From markw at illuminae.com Mon Nov 3 12:57:00 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Nov 3 13:55:06 2003 Subject: [MOBY-dev] Re: [MISC] hi In-Reply-To: <3FA61CF5.1060104@ebi.ac.uk> References: <3FA61CF5.1060104@ebi.ac.uk> Message-ID: <1067885820.2522.91.camel@localhost.localdomain> Dear GO Consortium members, I am writing to you as project leader of the BioMOBY interoperability project - an open-source project aimed at building a platform for the representation, discovery, and transaction of biological data services. One of the ontologies that we require in this project is a "Namespace" ontology; this is effectively an ontology of various data types as represented by common ID numbers. The Namespace Ontology maps conceptually onto the existing Gene Ontology Cross-Reference Abbreviations List, where you enumerate all of the different "prefixes" that are assigned to GO Xref's (e.g. NCBI_gi is the abbreviation for genbank records). Rather than create a list of our own de novo, we have imported the existing GO Xref Abbs into our ontology, however since MOBY is currently representing data-types that are not part of your Xref Abbs list, we have extended this list to include additional Namespaces that we require. We have also extended the specification such that each Namespace can be represented by a Life Sciences Identifier (LSID), and have set up an LSID meta-data resolution service on our project's server that is freely publicly accessible. It seems to me that it would be a shame (and a curatorial headache) to have two public lists of Namespaces that are not in-sync with each other. As such, I have raised with Michael Ashburner the possibility that the BioMOBY project take over the task of maintaining and curating this list, since we appear to edit it more frequently than you do. This came with several proviso's: 1) that we continue to offer all the data completely freely, both to you and everyone else. 2) that we build an interface (or make a regular dump) to provide you the data in the current GO Xrefs Abbs file format such that we do not break any of your existing tools 3) that we promise to give you back all relevant data and scripts in the event that the BioMOBY project expires for any reason. I hope that you will consider this and make a favourable decision! If there are any additional provisions, please let me know as I am certain that we can accommodate them. Sincerely, Mark Wilkinson -- Mark Wilkinson Illuminae From markw at illuminae.com Mon Nov 3 17:53:49 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Nov 3 18:51:49 2003 Subject: [MOBY-dev] heads up for biomoby.org flakeyness over the next few days! Message-ID: <1067903629.1711.43.camel@localhost.localdomain> Hi all, I've just moved the biomoby.org website over to the new open-bio server. The big headache was getting the Twiki moved over, but it looks like that is working now. I am going to ask Chris D. to update the DNS tomorrow. This will likely cause things to explode all over the place :-) As such, please *don't* send error reports for the next few days, including messages that the mailing list isn't working, or the website isn't working or the CVS isn't working, or whatever. I know, and I'm on it. It might take a day or two for everything to sort itself out. Moby Central is on a completely different server in a completely different country, so (barring another hurricane) there should be no problem in actually **using** MOBY during this transition - it is only the website, the CVS, and the mailing list that will be affected (he says, touching wood like mad!) So... take a deep breath and cross your fingers :-) Cheers all! Mark -- Mark Wilkinson Illuminae From yangclukey at suppedito.ipersonify.com Tue Nov 4 06:41:19 2003 From: yangclukey at suppedito.ipersonify.com (Females Update) Date: Mon Nov 3 19:39:31 2003 Subject: [MOBY-dev] Affordable L|p Plumper that works Message-ID: An HTML attachment was scrubbed... URL: http://pw600a.bioperl.org/pipermail/moby-dev/attachments/20031104/4c6fb2d4/attachment.htm From dag at sonsorol.org Mon Nov 3 20:42:17 2003 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon Nov 3 20:42:47 2003 Subject: [MOBY-dev] Re: [MOBY-l] heads up for biomoby.org flakeyness over the next few days! In-Reply-To: <1067903629.1711.43.camel@localhost.localdomain> References: <1067903629.1711.43.camel@localhost.localdomain> Message-ID: <3FA703F9.1050000@sonsorol.org> Hi all, Your mailing lists are tightly tied to the location of your website (because GNU Mailman is administered via http) so I need to relocate the moby-l and moby-dev lists and archives etc. at the same time you switch to the new server. Mark- I can move the lists over tonight -- if you get this and don't have any problems with the twiki config then we should just cut things over ASAP. Drop me an email giving me the OK if you are cool with this. List members -- the best/fastest way to report server related issues is to email "root-l@open-bio.org" at the same time you notify Mark. -Chris Mark Wilkinson wrote: > Hi all, > > I've just moved the biomoby.org website over to the new open-bio > server. The big headache was getting the Twiki moved over, but it looks > like that is working now. > > I am going to ask Chris D. to update the DNS tomorrow. This will likely > cause things to explode all over the place :-) > > As such, please *don't* send error reports for the next few days, > including messages that the mailing list isn't working, or the website > isn't working or the CVS isn't working, or whatever. I know, and I'm on > it. It might take a day or two for everything to sort itself out. > > Moby Central is on a completely different server in a completely > different country, so (barring another hurricane) there should be no > problem in actually **using** MOBY during this transition - it is only > the website, the CVS, and the mailing list that will be affected (he > says, touching wood like mad!) > > So... take a deep breath and cross your fingers :-) > > Cheers all! > > Mark > -- Chris Dagdigian, Independent life science IT & informatics consulting Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net From sender at tracewasher.com Wed Nov 5 09:48:47 2003 From: sender at tracewasher.com (Angeline O'Connor) Date: Wed Nov 5 09:55:52 2003 Subject: [MOBY-dev] www.biomoby.org Message-ID: <3328CR1000007486@s2h6a0w3.trafficglue.com> Hi, Newspaper Headlines:- 1. Consumer losses from identity theft grows to US$343 million 2. Employees' personal computers targeted by identity thieves 3. Cookies cumble online - privacy as advertisers track and exploit computer activities Your PC keeps records of all your online and off-line activity. Deleting "internet cache and history", will not protect you... Save your JOB, your MARRIAGE,and your FREEDOM! Get TraceWasher Now! Click at http://secure.tracewasher.com/buynow/form_signup.jsp to Buy now! Click at http://www.tracewasher.com/download/index.jsp to download a Free Trial! - Erase Internet Explorer Cache Files - Erase Internet Explorer Cookies - Erase Internet Explorer Visited/Typed URLs - Erase Internet Explorer Index.dat Files - Erase Internet Explorer AutoComplete Memory - Erase Windows Recent Documents History - Erase Windows Start Menu Run/Find History - Erase Windows Recycle Bin - Erase Windows Temporary Files Directory - Secure Erase Files - File Shredder - Plug-Ins Support - Free space on your Hard Drive! - Speed up your computer! Visit www.tracewasher.com to find out more! ----------------------------------------------------------------------- Not interested in buying our product? To be taken off our mailing list, please follow the instruction below: http://s2h6a0w3.trafficglue.com/mnkr/www/r?1000007486.3328.1.93cE8hvf3BMuKP From markw at illuminae.com Sat Nov 8 10:12:13 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 8 10:08:53 2003 Subject: [MOBY-dev] Change to the MOBY message format Message-ID: <1068304333.1708.49.camel@localhost.localdomain> Hi all, here's a heads-up that I am starting to implement a change to the MOBY-S messaging format that we decided on during the last MOBY-DIC meeting. It is the only one of the changes that is not fully backward-compatible with the existing message format, so I'm giving a bit of warning. I have made changes to the Perl CommonSubs library that makes all of this easy, and in fact, you likely wont break anything even if you continue using the old message structure, but... it wont be "correct" anymore :-) Here's the description of the change: The queryInput block(s) are now enumerated, and the queryResponse blocks are correspondingly enumerated such that inputs and outputs may be associated with each other Client-side. This is accomplished through a queryID attribute in the queryInput and queryResponse tags: ... ... This replaces the two rules in the 0.5 API that said: (1) outputs must appear in the same order in the response message as they appeared in the query message, and (2) services which change the namespace of the output object must provide an Invocation cross-reference pointing back at the originating query. Those two rules of the 0.5 API are now deprecated! The value you assign (client-side) to the queryID is completely arbitrary,and may be numeric, alphanumeric, or any other valid value of an XML attribute. It may also be blank, or absent (hence the backward compatibility), but be advised that you can no longer rely on the order of the outputs to map them back to your inputs, so... caveat emptor! Service providers MUST NOT try to interpret the value of the queryID attribute; it is an opaque value that they simply copy over into their queryResponse element. This change was made for two reasons: 1) the Invocation object was not sufficient to describe service inputs that consisted of Collections, or multiple Simple articles, and 2) the ordering of outputs was a pain in the butt for anyone providing services that did the underlying analysis in parallel, where the outputs might become available in an arbitrary order. I've just finished coding the various CommonSubs routines that will make this transition easy for the service provider, and I'm testing them now. As soon as they appear to be working properly (hopefully later today) I'll commit them. Hopefully this wont break anyone, but all existing services will have to be updated sooner or later anyway. Thankfully, this was the only seriously problematic part of the existing message format that we could identify during our discussions, so hopefully there wont be another major change like this for a long time! There are a few other changes to the API that we decided on, but these are simply extensions, and will not detrimentally affect anyone. I will implement those over the next week or so. Now that the Twiki has moved over to the new open-bio server I will also update the main API documentation so that we have a complete record of all changes. Cheers all! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 12:23:46 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 8 12:20:25 2003 Subject: [MOBY-dev] CommonSubs updated for new message structure Message-ID: <1068312226.1708.84.camel@localhost.localdomain> Okay, it looks like the new CommonSubs routine does not break the old routines, so people can begin to migrate over to the new message structure as they see fit. I will update all of my services in the LocalServices example module over the next few days, but below is a paradigmatic MOBY Service, using the various new routines in CommonSubs: sub myServiceName { my ($caller, $message) = @_; # get the incoming MOBY query XML my @queries = getInputs($message); # returns XML::DOM nodes my $RESPONSE = ""; # set empty response foreach my $query(@queries){ my $queryID = getInputID($query); # get the queryID attribute my @input_articles = getArticles($query); foreach my $input(@input_articles){ # input is a listref my ($articleName, $article) = @{$input}; # get the named article my $simple = isSimpleArticle($article); # simple or collection my $collection = isCollectionArticle($article); if ($collection){ # do something wtih the collection... # for example... my @simples = getCollectedSimples($article); # blah blah blah... } elsif ($simple){ # maybe you just need the ID of the incoming query: my ($id) = getSimpleArticleIDs('NCBI_gi', $article); # or maybe you are going to do something with the content? # for example, this will get the array of text lines # for the moby:String object with articleName 'SequenceString' # that is in this $article @s = getNodeContentWithArticle( $article, "String", "SequenceString"); # DO YOUR ANALYSIS HERE my $result = ""; #whatever you analysis says $RESPONSE .= simpleResponse($result, "someName", $queryID); } } } # note that responseHeader now takes an authority argument return responseHeader("my.authURI.com") . $RESPONSE . responseFooter; } M -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 19:02:46 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 8 18:59:23 2003 Subject: [MOBY-dev] Please introduce yourself. Message-ID: <1068336166.4275.6.camel@localhost.localdomain> mgruenb@gmx.net, please introduce yourself to the rest of the MOBY DEV list. No lurking ;-) Cheers! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 19:06:35 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 8 19:03:12 2003 Subject: [MOBY-dev] 0.6 API written up Message-ID: <1068336395.4275.11.camel@localhost.localdomain> Available on the TWiki. This contains the changes we made at the MOBY meeting; the change in enumeration of queryInput/Ouput blocks, the deprecation of the Invocation object, the addition of the Xref-type Cross Reference, and the revocation of the rule about ordered outputs. Old-style messages wont "break" anything, but they will not always be valid, so the sooner we migrate to the new API the better. I'm currently writing the CommonSubs code to handle Xref-type cross-references... it might already be working, but I can't remember if I tested it thoroughly in Hixton or not, so... hold your water.... M -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Sat Nov 8 20:59:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Sat Nov 8 20:55:36 2003 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068336395.4275.11.camel@localhost.localdomain> Message-ID: Mark, Ken and others, After some struggling (with firewalls etc.) I hope to have a reasonably ready version of Moby Graphs. The main page is here: http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html This page does a bit of explaining - and it should link you to the servlet-based service where you can play with creating various graphs (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). I will be glad to hear your comments. Mark, let me know when is the time to announce it to moby-l (or do it yourself if you wish because I will be travelling the whole week and not sure how I will be connected). Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Sat Nov 8 22:43:18 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 8 22:39:56 2003 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <1068349257.1994.56.camel@localhost.localdomain> Hey Martin! What an enormous amount of work you have done! Thank you! I'm going to spend a couple of hours tomorrow playing :-) It looks SO COOL! Everyone, you should check this out!! I'm off to the pub now, though, so I wont test it any more tonight... otherwise you would get some very peculiar feedback ;-) Tonight I'm celebrating the Lunar Eclipse (which was trez groovy!!), and the farewell/retirement party of our Prime Minister, Jean Cretien (YAAAAY! He's GONE!). Hopefully we can start rebuilding the country on Monday morning... Chat tomorrow! Mark On Sat, 2003-11-08 at 19:59, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Mark Wilkinson Illuminae From mgruenb at gmx.net Sun Nov 9 08:32:02 2003 From: mgruenb at gmx.net (Michael Gruenberger) Date: Sun Nov 9 08:28:48 2003 Subject: [MOBY-dev] Re: Please introduce yourself. In-Reply-To: <1068336166.4275.6.camel@localhost.localdomain> References: <1068336166.4275.6.camel@localhost.localdomain> Message-ID: <1068384721.2672.15.camel@vogel> Hello Moby developers, my name is Michael Gruenberger and I work as developer on Pathbase, which is a database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice and we are based at the Department of Anatomy, University of Cambridge. We have already implemented 5 ontologies (from GO + OBO) to describe our data and the next step will be to create a SOAP service and register it with Moby. If you are interested in more info, please have a look at: http://www.pathbase.net I will probably be lurking for a while to see what's going on, but mainly I want to create a Moby service for our database and use some other services as client. As I have written most of our web application / services in PHP I might want to port the Moby API to PHP or maybe write some wrapper functions to call the Perl API. But maybe I misunderstood Moby completely and this doesn't make any sense at all?! Anyway, I thought I'll subscribe to the moby-dev list to see what's happening in the development area of Moby and if it would be feasible or useful to port Moby to PHP. So it would be great if you could let me know what you think about the idea! Cheers, Michael. On Sun, 2003-11-09 at 00:02, Mark Wilkinson wrote: > mgruenb@gmx.net, please introduce yourself to the rest of the MOBY DEV > list. No lurking ;-) > > Cheers! > > Mark -- Michael Gruenberger Computer Officer, University of Cambridge Developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://portal.open-bio.org/pipermail/moby-dev/attachments/20031109/607bffa9/attachment.bin From lstein at cshl.edu Sun Nov 9 12:50:36 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sun Nov 9 12:47:12 2003 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <200311091250.36344.lstein@cshl.edu> That is SO cool! Lincoln On Saturday 08 November 2003 08:59 pm, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From lstein at cshl.edu Sun Nov 9 12:50:36 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sun Nov 9 12:47:14 2003 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <200311091250.36344.lstein@cshl.edu> That is SO cool! Lincoln On Saturday 08 November 2003 08:59 pm, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From markw at illuminae.com Sun Nov 9 15:57:55 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sun Nov 9 15:54:30 2003 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <1068411475.1706.23.camel@localhost.localdomain> Hey Martin, I'm having a lot of fun playing with these graphs :-) I've noticed a couple of things that strike me as odd: 1) build a graph from GenbankAccSequenceRetrieve to PBI_Parse_Blast. If you follow the path from GenbankAccSequenceRetrieve to GenbankAccVirtualSequenceRetrieve to GenbankCompleteSequenceRetrieve you will notice that the first two don't feedback on each other, but the GenbankCompleteSequenceRetrieve does. I think all three of them should feedback on each other (though in the context of finding a path the correct behaviour is probably to suppress this)... so I guess the question is why is it that some services are shown to feed-back, and others, don't even though they could? 