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From mmhohman@northwestern.edu Thu Jan 2 07:33:56 2003 From: mmhohman@northwestern.edu (Moses Hohman) Date: Thu, 2 Jan 2003 01:33:56 -0600 Subject: [Biojava-dev] moderation of the mailing list Message-ID: <8D3459D3-1E24-11D7-9422-000393DB7722@northwestern.edu> Hi all, Just wondering if there's some way to stop these spam postings. They're kind of out of control. List servers I've worked with in the past have ways of restricting this, by restricting posts to members only and then managing the member list, either by some approval process or just banishing bad behavers (the latter doesn't work for spammers that create bogus memberships on a per message basis, but I've only ever seen those spammers target things like yahoo egroups). thanks, Moses From matthew_pocock@yahoo.co.uk Wed Jan 8 11:27:26 2003 From: matthew_pocock@yahoo.co.uk (=?iso-8859-1?q?Matthew=20Pocock?=) Date: Wed, 8 Jan 2003 11:27:26 +0000 (GMT) Subject: [Biojava-dev] Fwd: Re: [Biojava-l] locating genes in a genomic sequence Message-ID: <20030108112726.81344.qmail@web14912.mail.yahoo.com> --0-528303563-1042025246=:80883 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Content-Disposition: inline In practice, how far from a 1.3.0 release are we? Matthew Note: forwarded message attached. __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com --0-528303563-1042025246=:80883 Content-Type: message/rfc822 X-Apparently-To: matthew_pocock@yahoo.co.uk via 216.136.225.241; 08 Jan 2003 01:20:38 -0800 (PST) X-Track: 1: 100 Return-Path: Received: from 155.94.54.80 (EHLO pw600a.bioperl.org) (155.94.54.80) by mta445.mail.yahoo.com with SMTP; 08 Jan 2003 01:20:37 -0800 (PST) Received: from pw600a.bioperl.org (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h088emSQ001503; Wed, 8 Jan 2003 03:40:48 -0500 Received: from pat.uio.no (IDENT:7411@pat.uio.no [129.240.130.16]) by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h088dvSQ001477 for ; Wed, 8 Jan 2003 03:39:58 -0500 Received: from uracil.uio.no ([129.240.220.11]) by pat.uio.no with esmtp (Exim 2.12 #7) id 18WBlN-0007ky-00; Wed, 8 Jan 2003 09:40:37 +0100 Received: from karinlag by uracil.uio.no with local (Exim 2.12 #1) id 18WBlM-0005q8-00; Wed, 8 Jan 2003 09:40:36 +0100 From: Karin Lagesen To: "Schreiber, Mark" Cc: biojava-l@biojava.org Subject: Re: [Biojava-l] locating genes in a genomic sequence References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i X-Spam-Status: No X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) Sender: biojava-l-admin@biojava.org Errors-To: biojava-l-admin@biojava.org X-BeenThere: biojava-l@biojava.org X-Mailman-Version: 2.0.12 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Biojava discussion list List-Unsubscribe: , List-Archive: Date: Wed, 8 Jan 2003 09:40:36 +0100 Content-Length: 659 On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote: > Hi - > > If you already have the SimpleGene features constructed these will > contain a Location object. However, I think you are saying how can I > find a subsequence in my Genomic sequence and locate the gene that way? > > To rapidly find exact matches you can use the biojava > KnuthMorrisPrattSearch object from the org.biojava.bio.search package. > It contains a main method that demonstrates it's use. This is a very > efficient algorithm for finding exact matches. Thankyou for your help. However, I seem to have a different version of biojava than you, since I cannot find that class in that package (and not in none of the others either). The biojava I am using is version 1.22 downloaded from biojava.org. I did however discover a KnuthMorrisPrattSearch in a biojava API at http://rosetteer.icu.ac.kr/, however, I could not figure out how to get at the actual class.... Am I missing something again? Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l --0-528303563-1042025246=:80883-- From mark.schreiber@agresearch.co.nz Wed Jan 8 20:07:30 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Thu, 9 Jan 2003 09:07:30 +1300 Subject: [Biojava-dev] Fwd: Re: [Biojava-l] locating genes in a genomic sequence Message-ID: Maybe we should do a survey of the bits that are not well covered by unit testing and the bits that do not support minimal javadoc. In the meantime, how about a snapshot? - Mark > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Thursday, 9 January 2003 12:27 a.m. > To: biojava-dev@biojava.org > Subject: [Biojava-dev] Fwd: Re: [Biojava-l] locating genes in > a genomic sequence > > > In practice, how far from a 1.3.0 release are we? > > Matthew > > Note: forwarded message attached. > > __________________________________________________ > Do You Yahoo!? > Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From russell_smithies@hotmail.com Wed Jan 8 22:24:33 2003 From: russell_smithies@hotmail.com (Russell Smithies) Date: Wed, 08 Jan 2003 22:24:33 +0000 Subject: [Biojava-dev] anonymous cvs down? Message-ID: It looks like the anonymous cvs server may be down :-( It doesn't work using the commands from the webpage: cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login Can someone please try it or see what the problem is? It seems to timeout after asking for and receiving the password (cvs). The server seems to be running OK (it can be pinged OK) but won't login. thanx Russell _________________________________________________________________ MSN 8: advanced junk mail protection and 2 months FREE*. http://join.msn.com/?page=features/junkmail From russell.smithies@xtra.co.nz Thu Jan 9 19:16:52 2003 From: russell.smithies@xtra.co.nz (Russell Smithies) Date: Fri, 10 Jan 2003 08:16:52 +1300 Subject: [Biojava-dev] re: anonymous cvs down? References: <20030109170008.14713.84901.Mailman@pw600a.bioperl.org> Message-ID: <001401c2b813$aade25d0$0100a8c0@lexx> Problem solved, it looks like our company may have the port may be blocked :-) It works fine from home but not at work. and cvs works fine from JBuilder7 Russell > Message: 2 > From: "Russell Smithies" > To: biojava-dev@biojava.org, biojava-l@biojava.org > Date: Wed, 08 Jan 2003 22:24:33 +0000 > Subject: [Biojava-dev] anonymous cvs down? > > It looks like the anonymous cvs server may be down :-( > It doesn't work using the commands from the webpage: > cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login > > Can someone please try it or see what the problem is? > > It seems to timeout after asking for and receiving the password (cvs). > The server seems to be running OK (it can be pinged OK) but won't > login. > > thanx > Russell > From mark.schreiber@agresearch.co.nz Mon Jan 13 20:12:02 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Tue, 14 Jan 2003 09:12:02 +1300 Subject: [Biojava-dev] New Snapshot Message-ID: Hi - Could I request a new snapshot of the current codebase? I have been getting a lot of enquiries about people not being able to compile