2) On your interface page, you have the option to show paths between selected services, where you have the service names in the drop-down menu. Be careful with this, because service name alone isn't sufficient to specify a service. The unique key is authURI + serviceName. What's already striking to me is how many paths I know exist, but are not shown because (a) we don't specify in the registry what Cross-references a service provides, or (b) the output namespace isn't unknown until run-time (e.g. the getGoTermAssociations should, in fact, be able to lead to one or more sequence retrievals because what comes out are usually EMBL ID's or some such thing). This is not a criticism of the graphing, but a criticism of the somewhat impoverished representation of service outputs in the registry... but I don't see a way around that because it is genuinely the case that sometimes you don't know what you are going to get until you run the service. Anyway, it's great fun! Thank you again for spending the time to build this! I wonder if, rather than a service -> service graph, a more useful graph might be from input data-type to output data-type? I only say "more useful" because service names are "officially" meant to be opaque, so the drop-down list of services might not always make as much sense as it currently does when all of our services are "sensibly" named. Is that a more difficult query to execute? In any case, this rocks! Thanks so much for your efforts - I really should repay you by writing that DUMP method that you asked me for last week... you're still too hairy to kiss ;-) Cheers! M On Sat, 2003-11-08 at 19:59, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Mon Nov 10 01:16:37 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Nov 10 01:13:11 2003 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Many thanks for encouragement and for detailed feedback. I will go throught all your comments and observations but perhaps not this week being in Tokyo. But soon! Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From shontaswander at reditus.raiseyou.com Tue Nov 11 06:14:38 2003 From: shontaswander at reditus.raiseyou.com (Cosmetic Forum) Date: Tue Nov 11 07:15:45 2003 Subject: [MOBY-dev] Get Gorgeous, Healthy L|ps - no man can resist! Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031111/b9e68136/attachment.htm From tressiehove at attollo.tubemaker.com Tue Nov 18 05:55:22 2003 From: tressiehove at attollo.tubemaker.com (Females Health News) Date: Tue Nov 18 06:55:26 2003 Subject: [MOBY-dev] Non-surgical L|p Plumping Treatment Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031118/8bece078/attachment-0001.htm From jessica.hekman at prov.ingenta.com Tue Nov 18 17:35:53 2003 From: jessica.hekman at prov.ingenta.com (Jessica P. Hekman) Date: Tue Nov 18 17:32:13 2003 Subject: [MOBY-dev] Web page and dist issues Message-ID: Sorry if this is the wrong place to send this, but it wasn't clear where would be better. The link to the Java API docs is broken. The page with the bad link is: http://www.biomoby.org/moby-live/Java/docs/index.html and the link which doesn't work is: http://www.biomoby.org/moby-live/Java/docs/API/index.html Wanting the Java API, I then went to download the dist, hoping it would be in there (looks like it is). I untarred the .tar.gz dist, and it dropped files all over the directory I was in; usually it's best for it to create a subdirectory and stick stuff in there. Neither is a really big problem but I thought I'd drop a line to let you know! Jessica From markw at illuminae.com Tue Nov 18 18:03:47 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Nov 18 18:00:06 2003 Subject: [MOBY] [MOBY-dev] Web page and dist issues In-Reply-To: References: Message-ID: <1069196627.1715.63.camel@localhost.localdomain> Hi Jessica, Yes, we are having "issues" with the Java documentation :-) We need to build the documentation (generated by Java's Ant), but Java isn't yet installed on the new server we just moved to. I've just sent a request to do so. please give it a day or two... sorry about that! Mark On Tue, 2003-11-18 at 16:35, Jessica P. Hekman wrote: > Sorry if this is the wrong place to send this, but it wasn't clear where > would be better. > > The link to the Java API docs is broken. The page with the bad link is: > > http://www.biomoby.org/moby-live/Java/docs/index.html > > and the link which doesn't work is: > > http://www.biomoby.org/moby-live/Java/docs/API/index.html > > Wanting the Java API, I then went to download the dist, hoping it would be > in there (looks like it is). I untarred the .tar.gz dist, and it dropped > files all over the directory I was in; usually it's best for it to create > a subdirectory and stick stuff in there. > > Neither is a really big problem but I thought I'd drop a line to let you > know! > > Jessica > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson Illuminae From markw at illuminae.com Tue Nov 18 18:03:47 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Nov 18 18:00:06 2003 Subject: [MOBY] [MOBY-dev] Web page and dist issues In-Reply-To: References: Message-ID: <1069196627.1715.63.camel@localhost.localdomain> Hi Jessica, Yes, we are having "issues" with the Java documentation :-) We need to build the documentation (generated by Java's Ant), but Java isn't yet installed on the new server we just moved to. I've just sent a request to do so. please give it a day or two... sorry about that! Mark On Tue, 2003-11-18 at 16:35, Jessica P. Hekman wrote: > Sorry if this is the wrong place to send this, but it wasn't clear where > would be better. > > The link to the Java API docs is broken. The page with the bad link is: > > http://www.biomoby.org/moby-live/Java/docs/index.html > > and the link which doesn't work is: > > http://www.biomoby.org/moby-live/Java/docs/API/index.html > > Wanting the Java API, I then went to download the dist, hoping it would be > in there (looks like it is). I untarred the .tar.gz dist, and it dropped > files all over the directory I was in; usually it's best for it to create > a subdirectory and stick stuff in there. > > Neither is a really big problem but I thought I'd drop a line to let you > know! > > Jessica > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Wed Nov 19 01:11:15 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 19 01:07:43 2003 Subject: [MOBY-dev] Web page and dist issues In-Reply-To: Message-ID: > The link to the Java API docs is broken. > Yes, Mark is completely right - it's been a "work in progress" (in order to fix it). In the meantime, use my mirror, please: http://industry.ebi.ac.uk/~senger/jMoby/API/index.html. Mark, thanks very much for taking care about the Java questions on the new web server. 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Thanks, CSHL's MOBY team From markw at illuminae.com Fri Nov 21 19:03:50 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Nov 21 19:00:02 2003 Subject: [MOBY] Re: [MOBY-dev] meeting minutes under construction In-Reply-To: References: Message-ID: <1069459430.1709.98.camel@localhost.localdomain> Hi Shuly, Since this is addressed to me, I don't know if you intentionally sent this to all of the mailing lists or not... but you did :-) I've just made a small fix that will allow you to run a local MOBY Central, but the error message you are describing isn't consistent with the error that resulted from this bug, so I don't know what is going wrong. Please send me the line of code you are using to connect to your local registry, and any other details that may be important. M On Fri, 2003-11-21 at 16:53, Shuly Avraham wrote: > Hey Mark, > Fiona, Ardi and myself are trying to install the new Moby Central (0.6) > and > write new services. > We followed the local installation procedures, and whenever we run > testMOBYClientCentral_v05.pl pointing to the local moby central server we > get the following error message: > Unexpected Content-Type '' returned > We tested SOAP::Lite and it works fine. > > In addition testMOBYCentral_v05.pl works fine. > > We appreciate any help we can get on this. > > > Thanks, CSHL's MOBY team > > -- Mark Wilkinson Illuminae From v968rvhjte at hotmail.com Sat Nov 22 05:27:39 2003 From: v968rvhjte at hotmail.com (Kellie Greenberg) Date: Sat Nov 22 04:28:15 2003 Subject: [MOBY-dev] It takes overnight to get to your front door ajw yievdql me Message-ID: <6dhg$d5mcv4487u9l338512$5w-co@qp8f91.n.7o> beebread Online prescriptions for FDA approved medication. 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(I need to tell the EU the participants for this meeting) Rebecca. -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst@gsf.de From markw at illuminae.com Mon Nov 24 13:07:09 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Mon Nov 24 13:13:42 2003 Subject: [MOBY-dev] bug still there Message-ID: <1069697228.2339.86.camel@localhost.localdomain> Hey Martin, I have fixed the Relationships call so that it only returns the relationship type that you ask for, and it does respond to the expandRelationship flag, but it still returns a redundant list of parent types... I can't see where that redundancy is coming from at the moment, but I'll keep exploring. Hopefully it doesn't do you too much harm to have it there in the short-term the Client library (perl) still does not handle this call properly. I'll get around to that soon, M -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Mon Nov 24 13:29:16 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Nov 24 13:35:48 2003 Subject: [MOBY-dev] bug still there In-Reply-To: <1069697228.2339.86.camel@localhost.localdomain> Message-ID: > I have fixed the Relationships call so that it only returns the > relationship type that you ask for > Yes, it works... I have tried at once after I saw your commit, thanks from the lightning speed... > but it still returns a redundant list of parent > types... I can't see where that redundancy is coming from at the moment, > but I'll keep exploring. Hopefully it doesn't do you too much harm to > have it there in the short-term > that's fine with me, no harm... Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From bvhh69waq at hotmail.com Tue Nov 25 01:58:46 2003 From: bvhh69waq at hotmail.com (Joey Hanson) Date: Mon Nov 24 23:03:35 2003 Subject: [MOBY-dev] Reach for the ceiling without side effects w Message-ID: <6bhiu49y-o9-1$n569e5@jyyv.1.7e66m> anachronistic Moby-dev Want A Bigger Pen1s? Want A Bigger Pen1s? Gain Up to 3+ Full Inches In Length Increase Your Penis Width (Girth) By 20% Stop Premature Ejaculation! Produce Stronger, Rock Hard Erections A Larger, Harder Penis During Sex 100% Safe To Take, With NO Side Effects Fast Priority Shipping WorldWide Doctor Approved And Recommended No Pumps! No Surgery! 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It's a small and unexciting graph because we have not many service types - but perhaps it can be useful in the future. Both buglist and the new service types graphs will appear on the pages later today or tomorrow after I deploy it. I will send another message when it is done. I am really sorry that I cannot fix all pointed bugs now... Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From info at artinfobank.net Tue Nov 25 12:07:29 2003 From: info at artinfobank.net (Private Banking) Date: Tue Nov 25 12:07:54 2003 Subject: [MOBY-dev] [ADV] The World Leader in Art Market information Message-ID: <200311251707.hAPH7Tg0024599@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031125/aeb04bb5/attachment-0001.htm From senger at ebi.ac.uk Tue Nov 25 12:06:32 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Nov 25 12:13:03 2003 Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: <1068336395.4275.11.camel@localhost.localdomain> Message-ID: Mark et al, I am slowly getting into understanding what was discussed on the last Moby meeting about service invocations. Please be patient with me... I am working now on the Java API of the service invocation - and I need some answers. 1) I understand that there are two usages for the tag . It is used once when one registers a service by Moby Central. And there is another one that is used in the service invocation. The former contains definition of data type, the latter contain a run-time value (of this type). i think that it would be much clearer if we use different tags - for example and . The same applies for collections. Is my understanding correct? 2) The same as above applies also to the secondary parameters. but in this case it is worse because the API does not define (at least I have not found it) what is the structure of the tag "secondaryParameters" (the tag used in run-time to carry value/values of the secondary parameters). 3) Finally, I had to mis a lot - but I do not understand why all those sample (XML) objects in the API table of the hypotetical examples do not have any names (or article names). For example, how one can distringuish between two Strings in the GO_Term object? Thanks for your help and patience, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From 21CFR11 at biozak.com Tue Nov 25 15:08:49 2003 From: 21CFR11 at biozak.com (21CFR11@biozak.com) Date: Tue Nov 25 14:41:03 2003 Subject: [MOBY-dev] We have emails of thousands of your prospective customers - life science executives Message-ID: <200311252008.MAA12783@main.biozak.com> Our CD-ROM databases contain detailed contact information on 29,000+ life science executives worldwide. Limited time offer: Contact us now to get 15% off the regular price - mention promotion code int_service_providers_gen when you order. 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URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031125/9652532c/attachment.htm From steube at sdsc.edu Tue Nov 25 17:07:21 2003 From: steube at sdsc.edu (Ken Steube) Date: Tue Nov 25 17:13:53 2003 Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: I don't know about 1), but here's some info on the other two: For 2) the API does describe secondary params. Go to http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for 'Secondary'. It has max, min and some other tags. I haven't tried to write any services that use secondary params. Has anyone else? For 3) the strings in GO_Term have been given names. Go to this URL to see them: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=GO_Term Ken On Tue, 25 Nov 2003, Martin Senger wrote: > Mark et al, > I am slowly getting into understanding what was discussed on the last > Moby meeting about service invocations. Please be patient with me... I am > working now on the Java API of the service invocation - and I need some > answers. > > 1) I understand that there are two usages for the tag . It is > used once when one registers a service by Moby Central. And there is > another one that is used in the service invocation. The former contains > definition of data type, the latter contain a run-time value (of this > type). i think that it would be much clearer if we use different tags - > for example and . > The same applies for collections. > Is my understanding correct? > > 2) The same as above applies also to the secondary parameters. but in > this case it is worse because the API does not define (at least I have not > found it) what is the structure of the tag "secondaryParameters" (the tag > used in run-time to carry value/values of the secondary parameters). > > 3) Finally, I had to mis a lot - but I do not understand why all those > sample (XML) objects in the API table of the hypotetical examples do not > have any names (or article names). For example, how one can distringuish > between two Strings in the GO_Term object? > > Thanks for your help and patience, > Martin > > -- ------------------------------------- Ken Steube steube@sdsc.edu San Diego Supercomputer Center @ UCSD San Diego, California USA From steube at sdsc.edu Tue Nov 25 17:07:21 2003 From: steube at sdsc.edu (Ken Steube) Date: Tue Nov 25 17:13:56 2003 Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: I don't know about 1), but here's some info on the other two: For 2) the API does describe secondary params. Go to http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for 'Secondary'. It has max, min and some other tags. I haven't tried to write any services that use secondary params. Has anyone else? For 3) the strings in GO_Term have been given names. Go to this URL to see them: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=GO_Term Ken On Tue, 25 Nov 2003, Martin Senger wrote: > Mark et al, > I am slowly getting into understanding what was discussed on the last > Moby meeting about service invocations. Please be patient with me... I am > working now on the Java API of the service invocation - and I need some > answers. > > 1) I understand that there are two usages for the tag . It is > used once when one registers a service by Moby Central. And there is > another one that is used in the service invocation. The former contains > definition of data type, the latter contain a run-time value (of this > type). i think that it would be much clearer if we use different tags - > for example and . > The same applies for collections. > Is my understanding correct? > > 2) The same as above applies also to the secondary parameters. but in > this case it is worse because the API does not define (at least I have not > found it) what is the structure of the tag "secondaryParameters" (the tag > used in run-time to carry value/values of the secondary parameters). > > 3) Finally, I had to mis a lot - but I do not understand why all those > sample (XML) objects in the API table of the hypotetical examples do not > have any names (or article names). For example, how one can distringuish > between two Strings in the GO_Term object? > > Thanks for your help and patience, > Martin > > -- ------------------------------------- Ken Steube steube@sdsc.edu San Diego Supercomputer Center @ UCSD San Diego, California USA From 4kvwsqn at prodigy.com Tue Nov 25 17:18:11 2003 From: 4kvwsqn at prodigy.com (Barbra Lackey) Date: Tue Nov 25 17:20:13 2003 Subject: [MOBY-dev] Looking For A Crisis Proof Investment? b Message-ID: <7-59$7eh98-7$na27$6-$ums-po6y1y@0udzxz.ww> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031125/e1efb460/attachment.htm From senger at ebi.ac.uk Tue Nov 25 17:19:03 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Nov 25 17:25:41 2003 Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Tue Nov 25 17:19:03 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Nov 25 17:25:42 2003 Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Tue Nov 25 17:18:05 2003 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Tue Nov 25 17:28:35 2003 Subject: [MOBY-dev] questions (mostly) on service invocation Message-ID: <200311252228.hAPMSXg0028235@portal.open-bio.org> It may be that the examples are wrong. I'm on my blackberry right now so I can't check, but I'll have a look later. M -----Original Message----- From: Martin Senger Date: Tue, 25 Nov 2003 22:19:03 To:Ken Steube Cc:Core developer announcements , Mark Wilkinson , mobydev Subject: Re: [MOBY-dev] questions (mostly) on service invocation > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger _______________________________________________ MOBY-dev mailing list MOBY-dev@biomoby.org http://www.biomoby.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Nov 25 20:43:10 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Nov 25 20:49:43 2003 Subject: [MOBY-dev] java docs built on biomoby.org Message-ID: <1069810989.5387.3.camel@localhost.localdomain> Hey martin, I built your documentation last night. Sorry for the delay - we just got Java installed yesterday. I hope this isn't something that needs to be done often, as it took about 1/2 hour to complete...?? Cheers! Mark -- Mark Wilkinson Illuminae From npsshl at tim.it Wed Nov 26 06:56:21 2003 From: npsshl at tim.it (Terrie Gee) Date: Wed Nov 26 03:05:15 2003 Subject: [MOBY-dev] masters, MBA, and doctorate (PhD) diplomas available b zxkjuazy Message-ID: U N I V E R S I T Y D I P L O M A ' S Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. Bachelors, masters, MBA, and doctorate (PhD) diplomas available in the field of your choice. Obtain a prosperous future, money earning power, and the admiration of all. No one is turned down. Confidentiality assured. No required tests, classes, books, or interviews. CALL NOW to receive your diploma within days!!! 1-425-669-4485 Call 24 hours a day, 7 days a week, including Sundays and holidays - pc pzan pkqjc fx pig From senger at ebi.ac.uk Wed Nov 26 03:24:05 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 03:30:32 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: <1069810989.5387.3.camel@localhost.localdomain> Message-ID: > I built your documentation last night. Sorry for the delay - we just > got Java installed yesterday. > Perfect, thanks! > I hope this isn't something that needs to be done often, as it took > about 1/2 hour to complete...?? > The first build downloads a lot from the inet. Next builds should be much faster (on my laptop it takes tens of seconds, max 1 minute). And we can still optimalize by building only some build targets if necessary. Let me know if the next build takes also long please. How often? Well, ideally after every cvs update. But in praxis it would be enough to run it much less often. BTW, is there an automatic way to check whether anything changed from the last update? I know that there is a cvs status but I have never used it much (Phil Lord, are you listening on this list? Have you a suggestion for us?) If ther is then we can build only if something changed. Thanks again for taking care about it, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 03:24:05 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 03:30:34 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: <1069810989.5387.3.camel@localhost.localdomain> Message-ID: > I built your documentation last night. Sorry for the delay - we just > got Java installed yesterday. > Perfect, thanks! > I hope this isn't something that needs to be done often, as it took > about 1/2 hour to complete...?? > The first build downloads a lot from the inet. Next builds should be much faster (on my laptop it takes tens of seconds, max 1 minute). And we can still optimalize by building only some build targets if necessary. Let me know if the next build takes also long please. How often? Well, ideally after every cvs update. But in praxis it would be enough to run it much less often. BTW, is there an automatic way to check whether anything changed from the last update? I know that there is a cvs status but I have never used it much (Phil Lord, are you listening on this list? Have you a suggestion for us?) If ther is then we can build only if something changed. Thanks again for taking care about it, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From p.lord at russet.org.uk Wed Nov 26 05:29:21 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: Wed Nov 26 05:35:50 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: Martin> BTW, is there an automatic way to check whether anything Martin> changed from the last update? I know that there is a cvs Martin> status but I have never used it much (Phil Lord, are you Martin> listening on this list? Have you a suggestion for us?) If Martin> ther is then we can build only if something changed. I am listening, but I'm not sure why I get the arch geek question! I am not sure quite what you want. You want to update the documentation after the CVS has undergone a checkin? You can certainly do this by adding a watch to the file(s) in question. Or you could run "cvs status" and look for the line "Status: Need". Or trawl through the commit logs. Or you could use something like anthill which will rebuild automatically, every night (or whenever), after something has changed. Cheers Phil From senger at ebi.ac.uk Wed Nov 26 06:43:51 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 06:50:20 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > I am listening, but I'm not sure why I get the arch geek question! > Because I thought that you may know. Sorry, I will never ask again... > I am not sure quite what you want. > I want to run a script (build.sh) after every 'cvs update' (which is invoked automatically every something) if this 'cvs update' brought any change, in any file. And I was asking if such script/program exists or if I need to write it myself. So much for geekness in the question... Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 06:43:51 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 06:50:23 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > I am listening, but I'm not sure why I get the arch geek question! > Because I thought that you may know. Sorry, I will never ask again... > I am not sure quite what you want. > I want to run a script (build.sh) after every 'cvs update' (which is invoked automatically every something) if this 'cvs update' brought any change, in any file. And I was asking if such script/program exists or if I need to write it myself. So much for geekness in the question... Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From yxknpbe3m at hotmail.com Wed Nov 26 00:54:56 2003 From: yxknpbe3m at hotmail.com (Myles Patton) Date: Wed Nov 26 07:05:43 2003 Subject: [MOBY-dev] info you wanted s vaeui ajf Message-ID: U N I V E R S I T Y D I P L O M A ' S Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. Bachelors, masters, MBA, and doctorate (PhD) diplomas available in the field of your choice. Obtain a prosperous future, money earning power, and the admiration of all. No one is turned down. Confidentiality assured. No required tests, classes, books, or interviews. CALL NOW to receive your diploma within days!!! 1-425-669-4485 Call 24 hours a day, 7 days a week, including Sundays and holidays - l gljfhzi h From p.lord at russet.org.uk Wed Nov 26 07:27:14 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: Wed Nov 26 07:34:09 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> I am listening, but I'm not sure why I get the arch geek >> question! >> Martin> Because I thought that you may know. Sorry, I will never Martin> ask again... >> I am not sure quite what you want. >> Martin> I want to run a script (build.sh) after every 'cvs Martin> update' (which is Martin> invoked automatically every something) if this 'cvs update' Martin> brought any change, in any file. And I was asking if such Martin> script/program exists or if I need to write it myself. So Martin> much for geekness in the question... Ah, okay. If you are happy for it to run on the server, then you just add a line to the "loginfo" file, which is found in the CVSROOT See for instance... http://olympus.het.brown.edu/cgi-bin/info2www?(cvsbook)Commit+Emails which sets up commit emails. Of course this could also rebuild things. Is this what you were asking for? Cheers Phil From p.lord at russet.org.uk Wed Nov 26 07:27:14 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: Wed Nov 26 07:34:10 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> I am listening, but I'm not sure why I get the arch geek >> question! >> Martin> Because I thought that you may know. Sorry, I will never Martin> ask again... >> I am not sure quite what you want. >> Martin> I want to run a script (build.sh) after every 'cvs Martin> update' (which is Martin> invoked automatically every something) if this 'cvs update' Martin> brought any change, in any file. And I was asking if such Martin> script/program exists or if I need to write it myself. So Martin> much for geekness in the question... Ah, okay. If you are happy for it to run on the server, then you just add a line to the "loginfo" file, which is found in the CVSROOT See for instance... http://olympus.het.brown.edu/cgi-bin/info2www?(cvsbook)Commit+Emails which sets up commit emails. Of course this could also rebuild things. Is this what you were asking for? Cheers Phil From senger at ebi.ac.uk Wed Nov 26 07:34:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 07:40:30 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > Is this what you were asking for? > That's EXACTLY what I was asking for. And obviously I have asked a right person :-) Many thanks, I will investigate in this direction and let Mark know a suggestion what to do. Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 07:34:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 07:40:32 2003 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > Is this what you were asking for? > That's EXACTLY what I was asking for. And obviously I have asked a right person :-) Many thanks, I will investigate in this direction and let Mark know a suggestion what to do. Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From wf at world-foundation.org Wed Nov 26 08:05:40 2003 From: wf at world-foundation.org (SN World Foundation) Date: Wed Nov 26 09:25:53 2003 Subject: [MOBY-dev] New Technology for the Third World Message-ID: New Technology for the Third World, November 2003 Production Mini-plants in mobile containers. Worldwide Partners program SN World Foundation will supply to countries and developing regions the technology and necessary support for production in series of Mini-plants in mobile containers (40-foot). The Mini-plant system is designed in such a way that all the production machinery is fixed on the platform of the container, with all wiring, piping, and installation parts; that is, they are fully equipped... and the mini-plant is ready for production." More than 700 portable production systems: Bakeries, Water purification, Dehydrated food, Steel Nails, Fruit juice preparation, Tire Retreading, Reinforcement Bar Bending for Construction Framework, Sheeting for Roofing, Ceilings and Fa?ades, Plated Drums, Aluminum Buckets, Injected Polypropylene Housewares, Pressed Melamine Items (Glasses, Cups, Plates, Mugs, etc.), Mufflers, Construction Electrically Welded Mesh, Plastic Bags and Packaging, Medical assistance mobile units, Sanitary Material, Hypodermic Syringes, Hemostatic Clamps, etc. SN World Foundation has started a Co-investment program for the installation of small Assembly plants to manufacture in series the Mini-plants of portable production on site, region or country where required. One of the most relevant features is the fact that these plants will be connected to the International Trade System, with access to more than 50 million raw materials, products and services and automatic transactions for world trade. Due to financial reasons, involving cost and social impact, the best solution is setting up assembly plants on the same countries and regions, using local resources (labor, some equipment, etc.) SN World Foundation participates at 50% (fifty percent) for investment of each Assembly plant. If you are interested in being a partner in your country or region, you can send your CV to: SN World Foundation (click here) Worldwide Partners Program By Sarah Mathews, Manager Program ------------------------------------------------------------------------- If you received this in error or would like to be removed from our list, please return us indicating: remove or un-subscribe in subject field, Thanks. Manager Program ? 2003 SN World Foundation. All rights reserved. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031126/41af24da/attachment-0001.htm From markw at illuminae.com Wed Nov 26 11:37:56 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Nov 26 11:44:28 2003 Subject: [MOBY-dev] website revamped Message-ID: <3FC4D6E4.1000104@illuminae.com> Hi all, I'm going to a "cleaner & cooler" look on the website. Please have a look and let me know what you think. I haven't yet updated all of the pages, but most of them are now in keeping with the new style. If I have missed referencing anyone's stuff (sorry!) please send me the info, URL, or whatever, and I'll be sure to put it up right away! Cheers, Mark From ddg at ncgr.org Wed Nov 26 12:40:52 2003 From: ddg at ncgr.org (Damian Gessler) Date: Wed Nov 26 12:47:21 2003 Subject: [MOBY-dev] website revamped References: <3FC4D6E4.1000104@illuminae.com> Message-ID: <3FC4E5A4.6858DEBE@ncgr.org> Fabulous improvement, Mark. Nice job. D. Mark Wilkinson wrote: > Hi all, > > I'm going to a "cleaner & cooler" look on the website. Please have a > look and let me know what you think. I haven't yet updated all of the > pages, but most of them are now in keeping with the new style. > > If I have missed referencing anyone's stuff (sorry!) please send me the > info, URL, or whatever, and I'll be sure to put it up right away! > > Cheers, > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev From 240754 at delphi.com Thu Nov 27 00:28:18 2003 From: 240754 at delphi.com (240754@delphi.com) Date: Wed Nov 26 16:39:04 2003 Subject: [MOBY-dev] =?iso-8859-1?q?=EE=E1=F4=F1=F6=EE=F9=E5_=F0=EF=F4=EF?= =?iso-8859-1?q?=EC=EB=E9_=EF=F4_=2418/=ED_______240754?= Message-ID: <200311262139.hAQLcwg0004520@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/moby-dev/attachments/20031127/a46d1707/attachment.htm From senger at ebi.ac.uk Wed Nov 26 19:33:57 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Nov 26 19:40:25 2003 Subject: [MOBY-dev] Re: [MOBY-l] website revamped In-Reply-To: <3FC4D6E4.1000104@illuminae.com> Message-ID: > If I have missed referencing anyone's stuff (sorry!) please send me the > info, URL, or whatever, and I'll be sure to put it up right away! > Page "Connecting to MOBY-Central" could have also an example in Java. Here it is: --- begin --- import org.biomoby.shared.*; import org.biomoby.client.*; import java.util.*; public class RetrieveServiceTypes { public static void main (String [] args) { try { Central worker = new CentralImpl (CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE); System.out.println ("KNOWN SERVICE TYPES\n"); Map types = worker.getServiceTypes(); for (Iterator it = types.entrySet().iterator(); it.hasNext();) { Map.Entry entry = (Map.Entry)it.next(); System.out.println (entry.getKey()); System.out.println ("\t" + entry.getValue()); } } catch (Exception e) { System.err.println ("===ERROR==="); System.err.println (e.toString()); System.err.println ("==========="); } } } --- end --- Also the Perl example is not complete (and should be). It needs: a) to add use MOBY::Client::Central; b) to add semicolon at the end, and c) print better the result (now it prints just: KNOWN SERVICE TYPES HASH(0x867aed8) Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Wed Nov 26 21:36:41 2003 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Wed Nov 26 21:47:22 2003 Subject: [MOBY-dev] Re: [MOBY-l] website revamped Message-ID: <200311270247.hAR2lJg0005949@portal.open-bio.org> Done. M From c071kj at hotmail.it Wed Nov 26 15:03:15 2003 From: c071kj at hotmail.it (Claire Lloyd) Date: Wed Nov 26 22:16:53 2003 Subject: [MOBY-dev] Moby-dev Information You need Message-ID: <5-9$k9-77z3$u702-hc6@qpd8p> crate Moby-dev Want A Bigger Pen1s? Want A Bigger Pen1s? 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To be taken off our mailing list, please follow the instruction below: http://s2h6a0w3.trafficglue.com/mnkr/www/r?1000007486.3328.1.93cE8hvf3BMuKP From markw at illuminae.com Sat Nov 8 10:12:13 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 09:12:13 -0600 Subject: [MOBY-dev] Change to the MOBY message format Message-ID: <1068304333.1708.49.camel@localhost.localdomain> Hi all, here's a heads-up that I am starting to implement a change to the MOBY-S messaging format that we decided on during the last MOBY-DIC meeting. It is the only one of the changes that is not fully backward-compatible with the existing message format, so I'm giving a bit of warning. I have made changes to the Perl CommonSubs library that makes all of this easy, and in fact, you likely wont break anything even if you continue using the old message structure, but... it wont be "correct" anymore :-) Here's the description of the change: The queryInput block(s) are now enumerated, and the queryResponse blocks are correspondingly enumerated such that inputs and outputs may be associated with each other Client-side. This is accomplished through a queryID attribute in the queryInput and queryResponse tags: ... ... This replaces the two rules in the 0.5 API that said: (1) outputs must appear in the same order in the response message as they appeared in the query message, and (2) services which change the namespace of the output object must provide an Invocation cross-reference pointing back at the originating query. Those two rules of the 0.5 API are now deprecated! The value you assign (client-side) to the queryID is completely arbitrary,and may be numeric, alphanumeric, or any other valid value of an XML attribute. It may also be blank, or absent (hence the backward compatibility), but be advised that you can no longer rely on the order of the outputs to map them back to your inputs, so... caveat emptor! Service providers MUST NOT try to interpret the value of the queryID attribute; it is an opaque value that they simply copy over into their queryResponse element. This change was made for two reasons: 1) the Invocation object was not sufficient to describe service inputs that consisted of Collections, or multiple Simple articles, and 2) the ordering of outputs was a pain in the butt for anyone providing services that did the underlying analysis in parallel, where the outputs might become available in an arbitrary order. I've just finished coding the various CommonSubs routines that will make this transition easy for the service provider, and I'm testing them now. As soon as they appear to be working properly (hopefully later today) I'll commit them. Hopefully this wont break anyone, but all existing services will have to be updated sooner or later anyway. Thankfully, this was the only seriously problematic part of the existing message format that we could identify during our discussions, so hopefully there wont be another major change like this for a long time! There are a few other changes to the API that we decided on, but these are simply extensions, and will not detrimentally affect anyone. I will implement those over the next week or so. Now that the Twiki has moved over to the new open-bio server I will also update the main API documentation so that we have a complete record of all changes. Cheers all! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 12:23:46 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 11:23:46 -0600 Subject: [MOBY-dev] CommonSubs updated for new message structure Message-ID: <1068312226.1708.84.camel@localhost.localdomain> Okay, it looks like the new CommonSubs routine does not break the old routines, so people can begin to migrate over to the new message structure as they see fit. I will update all of my services in the LocalServices example module over the next few days, but below is a paradigmatic MOBY Service, using the various new routines in CommonSubs: sub myServiceName { my ($caller, $message) = @_; # get the incoming MOBY query XML my @queries = getInputs($message); # returns XML::DOM nodes my $RESPONSE = ""; # set empty response foreach my $query(@queries){ my $queryID = getInputID($query); # get the queryID attribute my @input_articles = getArticles($query); foreach my $input(@input_articles){ # input is a listref my ($articleName, $article) = @{$input}; # get the named article my $simple = isSimpleArticle($article); # simple or collection my $collection = isCollectionArticle($article); if ($collection){ # do something wtih the collection... # for example... my @simples = getCollectedSimples($article); # blah blah blah... } elsif ($simple){ # maybe you just need the ID of the incoming query: my ($id) = getSimpleArticleIDs('NCBI_gi', $article); # or maybe you are going to do something with the content? # for example, this will get the array of text lines # for the moby:String object with articleName 'SequenceString' # that is in this $article @s = getNodeContentWithArticle( $article, "String", "SequenceString"); # DO YOUR ANALYSIS HERE my $result = ""; #whatever you analysis says $RESPONSE .= simpleResponse($result, "someName", $queryID); } } } # note that responseHeader now takes an authority argument return responseHeader("my.authURI.com") . $RESPONSE . responseFooter; } M -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 19:02:46 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 18:02:46 -0600 Subject: [MOBY-dev] Please introduce yourself. Message-ID: <1068336166.4275.6.camel@localhost.localdomain> mgruenb at gmx.net, please introduce yourself to the rest of the MOBY DEV list. No lurking ;-) Cheers! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 19:06:35 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 18:06:35 -0600 Subject: [MOBY-dev] 0.6 API written up Message-ID: <1068336395.4275.11.camel@localhost.localdomain> Available on the TWiki. This contains the changes we made at the MOBY meeting; the change in enumeration of queryInput/Ouput blocks, the deprecation of the Invocation object, the addition of the Xref-type Cross Reference, and the revocation of the rule about ordered outputs. Old-style messages wont "break" anything, but they will not always be valid, so the sooner we migrate to the new API the better. I'm currently writing the CommonSubs code to handle Xref-type cross-references... it might already be working, but I can't remember if I tested it thoroughly in Hixton or not, so... hold your water.... M -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Sat Nov 8 20:59:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 9 Nov 2003 01:59:01 +0000 (GMT) Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068336395.4275.11.camel@localhost.localdomain> Message-ID: Mark, Ken and others, After some struggling (with firewalls etc.) I hope to have a reasonably ready version of Moby Graphs. The main page is here: http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html This page does a bit of explaining - and it should link you to the servlet-based service where you can play with creating various graphs (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). I will be glad to hear your comments. Mark, let me know when is the time to announce it to moby-l (or do it yourself if you wish because I will be travelling the whole week and not sure how I will be connected). Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Sat Nov 8 22:43:18 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 21:43:18 -0600 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <1068349257.1994.56.camel@localhost.localdomain> Hey Martin! What an enormous amount of work you have done! Thank you! I'm going to spend a couple of hours tomorrow playing :-) It looks SO COOL! Everyone, you should check this out!! I'm off to the pub now, though, so I wont test it any more tonight... otherwise you would get some very peculiar feedback ;-) Tonight I'm celebrating the Lunar Eclipse (which was trez groovy!!), and the farewell/retirement party of our Prime Minister, Jean Cretien (YAAAAY! He's GONE!). Hopefully we can start rebuilding the country on Monday morning... Chat tomorrow! Mark On Sat, 2003-11-08 at 19:59, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Mark Wilkinson Illuminae From mgruenb at gmx.net Sun Nov 9 08:32:02 2003 From: mgruenb at gmx.net (Michael Gruenberger) Date: Sun, 09 Nov 2003 13:32:02 +0000 Subject: [MOBY-dev] Re: Please introduce yourself. In-Reply-To: <1068336166.4275.6.camel@localhost.localdomain> References: <1068336166.4275.6.camel@localhost.localdomain> Message-ID: <1068384721.2672.15.camel@vogel> Hello Moby developers, my name is Michael Gruenberger and I work as developer on Pathbase, which is a database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice and we are based at the Department of Anatomy, University of Cambridge. We have already implemented 5 ontologies (from GO + OBO) to describe our data and the next step will be to create a SOAP service and register it with Moby. If you are interested in more info, please have a look at: http://www.pathbase.net I will probably be lurking for a while to see what's going on, but mainly I want to create a Moby service for our database and use some other services as client. As I have written most of our web application / services in PHP I might want to port the Moby API to PHP or maybe write some wrapper functions to call the Perl API. But maybe I misunderstood Moby completely and this doesn't make any sense at all?! Anyway, I thought I'll subscribe to the moby-dev list to see what's happening in the development area of Moby and if it would be feasible or useful to port Moby to PHP. So it would be great if you could let me know what you think about the idea! Cheers, Michael. On Sun, 2003-11-09 at 00:02, Mark Wilkinson wrote: > mgruenb at gmx.net, please introduce yourself to the rest of the MOBY DEV > list. No lurking ;-) > > Cheers! > > Mark -- Michael Gruenberger Computer Officer, University of Cambridge Developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://www.biomoby.org/pipermail/moby-dev/attachments/20031109/607bffa9/attachment-0002.bin From lstein at cshl.edu Sun Nov 9 12:50:36 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sun, 09 Nov 2003 12:50:36 -0500 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <200311091250.36344.lstein@cshl.edu> That is SO cool! Lincoln On Saturday 08 November 2003 08:59 pm, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From lstein at cshl.edu Sun Nov 9 12:50:36 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sun, 09 Nov 2003 12:50:36 -0500 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <200311091250.36344.lstein@cshl.edu> That is SO cool! Lincoln On Saturday 08 November 2003 08:59 pm, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From markw at illuminae.com Sun Nov 9 15:57:55 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 09 Nov 2003 14:57:55 -0600 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <1068411475.1706.23.camel@localhost.localdomain> Hey Martin, I'm having a lot of fun playing with these graphs :-) I've noticed a couple of things that strike me as odd: 1) build a graph from GenbankAccSequenceRetrieve to PBI_Parse_Blast. If you follow the path from GenbankAccSequenceRetrieve to GenbankAccVirtualSequenceRetrieve to GenbankCompleteSequenceRetrieve you will notice that the first two don't feedback on each other, but the GenbankCompleteSequenceRetrieve does. I think all three of them should feedback on each other (though in the context of finding a path the correct behaviour is probably to suppress this)... so I guess the question is why is it that some services are shown to feed-back, and others, don't even though they could? 2) On your interface page, you have the option to show paths between selected services, where you have the service names in the drop-down menu. Be careful with this, because service name alone isn't sufficient to specify a service. The unique key is authURI + serviceName. What's already striking to me is how many paths I know exist, but are not shown because (a) we don't specify in the registry what Cross-references a service provides, or (b) the output namespace isn't unknown until run-time (e.g. the getGoTermAssociations should, in fact, be able to lead to one or more sequence retrievals because what comes out are usually EMBL ID's or some such thing). This is not a criticism of the graphing, but a criticism of the somewhat impoverished representation of service outputs in the registry... but I don't see a way around that because it is genuinely the case that sometimes you don't know what you are going to get until you run the service. Anyway, it's great fun! Thank you again for spending the time to build this! I wonder if, rather than a service -> service graph, a more useful graph might be from input data-type to output data-type? I only say "more useful" because service names are "officially" meant to be opaque, so the drop-down list of services might not always make as much sense as it currently does when all of our services are "sensibly" named. Is that a more difficult query to execute? In any case, this rocks! Thanks so much for your efforts - I really should repay you by writing that DUMP method that you asked me for last week... you're still too hairy to kiss ;-) Cheers! M On Sat, 2003-11-08 at 19:59, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Mon Nov 10 01:16:37 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 10 Nov 2003 06:16:37 +0000 (GMT) Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Many thanks for encouragement and for detailed feedback. I will go throught all your comments and observations but perhaps not this week being in Tokyo. But soon! Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From shontaswander at reditus.raiseyou.com Tue Nov 11 06:14:38 2003 From: shontaswander at reditus.raiseyou.com (Cosmetic Forum) Date: Tue, 11 Nov 2003 07:14:38 -0400 Subject: [MOBY-dev] Get Gorgeous, Healthy L|ps - no man can resist! Message-ID: An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031111/b9e68136/attachment.html From tressiehove at attollo.tubemaker.com Tue Nov 18 05:55:22 2003 From: tressiehove at attollo.tubemaker.com (Females Health News) Date: Tue, 18 Nov 2003 15:55:22 +0500 Subject: [MOBY-dev] Non-surgical L|p Plumping Treatment Message-ID: An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031118/8bece078/attachment.html From jessica.hekman at prov.ingenta.com Tue Nov 18 17:35:53 2003 From: jessica.hekman at prov.ingenta.com (Jessica P. Hekman) Date: Tue, 18 Nov 2003 17:35:53 -0500 (EST) Subject: [MOBY-dev] Web page and dist issues Message-ID: Sorry if this is the wrong place to send this, but it wasn't clear where would be better. The link to the Java API docs is broken. The page with the bad link is: http://www.biomoby.org/moby-live/Java/docs/index.html and the link which doesn't work is: http://www.biomoby.org/moby-live/Java/docs/API/index.html Wanting the Java API, I then went to download the dist, hoping it would be in there (looks like it is). I untarred the .tar.gz dist, and it dropped files all over the directory I was in; usually it's best for it to create a subdirectory and stick stuff in there. Neither is a really big problem but I thought I'd drop a line to let you know! Jessica From markw at illuminae.com Tue Nov 18 18:03:47 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 18 Nov 2003 17:03:47 -0600 Subject: [MOBY] [MOBY-dev] Web page and dist issues In-Reply-To: References: Message-ID: <1069196627.1715.63.camel@localhost.localdomain> Hi Jessica, Yes, we are having "issues" with the Java documentation :-) We need to build the documentation (generated by Java's Ant), but Java isn't yet installed on the new server we just moved to. I've just sent a request to do so. please give it a day or two... sorry about that! Mark On Tue, 2003-11-18 at 16:35, Jessica P. Hekman wrote: > Sorry if this is the wrong place to send this, but it wasn't clear where > would be better. > > The link to the Java API docs is broken. The page with the bad link is: > > http://www.biomoby.org/moby-live/Java/docs/index.html > > and the link which doesn't work is: > > http://www.biomoby.org/moby-live/Java/docs/API/index.html > > Wanting the Java API, I then went to download the dist, hoping it would be > in there (looks like it is). I untarred the .tar.gz dist, and it dropped > files all over the directory I was in; usually it's best for it to create > a subdirectory and stick stuff in there. > > Neither is a really big problem but I thought I'd drop a line to let you > know! > > Jessica > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson Illuminae From markw at illuminae.com Tue Nov 18 18:03:47 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 18 Nov 2003 17:03:47 -0600 Subject: [MOBY] [MOBY-dev] Web page and dist issues In-Reply-To: References: Message-ID: <1069196627.1715.63.camel@localhost.localdomain> Hi Jessica, Yes, we are having "issues" with the Java documentation :-) We need to build the documentation (generated by Java's Ant), but Java isn't yet installed on the new server we just moved to. I've just sent a request to do so. please give it a day or two... sorry about that! Mark On Tue, 2003-11-18 at 16:35, Jessica P. Hekman wrote: > Sorry if this is the wrong place to send this, but it wasn't clear where > would be better. > > The link to the Java API docs is broken. The page with the bad link is: > > http://www.biomoby.org/moby-live/Java/docs/index.html > > and the link which doesn't work is: > > http://www.biomoby.org/moby-live/Java/docs/API/index.html > > Wanting the Java API, I then went to download the dist, hoping it would be > in there (looks like it is). I untarred the .tar.gz dist, and it dropped > files all over the directory I was in; usually it's best for it to create > a subdirectory and stick stuff in there. > > Neither is a really big problem but I thought I'd drop a line to let you > know! > > Jessica > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Wed Nov 19 01:11:15 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 19 Nov 2003 06:11:15 +0000 (GMT) Subject: [MOBY-dev] Web page and dist issues In-Reply-To: Message-ID: > The link to the Java API docs is broken. > Yes, Mark is completely right - it's been a "work in progress" (in order to fix it). In the meantime, use my mirror, please: http://industry.ebi.ac.uk/~senger/jMoby/API/index.html. Mark, thanks very much for taking care about the Java questions on the new web server. 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Thanks, CSHL's MOBY team From markw at illuminae.com Fri Nov 21 19:03:50 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 21 Nov 2003 18:03:50 -0600 Subject: [MOBY] Re: [MOBY-dev] meeting minutes under construction In-Reply-To: References: Message-ID: <1069459430.1709.98.camel@localhost.localdomain> Hi Shuly, Since this is addressed to me, I don't know if you intentionally sent this to all of the mailing lists or not... but you did :-) I've just made a small fix that will allow you to run a local MOBY Central, but the error message you are describing isn't consistent with the error that resulted from this bug, so I don't know what is going wrong. Please send me the line of code you are using to connect to your local registry, and any other details that may be important. M On Fri, 2003-11-21 at 16:53, Shuly Avraham wrote: > Hey Mark, > Fiona, Ardi and myself are trying to install the new Moby Central (0.6) > and > write new services. > We followed the local installation procedures, and whenever we run > testMOBYClientCentral_v05.pl pointing to the local moby central server we > get the following error message: > Unexpected Content-Type '' returned > We tested SOAP::Lite and it works fine. > > In addition testMOBYCentral_v05.pl works fine. > > We appreciate any help we can get on this. > > > Thanks, CSHL's MOBY team > > -- Mark Wilkinson Illuminae From v968rvhjte at hotmail.com Sat Nov 22 05:27:39 2003 From: v968rvhjte at hotmail.com (Kellie Greenberg) Date: Sat, 22 Nov 03 10:27:39 GMT Subject: [MOBY-dev] It takes overnight to get to your front door ajw yievdql me Message-ID: <6dhg$d5mcv4487u9l338512$5w-co@qp8f91.n.7o> beebread Online prescriptions for FDA approved medication. 