some of the examples in biojava_in_anger with the current release. CVS is a possible solution but the public CVS is blocked by firewalls unless a certain port is open (I can't remember which). Thanks Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cmason@cmason.com Mon Jan 13 22:14:47 2003 From: cmason@cmason.com (Christopher Mason) Date: Mon, 13 Jan 2003 15:14:47 -0700 Subject: [Biojava-dev] Biojava GUI Message-ID: <2147483647.1042470887@[10.0.1.3]> Hi. I wonder what development work is being pursued on the GUI code in biojava, particularly that in org.biojava.bio.gui? I'm interested in working on GUI bits for biojava and have some ideas in this area, but I don't want to step on anyone's toes. I'm hoping to coordinate with anyone already working in this area. Thanks very much, -c [ Christopher Mason http://www.cmason.com/ ] From mark.schreiber@agresearch.co.nz Mon Jan 13 23:12:55 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Tue, 14 Jan 2003 12:12:55 +1300 Subject: [Biojava-dev] Location deprecated methods Message-ID: Hi - If nobody has any complaints I would to suggest that the deprecated Location methods be either removed or undeprecated. From memory they where all deprecated when we realized the system was buggy and switched all the operations to LocationTools. Now that the Locations methods actually use LocationTools the deprecated label is not really needed. Out of habit I use LocationTools as I was burned when Locations didn't work properly but it's probably more elegant to use the intersection, union etc operations from the Location. If this is the case the deprecations can be removed. If this is done the Location javadocs should be updated to strongly recommend that implementation of these methods is best left to LocationTools. The alternative would be to remove these methods from the interface altogether and get everyone using LocationTools. I tend to prefer this but probably its just due to habit. Finaly I see no reason why the symbols() method should be deprecated. It works and it's functionality of producing a SymbolList isn't really replaced by blockIterator(). I'd like to undeprecate it. Any strong views either way. - Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From kalle.naslund@genpat.uu.se Wed Jan 15 17:57:04 2003 From: kalle.naslund@genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Wed, 15 Jan 2003 18:57:04 +0100 Subject: [Biojava-dev] Biojava GUI References: <2147483647.1042470887@[10.0.1.3]> Message-ID: <3E25A0F0.5030509@genpat.uu.se> Christopher Mason wrote: > > Hi. > > I wonder what development work is being pursued on the GUI code in > biojava, particularly that in org.biojava.bio.gui? I'm interested in > working on GUI bits for biojava and have some ideas in this area, but > I don't want to step on anyone's toes. I'm hoping to coordinate with > anyone already working in this area. > > Thanks very much, > > -c > > [ Christopher Mason http://www.cmason.com/ ] > Hi, dunno if i am the person to answear to this, but as i dont see any other replies so far, i will give it a try =). Basicly, not that much have happened lately in the org.biojava.bio.gui part of the source tree, a few small changes here and there but nothing big. New code is always welcome, so my suggestion would be for you to drop another mail here, outlining what it is you want to do. Most likely that will generate some comments, suggestions and ideas for you to proceed with. I have some basic understanding of the org.biojava.bio.gui.seq classes ( i got the basic ideas sorted, but might not have all the small nitty gritty nasty details sorted ) So if needed, i might be able to help you out in the begining aswell. regards Kalle From support@biotaq.com Thu Jan 16 02:17:26 2003 From: support@biotaq.com (support@biotaq.com) Date: Wed, 15 Jan 2003 21:17:26 -0500 Subject: [Biojava-dev] SRI's Antibody World Summit Message-ID: <002702617021013VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net> Antibody World Summit to be Attended by Global Pharma & Biotech Industries in San Diego, CA Feb 24-28, 2003 Jan. 15, San Diego, CA. The world antibody community will convene in San Diego, CA on from February 24-28, 2003 to attend a series of four related antibody meetings in what promises to be the most comprehensive industry information, business development and networking extravaganza ever offered on this topic, announces Strategic Research Institute. The meeting schedule is as follows: Antibody Discovery & Pre-Clinical Drug Development, February 24-26 Antibody Clinical Development & Marketing, February 24-26 Trends in Antibody Deal-Making & Financing, February 27-28 Macromolecule Production & Economics, February 27-28 Detailed agenda and speaker list available at http://www.srinstitute.com/abworldsummit FEATURES: The Summit features over 100 speakers, dozens of exhibits, and will draw over 600+ attendees all focused on every aspect of the field. Research advances, emerging therapeutics, new technologies, antibody marketing, clinical cost optimization, production economics, large scale manufacturing, partnering and financing topics, intellectual property and the latest in the clinical pipeline are some of the Summit highlights. VENUE: The Summit will take place at the Wyndham U.S. Grant in San Diego, CA. Socializing and networking events are scheduled throughout the week. REGISTRATION: To register, call 1-888-666-8514, 646-336-7030, or online at http://www.srinstitute.com/abworldsummit. Mention Priority Code DEM002388 when registering. SPONSORSHIP & EXHIBITION OPPORTUNITIES: To register for the exposition or explore sponsorship opportunities to best suit your goals, please contact Mark Alexay at malexay@srinstitute.com or 212.967.0095 x251. Lead sponsors for the meeting are Amersham Biosciences and Bioforesight Strategies. CONTACT: Ed Drilon Strategic Research Institute 333 Seventh Avenue New York, NY 10001 Tel: 646-336-7030 Email: edrilon@srinstitute.com ******************************************************** This segmented email list tends to serve the people who are interested in news and product info in Proteomics sector. To edit or change your interest category selections or unsubscribe, simply reply to this email. BIOTAQ.COM's email news service is focused exclusively on biotech-related industry. Welcome to join BIOTAQ.COM at: http://www.biotaq.com/Joinbiotaq.htm ************************************************************************** **** From matthew_pocock@yahoo.co.uk Thu Jan 16 16:08:02 2003 From: matthew_pocock@yahoo.co.uk (Matthew Pocock) Date: Thu, 16 Jan 2003 16:08:02 +0000 Subject: [Biojava-dev] Location deprecated methods In-Reply-To: References: Message-ID: <3E26D8E2.6000102@yahoo.co.uk> Hi, My vote is to remove the deprecated methods prior to the 1.3 release. Matthew Schreiber, Mark wrote: > Hi - > > If nobody has any complaints I would to suggest