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(I need to tell the EU the participants for this meeting) Rebecca. -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From markw at illuminae.com Mon Nov 24 13:07:09 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 24 Nov 2003 12:07:09 -0600 Subject: [MOBY-dev] bug still there Message-ID: <1069697228.2339.86.camel@localhost.localdomain> Hey Martin, I have fixed the Relationships call so that it only returns the relationship type that you ask for, and it does respond to the expandRelationship flag, but it still returns a redundant list of parent types... I can't see where that redundancy is coming from at the moment, but I'll keep exploring. Hopefully it doesn't do you too much harm to have it there in the short-term the Client library (perl) still does not handle this call properly. I'll get around to that soon, M -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Mon Nov 24 13:29:16 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Nov 2003 18:29:16 +0000 (GMT) Subject: [MOBY-dev] bug still there In-Reply-To: <1069697228.2339.86.camel@localhost.localdomain> Message-ID: > I have fixed the Relationships call so that it only returns the > relationship type that you ask for > Yes, it works... I have tried at once after I saw your commit, thanks from the lightning speed... > but it still returns a redundant list of parent > types... I can't see where that redundancy is coming from at the moment, > but I'll keep exploring. Hopefully it doesn't do you too much harm to > have it there in the short-term > that's fine with me, no harm... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From bvhh69waq at hotmail.com Tue Nov 25 01:58:46 2003 From: bvhh69waq at hotmail.com (Joey Hanson) Date: Tue, 25 Nov 03 06:58:46 GMT Subject: [MOBY-dev] Reach for the ceiling without side effects w Message-ID: <6bhiu49y-o9-1$n569e5@jyyv.1.7e66m> anachronistic Moby-dev Want A Bigger Pen1s? Want A Bigger Pen1s? Gain Up to 3+ Full Inches In Length Increase Your Penis Width (Girth) By 20% Stop Premature Ejaculation! Produce Stronger, Rock Hard Erections A Larger, Harder Penis During Sex 100% Safe To Take, With NO Side Effects Fast Priority Shipping WorldWide Doctor Approved And Recommended No Pumps! No Surgery! 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No Exercises! 100% Money Back Guarantee Moby-dev Click Here http://www.waken.com at www.m-e-d-z.biz/vp/?ang2003 Opt-Off http://www.twaddle.com at www.m-e-d-z.biz/off.html cuj y ngysd lakfaxdo ju z uya p dn xp hlmq nkj wbhozzz usaskrj c From senger at ebi.ac.uk Tue Nov 25 08:04:53 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 13:04:53 +0000 (GMT) Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Many thanks for your detailed comments on graphs. Most of them (perhaps all) are bugs I need to work on. But because I cannot do it now (simply I do not have more working power, and other projects are waiting for my attention :-() I have put your comments into a buglist which will be soon available from the graphs main page. I have also added a new graph of service types (after discovering the Relationships method). It's a small and unexciting graph because we have not many service types - but perhaps it can be useful in the future. Both buglist and the new service types graphs will appear on the pages later today or tomorrow after I deploy it. I will send another message when it is done. I am really sorry that I cannot fix all pointed bugs now... Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From info at artinfobank.net Tue Nov 25 12:07:29 2003 From: info at artinfobank.net (Private Banking) Date: Tue, 25 Nov 2003 12:07:29 -0500 Subject: [MOBY-dev] [ADV] The World Leader in Art Market information Message-ID: <200311251707.hAPH7Tg0024599@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031125/aeb04bb5/attachment.html From senger at ebi.ac.uk Tue Nov 25 12:06:32 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 17:06:32 +0000 (GMT) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: <1068336395.4275.11.camel@localhost.localdomain> Message-ID: Mark et al, I am slowly getting into understanding what was discussed on the last Moby meeting about service invocations. Please be patient with me... I am working now on the Java API of the service invocation - and I need some answers. 1) I understand that there are two usages for the tag . It is used once when one registers a service by Moby Central. And there is another one that is used in the service invocation. The former contains definition of data type, the latter contain a run-time value (of this type). i think that it would be much clearer if we use different tags - for example and . The same applies for collections. Is my understanding correct? 2) The same as above applies also to the secondary parameters. but in this case it is worse because the API does not define (at least I have not found it) what is the structure of the tag "secondaryParameters" (the tag used in run-time to carry value/values of the secondary parameters). 3) Finally, I had to mis a lot - but I do not understand why all those sample (XML) objects in the API table of the hypotetical examples do not have any names (or article names). For example, how one can distringuish between two Strings in the GO_Term object? Thanks for your help and patience, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From 21CFR11 at biozak.com Tue Nov 25 15:08:49 2003 From: 21CFR11 at biozak.com (21CFR11@biozak.com) Date: Tue, 25 Nov 2003 20:08:49 UT Subject: [MOBY-dev] We have emails of thousands of your prospective customers - life science executives Message-ID: <200311252008.MAA12783@main.biozak.com> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20031125/32706a48/attachment.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031125/32706a48/attachment.html From 240734 at hotmail.com Tue Nov 25 23:48:52 2003 From: 240734 at hotmail.com (240734@hotmail.com) Date: Tue, 25 Nov 2003 23:48:52 -0500 Subject: [MOBY-dev] =?iso-8859-1?q?=CD=CE=C2=DB=C9_=C3=CE=C4_=C8_=D0=CE?= =?iso-8859-1?q?=C6=C4=C5=D1=D2=C2=CE_=C2_=D2=C0=CB=CB=C8=CD=C5___2?= =?iso-8859-1?q?40734?= Message-ID: <200311252059.hAPKxVg0027637@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031125/9652532c/attachment.html From steube at sdsc.edu Tue Nov 25 17:07:21 2003 From: steube at sdsc.edu (Ken Steube) Date: Tue, 25 Nov 2003 14:07:21 -0800 (PST) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: I don't know about 1), but here's some info on the other two: For 2) the API does describe secondary params. Go to http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for 'Secondary'. It has max, min and some other tags. I haven't tried to write any services that use secondary params. Has anyone else? For 3) the strings in GO_Term have been given names. Go to this URL to see them: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=GO_Term Ken On Tue, 25 Nov 2003, Martin Senger wrote: > Mark et al, > I am slowly getting into understanding what was discussed on the last > Moby meeting about service invocations. Please be patient with me... I am > working now on the Java API of the service invocation - and I need some > answers. > > 1) I understand that there are two usages for the tag . It is > used once when one registers a service by Moby Central. And there is > another one that is used in the service invocation. The former contains > definition of data type, the latter contain a run-time value (of this > type). i think that it would be much clearer if we use different tags - > for example and . > The same applies for collections. > Is my understanding correct? > > 2) The same as above applies also to the secondary parameters. but in > this case it is worse because the API does not define (at least I have not > found it) what is the structure of the tag "secondaryParameters" (the tag > used in run-time to carry value/values of the secondary parameters). > > 3) Finally, I had to mis a lot - but I do not understand why all those > sample (XML) objects in the API table of the hypotetical examples do not > have any names (or article names). For example, how one can distringuish > between two Strings in the GO_Term object? > > Thanks for your help and patience, > Martin > > -- ------------------------------------- Ken Steube steube at sdsc.edu San Diego Supercomputer Center @ UCSD San Diego, California USA From steube at sdsc.edu Tue Nov 25 17:07:21 2003 From: steube at sdsc.edu (Ken Steube) Date: Tue, 25 Nov 2003 14:07:21 -0800 (PST) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: I don't know about 1), but here's some info on the other two: For 2) the API does describe secondary params. Go to http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for 'Secondary'. It has max, min and some other tags. I haven't tried to write any services that use secondary params. Has anyone else? For 3) the strings in GO_Term have been given names. Go to this URL to see them: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=GO_Term Ken On Tue, 25 Nov 2003, Martin Senger wrote: > Mark et al, > I am slowly getting into understanding what was discussed on the last > Moby meeting about service invocations. Please be patient with me... I am > working now on the Java API of the service invocation - and I need some > answers. > > 1) I understand that there are two usages for the tag . It is > used once when one registers a service by Moby Central. And there is > another one that is used in the service invocation. The former contains > definition of data type, the latter contain a run-time value (of this > type). i think that it would be much clearer if we use different tags - > for example and . > The same applies for collections. > Is my understanding correct? > > 2) The same as above applies also to the secondary parameters. but in > this case it is worse because the API does not define (at least I have not > found it) what is the structure of the tag "secondaryParameters" (the tag > used in run-time to carry value/values of the secondary parameters). > > 3) Finally, I had to mis a lot - but I do not understand why all those > sample (XML) objects in the API table of the hypotetical examples do not > have any names (or article names). For example, how one can distringuish > between two Strings in the GO_Term object? > > Thanks for your help and patience, > Martin > > -- ------------------------------------- Ken Steube steube at sdsc.edu San Diego Supercomputer Center @ UCSD San Diego, California USA From 4kvwsqn at prodigy.com Tue Nov 25 17:18:11 2003 From: 4kvwsqn at prodigy.com (Barbra Lackey) Date: Tue, 25 Nov 2003 17:18:11 -0500 Subject: [MOBY-dev] Looking For A Crisis Proof Investment? b Message-ID: <7-59$7eh98-7$na27$6-$ums-po6y1y@0udzxz.ww> An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031125/e1efb460/attachment.html From senger at ebi.ac.uk Tue Nov 25 17:19:03 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 22:19:03 +0000 (GMT) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Tue Nov 25 17:19:03 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 22:19:03 +0000 (GMT) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Tue Nov 25 17:18:05 2003 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Tue, 25 Nov 2003 17:18:05 -0500 Subject: [MOBY-dev] questions (mostly) on service invocation Message-ID: <200311252228.hAPMSXg0028235@portal.open-bio.org> It may be that the examples are wrong. I'm on my blackberry right now so I can't check, but I'll have a look later. M -----Original Message----- From: Martin Senger Date: Tue, 25 Nov 2003 22:19:03 To:Ken Steube Cc:Core developer announcements , Mark Wilkinson , mobydev Subject: Re: [MOBY-dev] questions (mostly) on service invocation > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger _______________________________________________ MOBY-dev mailing list MOBY-dev at biomoby.org http://www.biomoby.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Nov 25 20:43:10 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 25 Nov 2003 19:43:10 -0600 Subject: [MOBY-dev] java docs built on biomoby.org Message-ID: <1069810989.5387.3.camel@localhost.localdomain> Hey martin, I built your documentation last night. Sorry for the delay - we just got Java installed yesterday. I hope this isn't something that needs to be done often, as it took about 1/2 hour to complete...?? Cheers! Mark -- Mark Wilkinson Illuminae From npsshl at tim.it Wed Nov 26 06:56:21 2003 From: npsshl at tim.it (Terrie Gee) Date: Wed, 26 Nov 03 11:56:21 GMT Subject: [MOBY-dev] masters, MBA, and doctorate (PhD) diplomas available b zxkjuazy Message-ID: U N I V E R S I T Y D I P L O M A ' S Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. Bachelors, masters, MBA, and doctorate (PhD) diplomas available in the field of your choice. Obtain a prosperous future, money earning power, and the admiration of all. No one is turned down. Confidentiality assured. No required tests, classes, books, or interviews. CALL NOW to receive your diploma within days!!! 1-425-669-4485 Call 24 hours a day, 7 days a week, including Sundays and holidays - pc pzan pkqjc fx pig From senger at ebi.ac.uk Wed Nov 26 03:24:05 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 08:24:05 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: <1069810989.5387.3.camel@localhost.localdomain> Message-ID: > I built your documentation last night. Sorry for the delay - we just > got Java installed yesterday. > Perfect, thanks! > I hope this isn't something that needs to be done often, as it took > about 1/2 hour to complete...?? > The first build downloads a lot from the inet. Next builds should be much faster (on my laptop it takes tens of seconds, max 1 minute). And we can still optimalize by building only some build targets if necessary. Let me know if the next build takes also long please. How often? Well, ideally after every cvs update. But in praxis it would be enough to run it much less often. BTW, is there an automatic way to check whether anything changed from the last update? I know that there is a cvs status but I have never used it much (Phil Lord, are you listening on this list? Have you a suggestion for us?) If ther is then we can build only if something changed. Thanks again for taking care about it, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 03:24:05 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 08:24:05 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: <1069810989.5387.3.camel@localhost.localdomain> Message-ID: > I built your documentation last night. Sorry for the delay - we just > got Java installed yesterday. > Perfect, thanks! > I hope this isn't something that needs to be done often, as it took > about 1/2 hour to complete...?? > The first build downloads a lot from the inet. Next builds should be much faster (on my laptop it takes tens of seconds, max 1 minute). And we can still optimalize by building only some build targets if necessary. Let me know if the next build takes also long please. How often? Well, ideally after every cvs update. But in praxis it would be enough to run it much less often. BTW, is there an automatic way to check whether anything changed from the last update? I know that there is a cvs status but I have never used it much (Phil Lord, are you listening on this list? Have you a suggestion for us?) If ther is then we can build only if something changed. Thanks again for taking care about it, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From p.lord at russet.org.uk Wed Nov 26 05:29:21 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: 26 Nov 2003 10:29:21 +0000 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: Martin> BTW, is there an automatic way to check whether anything Martin> changed from the last update? I know that there is a cvs Martin> status but I have never used it much (Phil Lord, are you Martin> listening on this list? Have you a suggestion for us?) If Martin> ther is then we can build only if something changed. I am listening, but I'm not sure why I get the arch geek question! I am not sure quite what you want. You want to update the documentation after the CVS has undergone a checkin? You can certainly do this by adding a watch to the file(s) in question. Or you could run "cvs status" and look for the line "Status: Need". Or trawl through the commit logs. Or you could use something like anthill which will rebuild automatically, every night (or whenever), after something has changed. Cheers Phil From senger at ebi.ac.uk Wed Nov 26 06:43:51 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 11:43:51 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > I am listening, but I'm not sure why I get the arch geek question! > Because I thought that you may know. Sorry, I will never ask again... > I am not sure quite what you want. > I want to run a script (build.sh) after every 'cvs update' (which is invoked automatically every something) if this 'cvs update' brought any change, in any file. And I was asking if such script/program exists or if I need to write it myself. So much for geekness in the question... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 06:43:51 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 11:43:51 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > I am listening, but I'm not sure why I get the arch geek question! > Because I thought that you may know. Sorry, I will never ask again... > I am not sure quite what you want. > I want to run a script (build.sh) after every 'cvs update' (which is invoked automatically every something) if this 'cvs update' brought any change, in any file. And I was asking if such script/program exists or if I need to write it myself. So much for geekness in the question... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From yxknpbe3m at hotmail.com Wed Nov 26 00:54:56 2003 From: yxknpbe3m at hotmail.com (Myles Patton) Date: Wed, 26 Nov 03 05:54:56 GMT Subject: [MOBY-dev] info you wanted s vaeui ajf Message-ID: U N I V E R S I T Y D I P L O M A ' S Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. Bachelors, masters, MBA, and doctorate (PhD) diplomas available in the field of your choice. Obtain a prosperous future, money earning power, and the admiration of all. No one is turned down. Confidentiality assured. No required tests, classes, books, or interviews. CALL NOW to receive your diploma within days!!! 1-425-669-4485 Call 24 hours a day, 7 days a week, including Sundays and holidays - l gljfhzi h From p.lord at russet.org.uk Wed Nov 26 07:27:14 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: 26 Nov 2003 12:27:14 +0000 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> I am listening, but I'm not sure why I get the arch geek >> question! >> Martin> Because I thought that you may know. Sorry, I will never Martin> ask again... >> I am not sure quite what you want. >> Martin> I want to run a script (build.sh) after every 'cvs Martin> update' (which is Martin> invoked automatically every something) if this 'cvs update' Martin> brought any change, in any file. And I was asking if such Martin> script/program exists or if I need to write it myself. So Martin> much for geekness in the question... Ah, okay. If you are happy for it to run on the server, then you just add a line to the "loginfo" file, which is found in the CVSROOT See for instance... http://olympus.het.brown.edu/cgi-bin/info2www?(cvsbook)Commit+Emails which sets up commit emails. Of course this could also rebuild things. Is this what you were asking for? Cheers Phil From p.lord at russet.org.uk Wed Nov 26 07:27:14 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: 26 Nov 2003 12:27:14 +0000 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> I am listening, but I'm not sure why I get the arch geek >> question! >> Martin> Because I thought that you may know. Sorry, I will never Martin> ask again... >> I am not sure quite what you want. >> Martin> I want to run a script (build.sh) after every 'cvs Martin> update' (which is Martin> invoked automatically every something) if this 'cvs update' Martin> brought any change, in any file. And I was asking if such Martin> script/program exists or if I need to write it myself. So Martin> much for geekness in the question... Ah, okay. If you are happy for it to run on the server, then you just add a line to the "loginfo" file, which is found in the CVSROOT See for instance... http://olympus.het.brown.edu/cgi-bin/info2www?(cvsbook)Commit+Emails which sets up commit emails. Of course this could also rebuild things. Is this what you were asking for? Cheers Phil From senger at ebi.ac.uk Wed Nov 26 07:34:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 12:34:01 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > Is this what you were asking for? > That's EXACTLY what I was asking for. And obviously I have asked a right person :-) Many thanks, I will investigate in this direction and let Mark know a suggestion what to do. Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 07:34:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 12:34:01 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > Is this what you were asking for? > That's EXACTLY what I was asking for. And obviously I have asked a right person :-) Many thanks, I will investigate in this direction and let Mark know a suggestion what to do. Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From wf at world-foundation.org Wed Nov 26 08:05:40 2003 From: wf at world-foundation.org (SN World Foundation) Date: Wed, 26 Nov 2003 14:05:40 +0100 Subject: [MOBY-dev] New Technology for the Third World Message-ID: New Technology for the Third World, November 2003 Production Mini-plants in mobile containers. Worldwide Partners program SN World Foundation will supply to countries and developing regions the technology and necessary support for production in series of Mini-plants in mobile containers (40-foot). The Mini-plant system is designed in such a way that all the production machinery is fixed on the platform of the container, with all wiring, piping, and installation parts; that is, they are fully equipped... and the mini-plant is ready for production." More than 700 portable production systems: Bakeries, Water purification, Dehydrated food, Steel Nails, Fruit juice preparation, Tire Retreading, Reinforcement Bar Bending for Construction Framework, Sheeting for Roofing, Ceilings and Fa?ades, Plated Drums, Aluminum Buckets, Injected Polypropylene Housewares, Pressed Melamine Items (Glasses, Cups, Plates, Mugs, etc.), Mufflers, Construction Electrically Welded Mesh, Plastic Bags and Packaging, Medical assistance mobile units, Sanitary Material, Hypodermic Syringes, Hemostatic Clamps, etc. SN World Foundation has started a Co-investment program for the installation of small Assembly plants to manufacture in series the Mini-plants of portable production on site, region or country where required. One of the most relevant features is the fact that these plants will be connected to the International Trade System, with access to more than 50 million raw materials, products and services and automatic transactions for world trade. Due to financial reasons, involving cost and social impact, the best solution is setting up assembly plants on the same countries and regions, using local resources (labor, some equipment, etc.) SN World Foundation participates at 50% (fifty percent) for investment of each Assembly plant. If you are interested in being a partner in your country or region, you can send your CV to: SN World Foundation (click here) Worldwide Partners Program By Sarah Mathews, Manager Program ------------------------------------------------------------------------- If you received this in error or would like to be removed from our list, please return us indicating: remove or un-subscribe in subject field, Thanks. Manager Program ? 2003 SN World Foundation. All rights reserved. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031126/41af24da/attachment.html From markw at illuminae.com Wed Nov 26 11:37:56 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 26 Nov 2003 10:37:56 -0600 Subject: [MOBY-dev] website revamped Message-ID: <3FC4D6E4.1000104@illuminae.com> Hi all, I'm going to a "cleaner & cooler" look on the website. Please have a look and let me know what you think. I haven't yet updated all of the pages, but most of them are now in keeping with the new style. If I have missed referencing anyone's stuff (sorry!) please send me the info, URL, or whatever, and I'll be sure to put it up right away! Cheers, Mark From ddg at ncgr.org Wed Nov 26 12:40:52 2003 From: ddg at ncgr.org (Damian Gessler) Date: Wed, 26 Nov 2003 10:40:52 -0700 Subject: [MOBY-dev] website revamped References: <3FC4D6E4.1000104@illuminae.com> Message-ID: <3FC4E5A4.6858DEBE@ncgr.org> Fabulous improvement, Mark. Nice job. D. Mark Wilkinson wrote: > Hi all, > > I'm going to a "cleaner & cooler" look on the website. Please have a > look and let me know what you think. I haven't yet updated all of the > pages, but most of them are now in keeping with the new style. > > If I have missed referencing anyone's stuff (sorry!) please send me the > info, URL, or whatever, and I'll be sure to put it up right away! > > Cheers, > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev From 240754 at delphi.com Thu Nov 27 00:28:18 2003 From: 240754 at delphi.com (240754@delphi.com) Date: Thu, 27 Nov 2003 00:28:18 -0500 Subject: [MOBY-dev] =?iso-8859-1?q?=EE=E1=F4=F1=F6=EE=F9=E5_=F0=EF=F4=EF?= =?iso-8859-1?q?=EC=EB=E9_=EF=F4_=2418/=ED_______240754?= Message-ID: <200311262139.hAQLcwg0004520@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://www.biomoby.org/pipermail/moby-dev/attachments/20031127/a46d1707/attachment.html From senger at ebi.ac.uk Wed Nov 26 19:33:57 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 27 Nov 2003 00:33:57 +0000 (GMT) Subject: [MOBY-dev] Re: [MOBY-l] website revamped In-Reply-To: <3FC4D6E4.1000104@illuminae.com> Message-ID: > If I have missed referencing anyone's stuff (sorry!) please send me the > info, URL, or whatever, and I'll be sure to put it up right away! > Page "Connecting to MOBY-Central" could have also an example in Java. Here it is: --- begin --- import org.biomoby.shared.*; import org.biomoby.client.*; import java.util.*; public class RetrieveServiceTypes { public static void main (String [] args) { try { Central worker = new CentralImpl (CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE); System.out.println ("KNOWN SERVICE TYPES\n"); Map types = worker.getServiceTypes(); for (Iterator it = types.entrySet().iterator(); it.hasNext();) { Map.Entry entry = (Map.Entry)it.next(); System.out.println (entry.getKey()); System.out.println ("\t" + entry.getValue()); } } catch (Exception e) { System.err.println ("===ERROR==="); System.err.println (e.toString()); System.err.println ("==========="); } } } --- end --- Also the Perl example is not complete (and should be). It needs: a) to add use MOBY::Client::Central; b) to add semicolon at the end, and c) print better the result (now it prints just: KNOWN SERVICE TYPES HASH(0x867aed8) Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Wed Nov 26 21:36:41 2003 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Wed, 26 Nov 2003 21:36:41 -0500 Subject: [MOBY-dev] Re: [MOBY-l] website revamped Message-ID: <200311270247.hAR2lJg0005949@portal.open-bio.org> Done. M From c071kj at hotmail.it Wed Nov 26 15:03:15 2003 From: c071kj at hotmail.it (Claire Lloyd) Date: Wed, 26 Nov 03 20:03:15 GMT Subject: [MOBY-dev] Moby-dev Information You need Message-ID: <5-9$k9-77z3$u702-hc6@qpd8p> crate Moby-dev Want A Bigger Pen1s? 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To be taken off our mailing list, please follow the instruction below: http://s2h6a0w3.trafficglue.com/mnkr/www/r?1000007486.3328.1.93cE8hvf3BMuKP From markw at illuminae.com Sat Nov 8 15:12:13 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 09:12:13 -0600 Subject: [MOBY-dev] Change to the MOBY message format Message-ID: <1068304333.1708.49.camel@localhost.localdomain> Hi all, here's a heads-up that I am starting to implement a change to the MOBY-S messaging format that we decided on during the last MOBY-DIC meeting. It is the only one of the changes that is not fully backward-compatible with the existing message format, so I'm giving a bit of warning. I have made changes to the Perl CommonSubs library that makes all of this easy, and in fact, you likely wont break anything even if you continue using the old message structure, but... it wont be "correct" anymore :-) Here's the description of the change: The queryInput block(s) are now enumerated, and the queryResponse blocks are correspondingly enumerated such that inputs and outputs may be associated with each other Client-side. This is accomplished through a queryID attribute in the queryInput and queryResponse tags: ... ... This replaces the two rules in the 0.5 API that said: (1) outputs must appear in the same order in the response message as they appeared in the query message, and (2) services which change the namespace of the output object must provide an Invocation cross-reference pointing back at the originating query. Those two rules of the 0.5 API are now deprecated! The value you assign (client-side) to the queryID is completely arbitrary,and may be numeric, alphanumeric, or any other valid value of an XML attribute. It may also be blank, or absent (hence the backward compatibility), but be advised that you can no longer rely on the order of the outputs to map them back to your inputs, so... caveat emptor! Service providers MUST NOT try to interpret the value of the queryID attribute; it is an opaque value that they simply copy over into their queryResponse element. This change was made for two reasons: 1) the Invocation object was not sufficient to describe service inputs that consisted of Collections, or multiple Simple articles, and 2) the ordering of outputs was a pain in the butt for anyone providing services that did the underlying analysis in parallel, where the outputs might become available in an arbitrary order. I've just finished coding the various CommonSubs routines that will make this transition easy for the service provider, and I'm testing them now. As soon as they appear to be working properly (hopefully later today) I'll commit them. Hopefully this wont break anyone, but all existing services will have to be updated sooner or later anyway. Thankfully, this was the only seriously problematic part of the existing message format that we could identify during our discussions, so hopefully there wont be another major change like this for a long time! There are a few other changes to the API that we decided on, but these are simply extensions, and will not detrimentally affect anyone. I will implement those over the next week or so. Now that the Twiki has moved over to the new open-bio server I will also update the main API documentation so that we have a complete record of all changes. Cheers all! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Nov 8 17:23:46 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 11:23:46 -0600 Subject: [MOBY-dev] CommonSubs updated for new message structure Message-ID: <1068312226.1708.84.camel@localhost.localdomain> Okay, it looks like the new CommonSubs routine does not break the old routines, so people can begin to migrate over to the new message structure as they see fit. I will update all of my services in the LocalServices example module over the next few days, but below is a paradigmatic MOBY Service, using the various new routines in CommonSubs: sub myServiceName { my ($caller, $message) = @_; # get the incoming MOBY query XML my @queries = getInputs($message); # returns XML::DOM nodes my $RESPONSE = ""; # set empty response foreach my $query(@queries){ my $queryID = getInputID($query); # get the queryID attribute my @input_articles = getArticles($query); foreach my $input(@input_articles){ # input is a listref my ($articleName, $article) = @{$input}; # get the named article my $simple = isSimpleArticle($article); # simple or collection my $collection = isCollectionArticle($article); if ($collection){ # do something wtih the collection... # for example... my @simples = getCollectedSimples($article); # blah blah blah... } elsif ($simple){ # maybe you just need the ID of the incoming query: my ($id) = getSimpleArticleIDs('NCBI_gi', $article); # or maybe you are going to do something with the content? # for example, this will get the array of text lines # for the moby:String object with articleName 'SequenceString' # that is in this $article @s = getNodeContentWithArticle( $article, "String", "SequenceString"); # DO YOUR ANALYSIS HERE my $result = ""; #whatever you analysis says $RESPONSE .= simpleResponse($result, "someName", $queryID); } } } # note that responseHeader now takes an authority argument return responseHeader("my.authURI.com") . $RESPONSE . responseFooter; } M -- Mark Wilkinson Illuminae From markw at illuminae.com Sun Nov 9 00:02:46 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 18:02:46 -0600 Subject: [MOBY-dev] Please introduce yourself. Message-ID: <1068336166.4275.6.camel@localhost.localdomain> mgruenb at gmx.net, please introduce yourself to the rest of the MOBY DEV list. No lurking ;-) Cheers! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Sun Nov 9 00:06:35 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 18:06:35 -0600 Subject: [MOBY-dev] 0.6 API written up Message-ID: <1068336395.4275.11.camel@localhost.localdomain> Available on the TWiki. This contains the changes we made at the MOBY meeting; the change in enumeration of queryInput/Ouput blocks, the deprecation of the Invocation object, the addition of the Xref-type Cross Reference, and the revocation of the rule about ordered outputs. Old-style messages wont "break" anything, but they will not always be valid, so the sooner we migrate to the new API the better. I'm currently writing the CommonSubs code to handle Xref-type cross-references... it might already be working, but I can't remember if I tested it thoroughly in Hixton or not, so... hold your water.... M -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Sun Nov 9 01:59:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 9 Nov 2003 01:59:01 +0000 (GMT) Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068336395.4275.11.camel@localhost.localdomain> Message-ID: Mark, Ken and others, After some struggling (with firewalls etc.) I hope to have a reasonably ready version of Moby Graphs. The main page is here: http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html This page does a bit of explaining - and it should link you to the servlet-based service where you can play with creating various graphs (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). I will be glad to hear your comments. Mark, let me know when is the time to announce it to moby-l (or do it yourself if you wish because I will be travelling the whole week and not sure how I will be connected). Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Sun Nov 9 03:43:18 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 08 Nov 2003 21:43:18 -0600 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <1068349257.1994.56.camel@localhost.localdomain> Hey Martin! What an enormous amount of work you have done! Thank you! I'm going to spend a couple of hours tomorrow playing :-) It looks SO COOL! Everyone, you should check this out!! I'm off to the pub now, though, so I wont test it any more tonight... otherwise you would get some very peculiar feedback ;-) Tonight I'm celebrating the Lunar Eclipse (which was trez groovy!!), and the farewell/retirement party of our Prime Minister, Jean Cretien (YAAAAY! He's GONE!). Hopefully we can start rebuilding the country on Monday morning... Chat tomorrow! Mark On Sat, 2003-11-08 at 19:59, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Mark Wilkinson Illuminae From mgruenb at gmx.net Sun Nov 9 13:32:02 2003 From: mgruenb at gmx.net (Michael Gruenberger) Date: Sun, 09 Nov 2003 13:32:02 +0000 Subject: [MOBY-dev] Re: Please introduce yourself. In-Reply-To: <1068336166.4275.6.camel@localhost.localdomain> References: <1068336166.4275.6.camel@localhost.localdomain> Message-ID: <1068384721.2672.15.camel@vogel> Hello Moby developers, my name is Michael Gruenberger and I work as developer on Pathbase, which is a database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice and we are based at the Department of Anatomy, University of Cambridge. We have already implemented 5 ontologies (from GO + OBO) to describe our data and the next step will be to create a SOAP service and register it with Moby. If you are interested in more info, please have a look at: http://www.pathbase.net I will probably be lurking for a while to see what's going on, but mainly I want to create a Moby service for our database and use some other services as client. As I have written most of our web application / services in PHP I might want to port the Moby API to PHP or maybe write some wrapper functions to call the Perl API. But maybe I misunderstood Moby completely and this doesn't make any sense at all?! Anyway, I thought I'll subscribe to the moby-dev list to see what's happening in the development area of Moby and if it would be feasible or useful to port Moby to PHP. So it would be great if you could let me know what you think about the idea! Cheers, Michael. On Sun, 2003-11-09 at 00:02, Mark Wilkinson wrote: > mgruenb at gmx.net, please introduce yourself to the rest of the MOBY DEV > list. No lurking ;-) > > Cheers! > > Mark -- Michael Gruenberger Computer Officer, University of Cambridge Developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From lstein at cshl.edu Sun Nov 9 17:50:36 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sun, 09 Nov 2003 12:50:36 -0500 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <200311091250.36344.lstein@cshl.edu> That is SO cool! Lincoln On Saturday 08 November 2003 08:59 pm, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From lstein at cshl.edu Sun Nov 9 17:50:36 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sun, 09 Nov 2003 12:50:36 -0500 Subject: [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <200311091250.36344.lstein@cshl.edu> That is SO cool! Lincoln On Saturday 08 November 2003 08:59 pm, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From markw at illuminae.com Sun Nov 9 20:57:55 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 09 Nov 2003 14:57:55 -0600 Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: References: Message-ID: <1068411475.1706.23.camel@localhost.localdomain> Hey Martin, I'm having a lot of fun playing with these graphs :-) I've noticed a couple of things that strike me as odd: 1) build a graph from GenbankAccSequenceRetrieve to PBI_Parse_Blast. If you follow the path from GenbankAccSequenceRetrieve to GenbankAccVirtualSequenceRetrieve to GenbankCompleteSequenceRetrieve you will notice that the first two don't feedback on each other, but the GenbankCompleteSequenceRetrieve does. I think all three of them should feedback on each other (though in the context of finding a path the correct behaviour is probably to suppress this)... so I guess the question is why is it that some services are shown to feed-back, and others, don't even though they could? 