that the deprecated > Location methods be either removed or undeprecated. From memory they > where all deprecated when we realized the system was buggy and switched > all the operations to LocationTools. > > Now that the Locations methods actually use LocationTools the deprecated > label is not really needed. > > Out of habit I use LocationTools as I was burned when Locations didn't > work properly but it's probably more elegant to use the intersection, > union etc operations from the Location. If this is the case the > deprecations can be removed. If this is done the Location javadocs > should be updated to strongly recommend that implementation of these > methods is best left to LocationTools. > > The alternative would be to remove these methods from the interface > altogether and get everyone using LocationTools. I tend to prefer this > but probably its just due to habit. > > Finaly I see no reason why the symbols() method should be deprecated. It > works and it's functionality of producing a SymbolList isn't really > replaced by blockIterator(). I'd like to undeprecate it. > > Any strong views either way. > > - Mark > > > Mark Schreiber PhD > Bioinformatics > AgResearch Invermay > PO Box 50034 > Mosgiel > New Zealand > > PH: +64 3 489 9175 > FAX: +64 3 489 3739 > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From mark.schreiber@agresearch.co.nz Thu Jan 16 20:31:53 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Fri, 17 Jan 2003 09:31:53 +1300 Subject: [Biojava-dev] RE: blast version support Message-ID: Hi - There is a method called setModeLazy() in the SaxLikeBlastParser, it doesn't actually seem to work though. Can someone else on the list confirm it's not just me? James? One way to get around it is to change the blast version to a supported version number. If you do this it's a good idea to check a few by eye as Blast output changes subtly between versions and the parser may not work properly. - Mark > -----Original Message----- > From: Staats, Brian (NIH/NCI) [mailto:staatsb@mail.nih.gov] > Sent: Friday, 17 January 2003 7:51 a.m. > To: Schreiber, Mark > Subject: RE: blast version support > > > I should of added that I have tried your examples in your > "cookbook" on BLAST parsing and I am not able to get anywhere > with the code. I still get errors of unsupported blastn version. > > Thanks again. > > > -----Original Message----- > > From: Staats, Brian (NIH/NCI) > > Sent: Thursday, January 16, 2003 1:46 PM > > To: 'mark.schreiber@agresearch.co.nz' > > Subject: blast version support > > > > Did you ever obtain a solution to parsing blastn files with > > unsupported version numbers with BioJava? Your help is greatly > > appreciated. > > > > Thank you > > > > Brian Staats > > Bioinformatics Programmer Analyst > > NIH/NCI/Core Genotyping Facility > > staatsb@mail.nih.gov > > 301.435.7617(V) > > 301.480.2235 (F) > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber@agresearch.co.nz Thu Jan 16 21:02:37 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Fri, 17 Jan 2003 10:02:37 +1300 Subject: [Biojava-dev] Location deprecated methods Message-ID: In the absence of other votes/ flames the deprecated tags have ceremoniously been deleted :) - Mark > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Friday, 17 January 2003 5:08 a.m. > To: Schreiber, Mark > Cc: biojava-dev@biojava.org > Subject: Re: [Biojava-dev] Location deprecated methods > > > Hi, > > My vote is to remove the deprecated methods prior to the 1.3 release. > > Matthew > > Schreiber, Mark wrote: > > Hi - > > > > If nobody has any complaints I would to suggest that the deprecated > > Location methods be either removed or undeprecated. From > memory they > > where all deprecated when we realized the system was buggy and > > switched all the operations to LocationTools. > > > > Now that the Locations methods actually use LocationTools the > > deprecated label is not really needed. > > > > Out of habit I use LocationTools as I was burned when > Locations didn't > > work properly but it's probably more elegant to use the > intersection, > > union etc operations from the Location. If this is the case the > > deprecations can be removed. If this is done the Location javadocs > > should be updated to strongly recommend that implementation > of these > > methods is best left to LocationTools. > > > > The alternative would be to remove these methods from the interface > > altogether and get everyone using LocationTools. I tend to > prefer this > > but probably its just due to habit. > > > > Finaly I see no reason why the symbols() method should be > deprecated. > > It works and it's functionality of producing a SymbolList > isn't really > > replaced by blockIterator(). I'd like to undeprecate it. > > > > Any strong views either way. > > > > - Mark > > > > > > Mark Schreiber PhD > > Bioinformatics > > AgResearch Invermay > > PO Box 50034 > > Mosgiel > > New Zealand > > > > PH: +64 3 489 9175 > > FAX: +64 3 489 3739 > > > > > ====================================================================== > > = > > Attention: The information contained in this message and/or > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential > and/or privileged > > material. Any review, retransmission, dissemination or > other use of, or > > taking of any action in reliance upon, this information by > persons or > > entities other than the intended recipients is prohibited > by AgResearch > > Limited. If you have received this message in error, please > notify the > > sender immediately. > > > ============================================================== > ========= > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev@biojava.org > > http://biojava.org/mailman/listinfo/biojava-dev > > > > > -- > BioJava Consulting LTD - Support and training for BioJava > http://www.biojava.co.uk > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From russell_smithies@hotmail.com Fri Jan 17 03:16:18 2003 From: russell_smithies@hotmail.com (Russell Smithies) Date: Fri, 17 Jan 2003 03:16:18 +0000 Subject: [Biojava-dev] reading pdb format or using tagvalue? Message-ID: Hi, Has anyone got an example of how to use Matthew's new biojava\bio\program\tagvalue package? I wantto read 'tags' off .pdb files and get the property (atom x,y,z coords) back and to do many(everything Brookhaven/RCSB has maybe?) files so converting to xml first is probably a bit time/resource-consuming. Maybe creating new Annotations is the better way to do it? Or can I trick SeqIOTools.readEmbl() to do it? Any ideas? thanx Russell _________________________________________________________________ MSN 8 helps eliminate e-mail viruses. Get 2 months FREE* http://join.msn.com/?page=features/virus From jourdren@dsvidf.cea.fr Thu Jan 16 11:05:42 2003 From: jourdren@dsvidf.cea.fr (Laurent Jourdren) Date: Thu, 16 Jan 2003 12:05:42 +0100 Subject: [Biojava-dev] patch: GenbankSequenceDB, Retrieved sequences in batch mode Message-ID: <200301161205.42902.jourdren@dsvidf.cea.fr> --------------Boundary-00=_I50TASCQH5IDH2N8Y303 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =09Hello, =09I make a patch to retrieve sequences objects from Entrez 'en masse', r= ather=20 than one at time using NCBI Entrez Programming Utilities. In this case, I= use=20 EFetch method with http post.=20 =20 =09Laurent. --=20 Laurent Jourdren Service de G=E9nomique Fonctionnelle Commissariat =E0 L'Energie Atomique 2 rue Gaston Cr=E9mieux - CP 22 91057 Evry Cedex Tel: 01.60.87.34.76 email: jourdren@dsvidf.cea.fr --------------Boundary-00=_I50TASCQH5IDH2N8Y303 Content-Type: text/x-diff; charset="us-ascii"; name="GenbankSequenceDB.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="GenbankSequenceDB.patch" *** GenbankSequenceDB.java.old 2003-01-16 11:35:41.000000000 +0100 --- GenbankSequenceDB.java 2003-01-16 11:48:05.000000000 +0100 *************** *** 22,27 **** --- 22,29 ---- import java.net.*; import java.io.*; + import java.util.Set; + import java.util.Iterator; import org.biojava.bio.symbol.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.seq.DNATools; *************** *** 29,34 **** --- 31,39 ---- import org.biojava.bio.seq.Sequence; import org.biojava.bio.BioException; import org.biojava.bio.seq.SequenceIterator; + import org.biojava.bio.seq.db.SequenceDB; + import org.biojava.bio.seq.db.HashSequenceDB; + import org.biojava.utils.ChangeVetoException; /** * This class contains functions accessing DNA sequences in Genbank format. *************** *** 42,47 **** --- 47,54 ---- private static String DBName="Genbank";//predefined the database name -- Genbank private boolean IOExceptionFound=false;//check if IOException is found private boolean ExceptionFound=false;//check if any exception is found + private static final String urlBatchSequences = + "http://www.ncbi.nlm.nih.gov:80/entrez/eutils/efetch.fcgi"; static { *************** *** 135,138 **** --- 142,260 ---- { return ExceptionFound; } + + /** + * Create the Http Post Request to fetch (in batch mode) a list of sequence + * with Genbank. + * @param url URL of the request + * @param list List of sequence identifier + * @return The Post request. + */ + private String makeBatchRequest(URL url, Set list) { + + StringBuffer params = new StringBuffer(); + params.append("db=nucleotide&rettype=gb&id="); + + for (Iterator i = list.iterator(); i.hasNext();) { + String idSequence = (String) i.next(); + params.append(idSequence); + params.append(","); + } + + StringBuffer header = new StringBuffer(); + header.append("POST "); + header.append(url.getPath()); + header.append( + " HTTP/1.0\r\n" + + "Connection: close\r\n" + + "Accept: text/html, text/plain\r\n" + + "Host: "); + + header.append(url.getHost()); + header.append( + "\r\n" + + "User-Agent: Biojava/GenbankSequenceDB\r\n" + + "Content-Type: application/x-www-form-urlencoded\r\n" + + "Content-Length: "); + header.append(params.length()); + header.append("\r\n\r\n"); + + StringBuffer request = new StringBuffer(); + request.append(header); + request.append(params); + + return request.toString(); + } + + /** + * Retrieve sequences from a Genbank + * + * @param list List of NCBI sequence number (GI), accession, accession.version, + * fasta or seqid. + * @return The database object (HashSequenceDB) with downloaded sequences. + */ + public SequenceDB getSequences(Set list) throws BioException { + + return getSequences(list, null); + } + + /** + * Retrieve sequences from a Genbank + * + * @param list List of NCBI sequence number (GI), accession, accession.version, + * fasta or seqid. + * @param database Where to store sequences. if database is null, use an + * HashSequenceDB Objet. + * @return The database object with downloaded sequences. + */ + public SequenceDB getSequences(Set list, SequenceDB database) + throws BioException { + + if (database == null) + database = new HashSequenceDB(); + + try { + + URL url = new URL(urlBatchSequences); + int port = url.getPort(); + String hostname = url.getHost(); + + //Open the connection and the streams + Socket s = new Socket(hostname, port); + + InputStream sin = s.getInputStream(); + BufferedReader fromServer = + new BufferedReader(new InputStreamReader(sin)); + OutputStream sout = s.getOutputStream(); + PrintWriter toServer = new PrintWriter(new OutputStreamWriter(sout)); + + // Put the Post request to the server + toServer.print(makeBatchRequest(url, list)); + toServer.flush(); + + // Delete response headers + boolean finEntete = false; + for (String l = null; + ((l = fromServer.readLine()) != null) && (!finEntete); + ) + if (l.equals("")) + finEntete = true; + + SequenceIterator seqI = SeqIOTools.readGenbank(fromServer); + + while (seqI.hasNext()) + database.addSequence(seqI.nextSequence()); + + } catch (MalformedURLException e) { + throw new BioException("Exception found in GenbankSequenceDB -- getSequences"); + } catch (IOException e) { + throw new BioException("Exception found in GenbankSequenceDB -- getSequences"); + } catch (BioException e) { + throw new BioException("Exception found in GenbankSequenceDB -- getSequences"); + } catch (ChangeVetoException e) { + throw new BioException("Exception found in GenbankSequenceDB -- getSequences"); + } + + return database; + } } --------------Boundary-00=_I50TASCQH5IDH2N8Y303-- From matthew_pocock@yahoo.co.uk Fri Jan 17 11:56:40 2003 From: matthew_pocock@yahoo.co.uk (Matthew Pocock) Date: Fri, 17 Jan 2003 11:56:40 +0000 Subject: [Biojava-dev] reading pdb format or using tagvalue? In-Reply-To: References: Message-ID: <3E27EF78.504@yahoo.co.uk> Hi Russell, The tag-value stuff assumes that each line can be broken into a single tag with a value. Things like pdb don't look quite like this (multiple types of values on some lines), but I recently added some handlers to fool the system. You will need the 1.3 snapshot, and a Java 1.4 or higher vm. Start off by creating a LineSplitParser instance. You will then have to configure it to match PDB. For example, each record seems to have a 6 char tag, so you need to call lsp.setSplitOffset(6). Also, every line is a new piece of data (unlike embl where multiple lines with the same tag are part of the same entry), so you need to call lsp.setMergeSameTag(false). Continue in this vein untill you think you have something that should process the skeleton of the file. Then, look at the demo code under demos-1.4/unigene/ParseUnigene.java for a simple skeleton for hooking your customized parser to some debug output. Once this is done, you should be able to see what kind of job it's made of the pdb entries. Now comes the fun bit. The values so far will be single strings for the entire bit of the line that's not a tag. This is next to useless. You realy need to tokenize each line. You do this using a combination of TagDelegator and RegexFieldFinder. Let's