2) On your interface page, you have the option to show paths between selected services, where you have the service names in the drop-down menu. Be careful with this, because service name alone isn't sufficient to specify a service. The unique key is authURI + serviceName. What's already striking to me is how many paths I know exist, but are not shown because (a) we don't specify in the registry what Cross-references a service provides, or (b) the output namespace isn't unknown until run-time (e.g. the getGoTermAssociations should, in fact, be able to lead to one or more sequence retrievals because what comes out are usually EMBL ID's or some such thing). This is not a criticism of the graphing, but a criticism of the somewhat impoverished representation of service outputs in the registry... but I don't see a way around that because it is genuinely the case that sometimes you don't know what you are going to get until you run the service. Anyway, it's great fun! Thank you again for spending the time to build this! I wonder if, rather than a service -> service graph, a more useful graph might be from input data-type to output data-type? I only say "more useful" because service names are "officially" meant to be opaque, so the drop-down list of services might not always make as much sense as it currently does when all of our services are "sensibly" named. Is that a more difficult query to execute? In any case, this rocks! Thanks so much for your efforts - I really should repay you by writing that DUMP method that you asked me for last week... you're still too hairy to kiss ;-) Cheers! M On Sat, 2003-11-08 at 19:59, Martin Senger wrote: > Mark, Ken and others, > After some struggling (with firewalls etc.) I hope to have a reasonably > ready version of Moby Graphs. The main page is here: > > http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/index.html > > This page does a bit of explaining - and it should link you to the > servlet-based service where you can play with creating various graphs > (http://www.ebi.ac.uk/collab/mygrid/service2/jmoby/graphs). > > I will be glad to hear your comments. Mark, let me know when is the time > to announce it to moby-l (or do it yourself if you wish because I will be > travelling the whole week and not sure how I will be connected). > > Regards, > Martin -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Mon Nov 10 06:16:37 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 10 Nov 2003 06:16:37 +0000 (GMT) Subject: [MOBY] [MOBY-dev] Moby Graphs version 1.0 (or 0.9?) In-Reply-To: <1068411475.1706.23.camel@localhost.localdomain> Message-ID: Mark, Many thanks for encouragement and for detailed feedback. I will go throught all your comments and observations but perhaps not this week being in Tokyo. But soon! Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From shontaswander at reditus.raiseyou.com Tue Nov 11 11:14:38 2003 From: shontaswander at reditus.raiseyou.com (Cosmetic Forum) Date: Tue, 11 Nov 2003 07:14:38 -0400 Subject: [MOBY-dev] Get Gorgeous, Healthy L|ps - no man can resist! Message-ID: An HTML attachment was scrubbed... URL: From tressiehove at attollo.tubemaker.com Tue Nov 18 10:55:22 2003 From: tressiehove at attollo.tubemaker.com (Females Health News) Date: Tue, 18 Nov 2003 15:55:22 +0500 Subject: [MOBY-dev] Non-surgical L|p Plumping Treatment Message-ID: An HTML attachment was scrubbed... URL: From jessica.hekman at prov.ingenta.com Tue Nov 18 22:35:53 2003 From: jessica.hekman at prov.ingenta.com (Jessica P. Hekman) Date: Tue, 18 Nov 2003 17:35:53 -0500 (EST) Subject: [MOBY-dev] Web page and dist issues Message-ID: Sorry if this is the wrong place to send this, but it wasn't clear where would be better. The link to the Java API docs is broken. The page with the bad link is: http://www.biomoby.org/moby-live/Java/docs/index.html and the link which doesn't work is: http://www.biomoby.org/moby-live/Java/docs/API/index.html Wanting the Java API, I then went to download the dist, hoping it would be in there (looks like it is). I untarred the .tar.gz dist, and it dropped files all over the directory I was in; usually it's best for it to create a subdirectory and stick stuff in there. Neither is a really big problem but I thought I'd drop a line to let you know! Jessica From markw at illuminae.com Tue Nov 18 23:03:47 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 18 Nov 2003 17:03:47 -0600 Subject: [MOBY] [MOBY-dev] Web page and dist issues In-Reply-To: References: Message-ID: <1069196627.1715.63.camel@localhost.localdomain> Hi Jessica, Yes, we are having "issues" with the Java documentation :-) We need to build the documentation (generated by Java's Ant), but Java isn't yet installed on the new server we just moved to. I've just sent a request to do so. please give it a day or two... sorry about that! Mark On Tue, 2003-11-18 at 16:35, Jessica P. Hekman wrote: > Sorry if this is the wrong place to send this, but it wasn't clear where > would be better. > > The link to the Java API docs is broken. The page with the bad link is: > > http://www.biomoby.org/moby-live/Java/docs/index.html > > and the link which doesn't work is: > > http://www.biomoby.org/moby-live/Java/docs/API/index.html > > Wanting the Java API, I then went to download the dist, hoping it would be > in there (looks like it is). I untarred the .tar.gz dist, and it dropped > files all over the directory I was in; usually it's best for it to create > a subdirectory and stick stuff in there. > > Neither is a really big problem but I thought I'd drop a line to let you > know! > > Jessica > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson Illuminae From markw at illuminae.com Tue Nov 18 23:03:47 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 18 Nov 2003 17:03:47 -0600 Subject: [MOBY] [MOBY-dev] Web page and dist issues In-Reply-To: References: Message-ID: <1069196627.1715.63.camel@localhost.localdomain> Hi Jessica, Yes, we are having "issues" with the Java documentation :-) We need to build the documentation (generated by Java's Ant), but Java isn't yet installed on the new server we just moved to. I've just sent a request to do so. please give it a day or two... sorry about that! Mark On Tue, 2003-11-18 at 16:35, Jessica P. Hekman wrote: > Sorry if this is the wrong place to send this, but it wasn't clear where > would be better. > > The link to the Java API docs is broken. The page with the bad link is: > > http://www.biomoby.org/moby-live/Java/docs/index.html > > and the link which doesn't work is: > > http://www.biomoby.org/moby-live/Java/docs/API/index.html > > Wanting the Java API, I then went to download the dist, hoping it would be > in there (looks like it is). I untarred the .tar.gz dist, and it dropped > files all over the directory I was in; usually it's best for it to create > a subdirectory and stick stuff in there. > > Neither is a really big problem but I thought I'd drop a line to let you > know! > > Jessica > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Wed Nov 19 06:11:15 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 19 Nov 2003 06:11:15 +0000 (GMT) Subject: [MOBY-dev] Web page and dist issues In-Reply-To: Message-ID: > The link to the Java API docs is broken. > Yes, Mark is completely right - it's been a "work in progress" (in order to fix it). In the meantime, use my mirror, please: http://industry.ebi.ac.uk/~senger/jMoby/API/index.html. Mark, thanks very much for taking care about the Java questions on the new web server. 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Thanks, CSHL's MOBY team From markw at illuminae.com Sat Nov 22 00:03:50 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 21 Nov 2003 18:03:50 -0600 Subject: [MOBY] Re: [MOBY-dev] meeting minutes under construction In-Reply-To: References: Message-ID: <1069459430.1709.98.camel@localhost.localdomain> Hi Shuly, Since this is addressed to me, I don't know if you intentionally sent this to all of the mailing lists or not... but you did :-) I've just made a small fix that will allow you to run a local MOBY Central, but the error message you are describing isn't consistent with the error that resulted from this bug, so I don't know what is going wrong. Please send me the line of code you are using to connect to your local registry, and any other details that may be important. M On Fri, 2003-11-21 at 16:53, Shuly Avraham wrote: > Hey Mark, > Fiona, Ardi and myself are trying to install the new Moby Central (0.6) > and > write new services. > We followed the local installation procedures, and whenever we run > testMOBYClientCentral_v05.pl pointing to the local moby central server we > get the following error message: > Unexpected Content-Type '' returned > We tested SOAP::Lite and it works fine. > > In addition testMOBYCentral_v05.pl works fine. > > We appreciate any help we can get on this. > > > Thanks, CSHL's MOBY team > > -- Mark Wilkinson Illuminae From v968rvhjte at hotmail.com Sat Nov 22 10:27:39 2003 From: v968rvhjte at hotmail.com (Kellie Greenberg) Date: Sat, 22 Nov 03 10:27:39 GMT Subject: [MOBY-dev] It takes overnight to get to your front door ajw yievdql me Message-ID: <6dhg$d5mcv4487u9l338512$5w-co@qp8f91.n.7o> beebread Online prescriptions for FDA approved medication. 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(I need to tell the EU the participants for this meeting) Rebecca. -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From markw at illuminae.com Mon Nov 24 18:07:09 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 24 Nov 2003 12:07:09 -0600 Subject: [MOBY-dev] bug still there Message-ID: <1069697228.2339.86.camel@localhost.localdomain> Hey Martin, I have fixed the Relationships call so that it only returns the relationship type that you ask for, and it does respond to the expandRelationship flag, but it still returns a redundant list of parent types... I can't see where that redundancy is coming from at the moment, but I'll keep exploring. Hopefully it doesn't do you too much harm to have it there in the short-term the Client library (perl) still does not handle this call properly. I'll get around to that soon, M -- Mark Wilkinson Illuminae From senger at ebi.ac.uk Mon Nov 24 18:29:16 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Nov 2003 18:29:16 +0000 (GMT) Subject: [MOBY-dev] bug still there In-Reply-To: <1069697228.2339.86.camel@localhost.localdomain> Message-ID: > I have fixed the Relationships call so that it only returns the > relationship type that you ask for > Yes, it works... I have tried at once after I saw your commit, thanks from the lightning speed... > but it still returns a redundant list of parent > types... I can't see where that redundancy is coming from at the moment, > but I'll keep exploring. Hopefully it doesn't do you too much harm to > have it there in the short-term > that's fine with me, no harm... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From bvhh69waq at hotmail.com Tue Nov 25 06:58:46 2003 From: bvhh69waq at hotmail.com (Joey Hanson) Date: Tue, 25 Nov 03 06:58:46 GMT Subject: [MOBY-dev] Reach for the ceiling without side effects w Message-ID: <6bhiu49y-o9-1$n569e5@jyyv.1.7e66m> anachronistic Moby-dev Want A Bigger Pen1s? Want A Bigger Pen1s? Gain Up to 3+ Full Inches In Length Increase Your Penis Width (Girth) By 20% Stop Premature Ejaculation! Produce Stronger, Rock Hard Erections A Larger, Harder Penis During Sex 100% Safe To Take, With NO Side Effects Fast Priority Shipping WorldWide Doctor Approved And Recommended No Pumps! No Surgery! 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It's a small and unexciting graph because we have not many service types - but perhaps it can be useful in the future. Both buglist and the new service types graphs will appear on the pages later today or tomorrow after I deploy it. I will send another message when it is done. I am really sorry that I cannot fix all pointed bugs now... Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From info at artinfobank.net Tue Nov 25 17:07:29 2003 From: info at artinfobank.net (Private Banking) Date: Tue, 25 Nov 2003 12:07:29 -0500 Subject: [MOBY-dev] [ADV] The World Leader in Art Market information Message-ID: <200311251707.hAPH7Tg0024599@portal.open-bio.org> An HTML attachment was scrubbed... URL: From senger at ebi.ac.uk Tue Nov 25 17:06:32 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 17:06:32 +0000 (GMT) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: <1068336395.4275.11.camel@localhost.localdomain> Message-ID: Mark et al, I am slowly getting into understanding what was discussed on the last Moby meeting about service invocations. Please be patient with me... I am working now on the Java API of the service invocation - and I need some answers. 1) I understand that there are two usages for the tag . It is used once when one registers a service by Moby Central. And there is another one that is used in the service invocation. The former contains definition of data type, the latter contain a run-time value (of this type). i think that it would be much clearer if we use different tags - for example and . The same applies for collections. Is my understanding correct? 2) The same as above applies also to the secondary parameters. but in this case it is worse because the API does not define (at least I have not found it) what is the structure of the tag "secondaryParameters" (the tag used in run-time to carry value/values of the secondary parameters). 3) Finally, I had to mis a lot - but I do not understand why all those sample (XML) objects in the API table of the hypotetical examples do not have any names (or article names). For example, how one can distringuish between two Strings in the GO_Term object? Thanks for your help and patience, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From 21CFR11 at biozak.com Tue Nov 25 20:08:49 2003 From: 21CFR11 at biozak.com (21CFR11 at biozak.com) Date: Tue, 25 Nov 2003 20:08:49 UT Subject: [MOBY-dev] We have emails of thousands of your prospective customers - life science executives Message-ID: <200311252008.MAA12783@main.biozak.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From 240734 at hotmail.com Wed Nov 26 04:48:52 2003 From: 240734 at hotmail.com (240734 at hotmail.com) Date: Tue, 25 Nov 2003 23:48:52 -0500 Subject: [MOBY-dev] =?iso-8859-1?q?=CD=CE=C2=DB=C9_=C3=CE=C4_=C8_=D0=CE?= =?iso-8859-1?q?=C6=C4=C5=D1=D2=C2=CE_=C2_=D2=C0=CB=CB=C8=CD=C5___2?= =?iso-8859-1?q?40734?= Message-ID: <200311252059.hAPKxVg0027637@portal.open-bio.org> An HTML attachment was scrubbed... URL: From steube at sdsc.edu Tue Nov 25 22:07:21 2003 From: steube at sdsc.edu (Ken Steube) Date: Tue, 25 Nov 2003 14:07:21 -0800 (PST) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: I don't know about 1), but here's some info on the other two: For 2) the API does describe secondary params. Go to http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for 'Secondary'. It has max, min and some other tags. I haven't tried to write any services that use secondary params. Has anyone else? For 3) the strings in GO_Term have been given names. Go to this URL to see them: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=GO_Term Ken On Tue, 25 Nov 2003, Martin Senger wrote: > Mark et al, > I am slowly getting into understanding what was discussed on the last > Moby meeting about service invocations. Please be patient with me... I am > working now on the Java API of the service invocation - and I need some > answers. > > 1) I understand that there are two usages for the tag . It is > used once when one registers a service by Moby Central. And there is > another one that is used in the service invocation. The former contains > definition of data type, the latter contain a run-time value (of this > type). i think that it would be much clearer if we use different tags - > for example and . > The same applies for collections. > Is my understanding correct? > > 2) The same as above applies also to the secondary parameters. but in > this case it is worse because the API does not define (at least I have not > found it) what is the structure of the tag "secondaryParameters" (the tag > used in run-time to carry value/values of the secondary parameters). > > 3) Finally, I had to mis a lot - but I do not understand why all those > sample (XML) objects in the API table of the hypotetical examples do not > have any names (or article names). For example, how one can distringuish > between two Strings in the GO_Term object? > > Thanks for your help and patience, > Martin > > -- ------------------------------------- Ken Steube steube at sdsc.edu San Diego Supercomputer Center @ UCSD San Diego, California USA From steube at sdsc.edu Tue Nov 25 22:07:21 2003 From: steube at sdsc.edu (Ken Steube) Date: Tue, 25 Nov 2003 14:07:21 -0800 (PST) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: I don't know about 1), but here's some info on the other two: For 2) the API does describe secondary params. Go to http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for 'Secondary'. It has max, min and some other tags. I haven't tried to write any services that use secondary params. Has anyone else? For 3) the strings in GO_Term have been given names. Go to this URL to see them: http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=GO_Term Ken On Tue, 25 Nov 2003, Martin Senger wrote: > Mark et al, > I am slowly getting into understanding what was discussed on the last > Moby meeting about service invocations. Please be patient with me... I am > working now on the Java API of the service invocation - and I need some > answers. > > 1) I