call the instance of TagDelegator td. Now, for example, call td.setListener("HEADER", headerHandler). You can make headerHandler an instance of RegexFieldFinder, configure it with a regex to match the name and date and ID, and name them sanely. Don't forget to pass in your debug listener as the delegate for headerHandler - that way the events will get dumped out. For entries like AUTHOR that are lists, you can associate a listener that splits the output up. Use ChangeTable, RegexSplitter and ValueChanger to describe the process. Sorry, this has got too long already. See how far you can get on your own and then pester me. It's not that hard to write these things once you're up to speed, but there's a steep learning curve. Matthew Russell Smithies wrote: > > Hi, > Has anyone got an example of how to use Matthew's new > biojava\bio\program\tagvalue package? > > I wantto read 'tags' off .pdb files and get the property (atom x,y,z > coords) back and to do many(everything Brookhaven/RCSB has maybe?) files > so converting to xml first is probably a bit time/resource-consuming. > > Maybe creating new Annotations is the better way to do it? > Or can I trick SeqIOTools.readEmbl() to do it? > > Any ideas? > > thanx > Russell > > > > > _________________________________________________________________ > MSN 8 helps eliminate e-mail viruses. Get 2 months FREE* > http://join.msn.com/?page=features/virus > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From jj@mail.ahc.umn.edu Fri Jan 17 21:19:15 2003 From: jj@mail.ahc.umn.edu (Jim Johnson (CCGB)) Date: Fri, 17 Jan 2003 15:19:15 -0600 Subject: [Biojava-dev] Biojava GUI In-Reply-To: <3E25A0F0.5030509@genpat.uu.se> References: <2147483647.1042470887@[10.0.1.3]> <3E25A0F0.5030509@genpat.uu.se> Message-ID: <3E287353.6040401@mail.med.umn.edu> Kalle Näslund wrote: > Christopher Mason wrote: > >> >> Hi. >> >> I wonder what development work is being pursued on the GUI code in >> biojava, particularly that in org.biojava.bio.gui? I'm interested in >> working on GUI bits for biojava and have some ideas in this area, but >> I don't want to step on anyone's toes. I'm hoping to coordinate with >> anyone already working in this area. >> >> Thanks very much, >> >> -c >> >> [ Christopher Mason http://www.cmason.com/ ] >> > Hi, dunno if i am the person to answear to this, but as i dont see any > other replies so far, i will give it a try =). > > Basicly, not that much have happened lately in the org.biojava.bio.gui > part of the source tree, a few small > changes here and there but nothing big. > > New code is always welcome, so my suggestion would be for you to drop > another mail here, outlining what it > is you want to do. Most likely that will generate some comments, > suggestions and ideas for you to proceed with. > > I have some basic understanding of the org.biojava.bio.gui.seq classes ( > i got the basic ideas sorted, but might not > have all the small nitty gritty nasty details sorted ) So if needed, i > might be able to help you out in the begining > aswell. > > regards Kalle > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > > I've been interested in adding more features to the biojava GUI. I would also like to see the development of applications that can be launched through JavaWebStart. I like Jalview as a model of what we could add in GUI package: Mutliple views of the datamodel. Coordinated selection that would be represented in all views. Properties such as various color models that could be coordinated across views. Article: http://acer.gen.tcd.ie/embnet.news/vol5_4/embnet/body_jalview.html/ Availability: http://circinus.ebi.ac.uk:6543/jalview/ and http://www2.ebi.ac.uk/clustalw JavaWebStart: http://mgd.ahc.umn.edu/java/apps/Jalview.jnlp I started prototyping some color schemes into a biojava demo last spring: JavaWebStart: http://mgd.ahc.umn.edu/java/apps/BiojavaDemo.jnlp Snaps: http://mgd.ahc.umn.edu/java/apps/BioJavaDemo_expanded.jpg http://mgd.ahc.umn.edu/java/apps/BioJavaDemo_scaled.jpg I thought it might make sense to have a StyleManager that would be the repository for color mapping schemes available for particular alphabets. Default color schemes could be loaded from resources in a similar fashion to the AlphabetManager. NCBI has started work on a Genome WorkBench. It looks similar in concept to the Sequence Feature viewer. I've employed the datamodel with muliple view and common selection in another project: http://ccgb.umn.edu/software/java/apps/TableView/ JJ -- James E. Johnson Center for Computational Genomics and Bioinformatics Mayo Mail Code 43, AHC, University of Minnesota 420 Delaware St SE Minneapolis, MN 55455 612-626-6937 From mark.schreiber@agresearch.co.nz Sun Jan 19 22:51:36 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Mon, 20 Jan 2003 11:51:36 +1300 Subject: [Biojava-dev] Two IndexStores??? Message-ID: Hi - Is it possible to not have two interfaces called IndexStore which are both involved in OBDC functionality? This is really confusing!!! - Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber@agresearch.co.nz Mon Jan 20 01:48:19 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Mon, 20 Jan 2003 14:48:19 +1300 Subject: [Biojava-dev] Biojava GUI Message-ID: > I like Jalview as a model of what we could add in GUI package: > > Mutliple views of the datamodel. > Coordinated selection that would be represented in all views. > Properties such as various color models that could be coordinated > across views. I'd like to add copy paste functionality to the list. PS your stuff looks really good. - Mark ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber@agresearch.co.nz Mon Jan 20 03:18:31 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Mon, 20 Jan 2003 16:18:31 +1300 Subject: [Biojava-dev] SequenceDBInstallation Message-ID: Hi - Is there a reason why SequenceDBInstallation cannot hold SequenceDBLite objects. The interface addSequenceDB method specifies SequenceDB but I can't see why it couldn't add SequenceDB lite. This would mean it could add things like BioFetch and GenbankSequenceDB objects. The real beauty is that changing it to SequenceDBLite won't break a thing! - Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From kalle.naslund@genpat.uu.se Mon Jan 20 10:46:12 2003 From: kalle.naslund@genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Mon, 20 Jan 2003 11:46:12 +0100 Subject: [Biojava-dev] Biojava GUI References: <2147483647.1042470887@[10.0.1.3]> <3E25A0F0.5030509@genpat.uu.se> <3E287353.6040401@mail.med.umn.edu> Message-ID: <3E2BD374.7040003@genpat.uu.se> Jim Johnson (CCGB) wrote: > > I've been interested in adding more features to the biojava GUI. > I would also like to see the development of applications that > can be launched through JavaWebStart. > > > I like Jalview as a model of what we could add in GUI package: > > Mutliple views of the datamodel. > Coordinated selection that would be represented in all views. > Properties such as various color models that could be coordinated > across views. In theory you can already have multiple views of the same datamodel =) ( i have just tried it a tiny bit so i dont know how well it works in reality, the code might need some polishing here and there ). Basicly, nothing stops you from connecting the same Sequence object to several SequencePanels and then just set different ranges and scales on those. When it comes to coordinate selection that can be represented in all views, a simple solution is just to make a simple SequenceRenderer that renders a BOX or similar to mark the selection, and just share that renderer between the different views. An alternative is to have different renderers but have them share a common swing data model. If i remember correctly i think i have something like this lying in some directory, i could try to dig it upp if people think it would be usefull. So, hopefully it wont be hard to get multiple views and selection working well. Standardized color models would be a good thing to have, i have always found it annoying to have to "mix" my colours myself, and i seem to always get the shade slightly different from other apps =). regards Kalle From matthew_pocock@yahoo.co.uk Mon Jan 20 11:09:55 2003 From: matthew_pocock@yahoo.co.uk (Matthew Pocock) Date: Mon, 20 Jan 2003 11:09:55 +0000 Subject: [Biojava-dev] SequenceDBInstallation In-Reply-To: References: Message-ID: <3E2BD903.3060604@yahoo.co.uk> I don't see why not. Do you want to make the change? Matthew Schreiber, Mark wrote: > Hi - > > Is there a reason why SequenceDBInstallation cannot hold SequenceDBLite > objects. The interface addSequenceDB method specifies SequenceDB but I > can't see why it couldn't add SequenceDB lite. This would mean it could > add things like BioFetch and GenbankSequenceDB objects. > > The real beauty is that changing it to SequenceDBLite won't break a > thing! > > - Mark > > > Mark Schreiber PhD > Bioinformatics > AgResearch Invermay > PO Box 50034 > Mosgiel > New Zealand > > PH: +64 3 489 9175 > FAX: +64 3 489 3739 > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From support@biotaq.com Tue Jan 21 01:29:25 2003 From: support@biotaq.com (support@biotaq.com) Date: Mon, 20 Jan 2003 20:29:25 -0500 Subject: [Biojava-dev] IBC Life Sciences Presents Protein Discovery & Engineering Message-ID: <004052529011513VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net> IBC Life Sciences Presents Protein Discovery & Engineering When: March 24-27, 2003 Where: San Francisco, CA, USA Learn more and register! http://www.LifeSciencesInfo.com/protein?source=2845btq IBC's Protein Discovery & Engineering event will bring together the technologies and tools enabling research in these 2 critical areas for a 4-day, 2-conference forum featuring: Protein Discovery Technologies: Directed Evolution Monday - Tuesday, March 24 - 25, 2003 Take a look at phage, yeast, ribosome and other technologies that enable the engineering and discovery of proteins, and implement evolutionary algorithms of mutation and selection to obtain new functional features. Evolving enzymes and functional peptides Protein-protein interactions Construction of libraries from new scaffolds Expression and folding of proteins from combinatorial libraries Engineered Protein Expression: The Latest Tools Wednesday - Thursday, March 26 - 27, 2003 Learn about the latest innovative advances occurring in protein expression for discovery purposes -- engineered expression hosts, the expression of multiple members of protein families, structural protein elements, membrane and signaling proteins as well as post-translational modifications and associated purification techniques. in vivo expression in vitro protein expression Expressing membrane associated proteins Expression systems and applications This combined event unites renowned scientists and researchers from disciplines including display technologies, molecular biology, cell biology, biochemistry, chemistry, target validation, protein engineering, protein expression, chemical engineering, drug discovery and proteomics. Join these industry leaders as they share their discoveries and new research initiatives at this 4-day combined event. Register Today! To review the complete program and to register online, please visit IBC's Protein Discovery & Engineering Web site at: http://www.lifesciencesinfo.com/protein?source=2845btq-reg Phone: (508) 616-5550 * Fax: (508) 616-5522 * E-Mail: inq@ibcusa.com ******************************************************** This segmented email list tends to serve the people who are interested in news and product info in Proteomics sector. To edit or change your interest category selections or unsubscribe, simply reply to this email. To distribute your news to this list, contact sales@biotaq.com. BIOTAQ.COM's email news service is focused exclusively on biotech-related industry. Welcome to join BIOTAQ.COM at: http://www.biotaq.com/Joinbiotaq.htm ************************************************************************** **** From mark.schreiber@agresearch.co.nz Tue Jan 21 03:32:29 2003 From: mark.schreiber@agresearch.co.nz (Schreiber, Mark) Date: Tue, 21 Jan 2003 16:32:29 +1300 Subject: [Biojava-dev] SequenceDBInstallation Message-ID: Hi - Made the changes, Unit tests seem to pass, let me know if I've broken anything and I'll change it back. - Mark > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Tuesday, 21 January 2003 12:10 a.m. > To: Schreiber, Mark > Cc: biojava-dev@biojava.org > Subject: Re: [Biojava-dev] SequenceDBInstallation > > > I don't see why not. Do you want to make the change? > > Matthew > > Schreiber, Mark wrote: > > Hi - > > > > Is there a reason why SequenceDBInstallation cannot hold > > SequenceDBLite objects. The interface addSequenceDB method > specifies > > SequenceDB but I can't see why it couldn't add SequenceDB > lite. This > > would mean it could add things like BioFetch and GenbankSequenceDB > > objects. > > > > The real beauty is that changing it to SequenceDBLite won't break a > > thing! > > > > - Mark > > > > > > Mark Schreiber PhD > > Bioinformatics > > AgResearch Invermay > > PO Box 50034 > > Mosgiel > > New Zealand > > > > PH: +64 3 489 9175 > > FAX: +64 3 489 3739 > > > > > ====================================================================== > > = > > Attention: The information contained in this message and/or > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential > and/or privileged > > material. Any review, retransmission, dissemination or > other use of, or > > taking of any action in reliance upon, this information by > persons or > > entities other than the intended recipients is prohibited > by AgResearch > > Limited. If you have received this message in error, please > notify the > > sender