understand that there are two usages for the tag . It is > used once when one registers a service by Moby Central. And there is > another one that is used in the service invocation. The former contains > definition of data type, the latter contain a run-time value (of this > type). i think that it would be much clearer if we use different tags - > for example and . > The same applies for collections. > Is my understanding correct? > > 2) The same as above applies also to the secondary parameters. but in > this case it is worse because the API does not define (at least I have not > found it) what is the structure of the tag "secondaryParameters" (the tag > used in run-time to carry value/values of the secondary parameters). > > 3) Finally, I had to mis a lot - but I do not understand why all those > sample (XML) objects in the API table of the hypotetical examples do not > have any names (or article names). For example, how one can distringuish > between two Strings in the GO_Term object? > > Thanks for your help and patience, > Martin > > -- ------------------------------------- Ken Steube steube at sdsc.edu San Diego Supercomputer Center @ UCSD San Diego, California USA From 4kvwsqn at prodigy.com Tue Nov 25 22:18:11 2003 From: 4kvwsqn at prodigy.com (Barbra Lackey) Date: Tue, 25 Nov 2003 17:18:11 -0500 Subject: [MOBY-dev] Looking For A Crisis Proof Investment? b Message-ID: <7-59$7eh98-7$na27$6-$ums-po6y1y@0udzxz.ww> An HTML attachment was scrubbed... URL: From senger at ebi.ac.uk Tue Nov 25 22:19:03 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 22:19:03 +0000 (GMT) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Tue Nov 25 22:19:03 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Nov 2003 22:19:03 +0000 (GMT) Subject: [MOBY-dev] questions (mostly) on service invocation In-Reply-To: Message-ID: > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Tue Nov 25 22:18:05 2003 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Tue, 25 Nov 2003 17:18:05 -0500 Subject: [MOBY-dev] questions (mostly) on service invocation Message-ID: <200311252228.hAPMSXg0028235@portal.open-bio.org> It may be that the examples are wrong. I'm on my blackberry right now so I can't check, but I'll have a look later. M -----Original Message----- From: Martin Senger Date: Tue, 25 Nov 2003 22:19:03 To:Ken Steube Cc:Core developer announcements , Mark Wilkinson , mobydev Subject: Re: [MOBY-dev] questions (mostly) on service invocation > For 2) the API does describe secondary params. Go to > http://www.biomoby.org/twiki/bin/view/TWiki/BioMOBYAPI and search for > 'Secondary'. It has max, min and some other tags. > No, that's a description of a service instance (or a data type). I am looking for an XML used in run-time if you really send a secondary parameter to a service. That's what I could not find. > For 3) the strings in GO_Term have been given names. > Does it mean that the table with examples in the API doc is old, or wrong? Thanks, Ken, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger _______________________________________________ MOBY-dev mailing list MOBY-dev at biomoby.org http://www.biomoby.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Nov 26 01:43:10 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 25 Nov 2003 19:43:10 -0600 Subject: [MOBY-dev] java docs built on biomoby.org Message-ID: <1069810989.5387.3.camel@localhost.localdomain> Hey martin, I built your documentation last night. Sorry for the delay - we just got Java installed yesterday. I hope this isn't something that needs to be done often, as it took about 1/2 hour to complete...?? Cheers! Mark -- Mark Wilkinson Illuminae From npsshl at tim.it Wed Nov 26 11:56:21 2003 From: npsshl at tim.it (Terrie Gee) Date: Wed, 26 Nov 03 11:56:21 GMT Subject: [MOBY-dev] masters, MBA, and doctorate (PhD) diplomas available b zxkjuazy Message-ID: U N I V E R S I T Y D I P L O M A ' S Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. Bachelors, masters, MBA, and doctorate (PhD) diplomas available in the field of your choice. Obtain a prosperous future, money earning power, and the admiration of all. No one is turned down. Confidentiality assured. No required tests, classes, books, or interviews. CALL NOW to receive your diploma within days!!! 1-425-669-4485 Call 24 hours a day, 7 days a week, including Sundays and holidays - pc pzan pkqjc fx pig From senger at ebi.ac.uk Wed Nov 26 08:24:05 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 08:24:05 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: <1069810989.5387.3.camel@localhost.localdomain> Message-ID: > I built your documentation last night. Sorry for the delay - we just > got Java installed yesterday. > Perfect, thanks! > I hope this isn't something that needs to be done often, as it took > about 1/2 hour to complete...?? > The first build downloads a lot from the inet. Next builds should be much faster (on my laptop it takes tens of seconds, max 1 minute). And we can still optimalize by building only some build targets if necessary. Let me know if the next build takes also long please. How often? Well, ideally after every cvs update. But in praxis it would be enough to run it much less often. BTW, is there an automatic way to check whether anything changed from the last update? I know that there is a cvs status but I have never used it much (Phil Lord, are you listening on this list? Have you a suggestion for us?) If ther is then we can build only if something changed. Thanks again for taking care about it, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 08:24:05 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 08:24:05 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: <1069810989.5387.3.camel@localhost.localdomain> Message-ID: > I built your documentation last night. Sorry for the delay - we just > got Java installed yesterday. > Perfect, thanks! > I hope this isn't something that needs to be done often, as it took > about 1/2 hour to complete...?? > The first build downloads a lot from the inet. Next builds should be much faster (on my laptop it takes tens of seconds, max 1 minute). And we can still optimalize by building only some build targets if necessary. Let me know if the next build takes also long please. How often? Well, ideally after every cvs update. But in praxis it would be enough to run it much less often. BTW, is there an automatic way to check whether anything changed from the last update? I know that there is a cvs status but I have never used it much (Phil Lord, are you listening on this list? Have you a suggestion for us?) If ther is then we can build only if something changed. Thanks again for taking care about it, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From p.lord at russet.org.uk Wed Nov 26 10:29:21 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: 26 Nov 2003 10:29:21 +0000 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: Martin> BTW, is there an automatic way to check whether anything Martin> changed from the last update? I know that there is a cvs Martin> status but I have never used it much (Phil Lord, are you Martin> listening on this list? Have you a suggestion for us?) If Martin> ther is then we can build only if something changed. I am listening, but I'm not sure why I get the arch geek question! I am not sure quite what you want. You want to update the documentation after the CVS has undergone a checkin? You can certainly do this by adding a watch to the file(s) in question. Or you could run "cvs status" and look for the line "Status: Need". Or trawl through the commit logs. Or you could use something like anthill which will rebuild automatically, every night (or whenever), after something has changed. Cheers Phil From senger at ebi.ac.uk Wed Nov 26 11:43:51 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 11:43:51 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > I am listening, but I'm not sure why I get the arch geek question! > Because I thought that you may know. Sorry, I will never ask again... > I am not sure quite what you want. > I want to run a script (build.sh) after every 'cvs update' (which is invoked automatically every something) if this 'cvs update' brought any change, in any file. And I was asking if such script/program exists or if I need to write it myself. So much for geekness in the question... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 11:43:51 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 11:43:51 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > I am listening, but I'm not sure why I get the arch geek question! > Because I thought that you may know. Sorry, I will never ask again... > I am not sure quite what you want. > I want to run a script (build.sh) after every 'cvs update' (which is invoked automatically every something) if this 'cvs update' brought any change, in any file. And I was asking if such script/program exists or if I need to write it myself. So much for geekness in the question... Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From yxknpbe3m at hotmail.com Wed Nov 26 05:54:56 2003 From: yxknpbe3m at hotmail.com (Myles Patton) Date: Wed, 26 Nov 03 05:54:56 GMT Subject: [MOBY-dev] info you wanted s vaeui ajf Message-ID: U N I V E R S I T Y D I P L O M A ' S Diplomas from prestigious non-accredited universities based on your present knowledge and life experience. Bachelors, masters, MBA, and doctorate (PhD) diplomas available in the field of your choice. Obtain a prosperous future, money earning power, and the admiration of all. No one is turned down. Confidentiality assured. No required tests, classes, books, or interviews. CALL NOW to receive your diploma within days!!! 1-425-669-4485 Call 24 hours a day, 7 days a week, including Sundays and holidays - l gljfhzi h From p.lord at russet.org.uk Wed Nov 26 12:27:14 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: 26 Nov 2003 12:27:14 +0000 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> I am listening, but I'm not sure why I get the arch geek >> question! >> Martin> Because I thought that you may know. Sorry, I will never Martin> ask again... >> I am not sure quite what you want. >> Martin> I want to run a script (build.sh) after every 'cvs Martin> update' (which is Martin> invoked automatically every something) if this 'cvs update' Martin> brought any change, in any file. And I was asking if such Martin> script/program exists or if I need to write it myself. So Martin> much for geekness in the question... Ah, okay. If you are happy for it to run on the server, then you just add a line to the "loginfo" file, which is found in the CVSROOT See for instance... http://olympus.het.brown.edu/cgi-bin/info2www?(cvsbook)Commit+Emails which sets up commit emails. Of course this could also rebuild things. Is this what you were asking for? Cheers Phil From p.lord at russet.org.uk Wed Nov 26 12:27:14 2003 From: p.lord at russet.org.uk (Phillip Lord) Date: 26 Nov 2003 12:27:14 +0000 Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> I am listening, but I'm not sure why I get the arch geek >> question! >> Martin> Because I thought that you may know. Sorry, I will never Martin> ask again... >> I am not sure quite what you want. >> Martin> I want to run a script (build.sh) after every 'cvs Martin> update' (which is Martin> invoked automatically every something) if this 'cvs update' Martin> brought any change, in any file. And I was asking if such Martin> script/program exists or if I need to write it myself. So Martin> much for geekness in the question... Ah, okay. If you are happy for it to run on the server, then you just add a line to the "loginfo" file, which is found in the CVSROOT See for instance... http://olympus.het.brown.edu/cgi-bin/info2www?(cvsbook)Commit+Emails which sets up commit emails. Of course this could also rebuild things. Is this what you were asking for? Cheers Phil From senger at ebi.ac.uk Wed Nov 26 12:34:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 12:34:01 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > Is this what you were asking for? > That's EXACTLY what I was asking for. And obviously I have asked a right person :-) Many thanks, I will investigate in this direction and let Mark know a suggestion what to do. Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Wed Nov 26 12:34:01 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Nov 2003 12:34:01 +0000 (GMT) Subject: [MOBY-dev] java docs built on biomoby.org In-Reply-To: Message-ID: > Is this what you were asking for? > That's EXACTLY what I was asking for. And obviously I have asked a right person :-) Many thanks, I will investigate in this direction and let Mark know a suggestion what to do. Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From wf at world-foundation.org Wed Nov 26 13:05:40 2003 From: wf at world-foundation.org (SN World Foundation) Date: Wed, 26 Nov 2003 14:05:40 +0100 Subject: [MOBY-dev] New Technology for the Third World Message-ID: New Technology for the Third World, November 2003 Production Mini-plants in mobile containers. Worldwide Partners program SN World Foundation will supply to countries and developing regions the technology and necessary support for production in series of Mini-plants in mobile containers (40-foot). 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More than 700 portable production systems: Bakeries, Water purification, Dehydrated food, Steel Nails, Fruit juice preparation, Tire Retreading, Reinforcement Bar Bending for Construction Framework, Sheeting for Roofing, Ceilings and Fa?ades, Plated Drums, Aluminum Buckets, Injected Polypropylene Housewares, Pressed Melamine Items (Glasses, Cups, Plates, Mugs, etc.), Mufflers, Construction Electrically Welded Mesh, Plastic Bags and Packaging, Medical assistance mobile units, Sanitary Material, Hypodermic Syringes, Hemostatic Clamps, etc. SN World Foundation has started a Co-investment program for the installation of small Assembly plants to manufacture in series the Mini-plants of portable production on site, region or country where required. One of the most relevant features is the fact that these plants will be connected to the International Trade System, with access to more than 50 million raw materials, products and services and automatic transactions for world trade. Due to financial reasons, involving cost and social impact, the best solution is setting up assembly plants on the same countries and regions, using local resources (labor, some equipment, etc.) SN World Foundation participates at 50% (fifty percent) for investment of each Assembly plant. If you are interested in being a partner in your country or region, you can send your CV to: SN World Foundation (click here) Worldwide Partners Program By Sarah Mathews, Manager Program ------------------------------------------------------------------------- If you received this in error or would like to be removed from our list, please return us indicating: remove or un-subscribe in subject field, Thanks. Manager Program ? 2003 SN World Foundation. All rights reserved. -------------- next part -------------- An HTML attachment was scrubbed... URL: From markw at illuminae.com Wed Nov 26 16:37:56 2003 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 26 Nov 2003 10:37:56 -0600 Subject: [MOBY-dev] website revamped Message-ID: <3FC4D6E4.1000104@illuminae.com> Hi all, I'm going to a "cleaner & cooler" look on the website. Please have a look and let me know what you think. I haven't yet updated all of the pages, but most of them are now in keeping with the new style. If I have missed referencing anyone's stuff (sorry!) please send me the info, URL, or whatever, and I'll be sure to put it up right away! Cheers, Mark From ddg at ncgr.org Wed Nov 26 17:40:52 2003 From: ddg at ncgr.org (Damian Gessler) Date: Wed, 26 Nov 2003 10:40:52 -0700 Subject: [MOBY-dev] website revamped References: <3FC4D6E4.1000104@illuminae.com> Message-ID: <3FC4E5A4.6858DEBE@ncgr.org> Fabulous improvement, Mark. Nice job. D. Mark Wilkinson wrote: > Hi all, > > I'm going to a "cleaner & cooler" look on the website. Please have a > look and let me know what you think. I haven't yet updated all of the > pages, but most of them are now in keeping with the new style. > > If I have missed referencing anyone's stuff (sorry!) please send me the > info, URL, or whatever, and I'll be sure to put it up right away! > > Cheers, > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev From 240754 at delphi.com Thu Nov 27 05:28:18 2003 From: 240754 at delphi.com (240754 at delphi.com) Date: Thu, 27 Nov 2003 00:28:18 -0500 Subject: [MOBY-dev] =?iso-8859-1?q?=EE=E1=F4=F1=F6=EE=F9=E5_=F0=EF=F4=EF?= =?iso-8859-1?q?=EC=EB=E9_=EF=F4_=2418/=ED_______240754?= Message-ID: <200311262139.hAQLcwg0004520@portal.open-bio.org> An HTML attachment was scrubbed... URL: From senger at ebi.ac.uk Thu Nov 27 00:33:57 2003 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 27 Nov 2003 00:33:57 +0000 (GMT) Subject: [MOBY-dev] Re: [MOBY-l] website revamped In-Reply-To: <3FC4D6E4.1000104@illuminae.com> Message-ID: > If I have missed referencing anyone's stuff (sorry!) please send me the > info, URL, or whatever, and I'll be sure to put it up right away! > Page "Connecting to MOBY-Central" could have also an example in Java. Here it is: --- begin --- import org.biomoby.shared.*; import org.biomoby.client.*; import java.util.*; public class RetrieveServiceTypes { public static void main (String [] args) { try { Central worker = new CentralImpl (CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE); System.out.println ("KNOWN SERVICE TYPES\n"); Map types = worker.getServiceTypes(); for (Iterator it = types.entrySet().iterator(); it.hasNext();) { Map.Entry entry = (Map.Entry)it.next(); System.out.println (entry.getKey()); System.out.println ("\t" + entry.getValue()); } } catch (Exception e) { System.err.println ("===ERROR==="); System.err.println (e.toString()); System.err.println ("==========="); } } } --- end --- Also the Perl example is not complete (and should be). It needs: a) to add use MOBY::Client::Central; b) to add semicolon at the end, and c) print better the result (now it prints just: KNOWN SERVICE TYPES HASH(0x867aed8) Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Thu Nov 27 02:36:41 2003 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Wed, 26 Nov 2003 21:36:41 -0500 Subject: [MOBY-dev] Re: [MOBY-l] website revamped Message-ID: <200311270247.hAR2lJg0005949@portal.open-bio.org> Done. M From c071kj at hotmail.it Wed Nov 26 20:03:15 2003 From: c071kj at hotmail.it (Claire Lloyd) Date: Wed, 26 Nov 03 20:03:15 GMT Subject: [MOBY-dev] Moby-dev Information You need Message-ID: <5-9$k9-77z3$u702-hc6@qpd8p> crate Moby-dev Want A Bigger Pen1s? 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