immediately. > > > ============================================================== > ========= > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev@biojava.org > > http://biojava.org/mailman/listinfo/biojava-dev > > > > > -- > BioJava Consulting LTD - Support and training for BioJava > http://www.biojava.co.uk > > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From kevin.echols@syngenta.com Wed Jan 22 22:30:28 2003 From: kevin.echols@syngenta.com (kevin.echols@syngenta.com) Date: Wed, 22 Jan 2003 17:30:28 -0500 Subject: [Biojava-dev] Multi Line Comments Message-ID: All Is it possible to get biojava to generate single comment lines? Currently Vector NTI does not handle mult-line comments. For example using the Biojava API "SeqIOTools.writeGenbank(OutputStream, Sequence)" The Genbank file is written as follows: =================================================== LOCUS 444444 55555 bp DNA circular 17-OCT-2002 SOURCE ORGANISM COMMENT werwerwerwerwe werwerwerwer werwerwerewrere ewrwerwrwerew werwerwerwer errewrwrew ewrrwerewrwer ==================================================== However Vector NTI expects it to look like this: ==================================================== LOCUS 444444 55555 bp DNA circular 17-OCT-2002 SOURCE ORGANISM COMMENT werwerwerwerwe COMMENT werwerwerwer COMMENT werwerwerewrere COMMENT ewrwerwrwerew COMMENT werwerwerwer COMMENT errewrwrew COMMENT ewrrwerewrwer ==================================================== From support@biotaq.com Thu Jan 23 01:30:48 2003 From: support@biotaq.com (support@biotaq.com) Date: Wed, 22 Jan 2003 20:30:48 -0500 Subject: [Biojava-dev] IBC Life Sciences 2003 Conference Collection Message-ID: <003ae4830011713VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net> IBC Life Sciences 2003 Conference Collection Information on the Knowledge You Need, Answers to the Challenges You Face Preview the Lineup Today Westborough, MA, January 23, 2003 -- From North America to Europe, IBC Life Sciences continues to supply the life science industry with specialized information through quality learning and networking events organized into three primary market sectors: Drug Discovery, Biopharmaceutical Production and Microtechnology. Read below for a select listing of conferences and see why we are recognized around the globe for quality, service and value. DRUG DISCOVERY SERIES Global events highlighting technological advancements and applications in niche areas of the drug discovery pipeline. Topics include genomics, proteomics, target validation, high-throughput screening, assay development, bioinformatics, ADME toxicology and more. Applications of RNA Interface February 10-11, 2003, San Diego, CA http://www.lifesciencesinfo.com/RNAi?source=btq-rnai Genomic & Proteomic Technological Advances in Cancer Research February 10-12, 2003, Bethesda, MD http://www.lifesciencesinfo.com/2808?source=btq-2808 BioTechniques(R) Live! March 5, 2003, Boston, MA http://www.biotechniqueslive.com/?source=btq-btlive Pharmacology for Drug Discovery & Development March 17-18, 2003, Boston, MA http://www.lifesciencesinfo.com/2840?source=btq-2840 ScreenTech(R) World Summit March 23-27, 2003, San Diego, CA http://www.lifesciencesinfo.com/screentech?source=btq-stech Four Events - One Venue · HTS & Assay Technologies · Protein Kinases & Phosphatases · Protease Inhibitors ·In Silico & Experimental Target Validation Protein Discovery & Engineering March 24-27, 2003, San Francisco, CA http://www.lifesciencesinfo.com/protein?source=btq-protein Four Days - Two Conferences Protein Discovery Technologies: Directed Evolution Engineered Protein Expression: The Latest Tools Drug Discovery Technology European Congress March 31-April 3, 2003, Stuttgart, Germany http://www.drugdisc.com/europe?source=btq-ddtuk Drug Discovery Technology™ World Congress August 10-15, 2003, Boston, MA http://www.drugdisc.com/us?source=btq-ddtus BIOPHARMACEUTICAL PRODUCTION SERIES Global conferences and courses covering the latest information on technologies, economics and regulatory strategies that facilitate the production of biopharmaceuticals. Subjects include upstream through downstream process design, development and scale-up; process validation; viral clearance; process optimization; project planning; drug development, formulation and stability. Process Validation for Biologicals March 3-4, 2003, La Jolla, CA http://www.lifesciencesinfo.com/process?source=btq-process Antibody Partnering & Collaboration March 3-4, 2003, La Jolla, CA http://www.lifesciencesinfo.com/2837?source=btq-2837 Antibody Production & Downstream Processing March 5-7, 2003, La Jolla, CA http://www.lifesciencesinfo.com/antibodyprod?source=btq-antiprod TIDES 2003: Oligonucleotide and Peptide(R) Technologies Conference April 28-May 1, 2003, Las Vegas, NV http://www.lifesciencesinfo.com/tides?source=btq-tides Recombinant Antibodies May 13-14, 2003, Munich, Germany http://www.ibc-lifesci.com/antibodies?source=btq-antibod MICROTECHNOLOGY SERIES Global events providing first-hand information on the latest emerging technology and applications. This series meets the informational needs of industry and academia by presenting the latest innovations and applications, as well as evaluation of emerging technologies. Subjects include microarray technologies, bioMEMs and microfluidics, informatics, molecular diagnostics and more. InfoTechPharma 2003 February 10-13, 2003, London, UK http://www.infotechpharma.com/?source=btq-infotech BioMEMs & Microfluidics April 30-May 2, 2003, San Diego, CA http://www.lifesciencesinfo.com/2881?source=btq-2881 EuroBiochips 2003 May 20-23, 2003, London, UK http://www.eurobiochips.com/?source=btq-eurobio Chips to Hits(R) October 27-31, 2003, Boston, MA http://www.chipstohits.com/?source=btq-chips For more information on these conferences or to register, visit the conference-specific Web site listed above, call (508) 616-5550, e-mail reg@ibcusa.com or visit our main Web site at www.LifeSciencesInfo.com?source=btq-lsi ABOUT IBC LIFE SCIENCES The worldwide leader in scientific, technical and business conferences and courses in the drug discovery arena. During the past year, IBC has experienced substantial growth and emerged as the premier information provider to the market. IBC Life Sciences actively researches the advancements, technologies and trends impacting and driving the race for new drugs and therapies. No other organization can make claim to the breadth and quality that IBC Life Sciences delivers in each event. ******************************************************** This segmented email list tends to serve the people who are interested in news and product info in Proteomics sector. To edit or change your interest category selections or unsubscribe, simply reply to this email. To distribute your news to this list, contact sales@biotaq.com. BIOTAQ.COM's email news service is focused exclusively on biotech-related industry. Welcome to join BIOTAQ.COM at: http://www.biotaq.com/Joinbiotaq.htm ************************************************************************** **** From mmhohman@northwestern.edu Thu Jan 23 16:53:45 2003 From: mmhohman@northwestern.edu (Moses Hohman) Date: Thu, 23 Jan 2003 10:53:45 -0600 Subject: [Biojava-dev] interested in helping where needed Message-ID: <3C241DF8-2EF3-11D7-827B-000393DB7722@northwestern.edu> Hi all, I'm interested in getting involved with biojava. A little about my background: I have a PhD in physics (2000, U Chicago); worked for 3 years thereafter as a Java developer doing web-based, J2EE business software, progressing to a mentor role; have extensive experience with unit testing/JUnit (I taught a class on programming and XP in Bangalore, India for my company at a post-bac institution there); and am currently working at Northwestern University's Center for Functional Genomics as a project/development manager on a project that is more informatics than bioinformatics but at least the business domain is biological/genetic in nature. In addition, I don't always speak in run-on sentences. How can I help? thanks, Moses From matthew_pocock@yahoo.co.uk Fri Jan 24 13:06:38 2003 From: matthew_pocock@yahoo.co.uk (Matthew Pocock) Date: Fri, 24 Jan 2003 13:06:38 +0000 Subject: [Biojava-dev] interested in helping where needed In-Reply-To: <3C241DF8-2EF3-11D7-827B-000393DB7722@northwestern.edu> References: <3C241DF8-2EF3-11D7-827B-000393DB7722@northwestern.edu> Message-ID: <3E313A5E.6030507@yahoo.co.uk> Hi Moses, Good to hear from you. We're always keen to hear from new developers. Is there anything that you are particularly interested in? We're gearing up for the 1.3 release. At this point, the main way you could contribute is by writing documentation and JUnit tests. I have no idea what the test coverage is like but it should be higher. Perhaps if you took a class without a test, read the docs, and then wrote better docs & a unit test. Matthew Moses Hohman wrote: > Hi all, > > I'm interested in getting involved with biojava. A little about my > background: I have a PhD in physics (2000, U Chicago); worked for 3 > years thereafter as a Java developer doing web-based, J2EE business > software, progressing to a mentor role; have extensive experience with > unit testing/JUnit (I taught a class on programming and XP in Bangalore, > India for my company at a post-bac institution there); and am currently > working at Northwestern University's Center for Functional Genomics as a > project/development manager on a project that is more informatics than > bioinformatics but at least the business domain is biological/genetic in > nature. In addition, I don't always speak in run-on sentences. > > How can I help? > > thanks, > > Moses > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From mark.schreiber at agresearch.co.nz Mon Jan 27 13:17:59 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sun Jan 26 19:09:37 2003 Subject: [Biojava-dev] Multi Line Comments Message-ID: Hi - It's actually perfectly valid GenBank to have only one Comment entry. Having said that I find this to be a problem with VectorNTI also so when I next have five minutes I will look into making a IO customization to support this problem. - Mark > -----Original Message----- > From: kevin.echols@syngenta.com [mailto:kevin.echols@syngenta.com] > Sent: Thursday, 23 January 2003 11:30 a.m. > To: biojava-dev@biojava.org > Subject: [Biojava-dev] Multi Line Comments > > > All > > Is it possible to get biojava to generate single comment lines? > > Currently Vector NTI does not handle mult-line comments. For > example using the Biojava API > "SeqIOTools.writeGenbank(OutputStream, Sequence)" The Genbank > file is written as follows: > > =================================================== > LOCUS 444444 55555 bp DNA circular > 17-OCT-2002 > SOURCE > ORGANISM > COMMENT werwerwerwerwe > werwerwerwer > werwerwerewrere > ewrwerwrwerew > werwerwerwer > errewrwrew > ewrrwerewrwer ==================================================== > > However Vector NTI expects it to look like this: > > > > ==================================================== > > > LOCUS 444444 55555 bp DNA circular > 17-OCT-2002 > SOURCE > ORGANISM > COMMENT werwerwerwerwe > COMMENT werwerwerwer > COMMENT werwerwerewrere > COMMENT ewrwerwrwerew > COMMENT werwerwerwer > COMMENT errewrwrew > COMMENT ewrrwerewrwer > ==================================================== > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Mon Jan 27 14:11:04 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Sun Jan 26 20:02:43 2003 Subject: [Biojava-dev] Nucleotide Alphabet? Message-ID: Hi - I noticed the arrival of the Nucleotide Alphabet and NucleotideTools in cvs. Can someone provide a quick overview of what they are for?? Cheers Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From matthew_pocock at yahoo.co.uk Mon Jan 27 18:36:55 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Mon Jan 27 13:45:59 2003 Subject: [Biojava-dev] GenebankSequenceDB patch Message-ID: <3E357C47.7090502@yahoo.co.uk> Hi all, I've just applied a patch to GenebankSeqeunceDB kindly provided by Laurent Jourden. It should allow batch-fetching of sequences. The code looks sane, but I don't know much about the current ncbi cgis. Could somebody better qualified than me review this code & see if the same patch can be applied to the other ncbi sequence DBs? Thanks, Matthew -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From mark.schreiber at agresearch.co.nz Tue Jan 28 09:24:05 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Jan 27 15:16:04 2003 Subject: [Biojava-dev] RE: [Biojava-l] BLAST Parser in Anger! Message-ID: Hi - There are some deficiencies in the blast parsing API. I know that there is some reluctance to add new methods to the interface as things will break, however blast parsing is a core task and it would be v good if we could make this more functional. One way to get around the interface thing is to simlply extend it and then make all the classes we have now implement the extended interface. Another way is to simply break the interface before bj1.3 is released and make it stable from there on. Can we please, please sort this out before bj1.3 is released? Perhaps the development team could get together over a beer at the hackathon and nut this one out. It really can't be that hard can it? Hear endeth the sermon. - Mark > -----Original Message----- > From: staatsb [mailto:staatsb@mail.nih.gov] > Sent: Tuesday, 28 January 2003 6:19 a.m. > To: biojava-l@biojava.org > Subject: [Biojava-l] BLAST Parser in Anger! > > > I was successful in getting the BLAST parser to work outlined by the > "BioJava in Anger" doc by changing the version number too > 2.0.11 (thank > you Mark Schreiber X2). However, a few of the APIs dont seem to > function i.e. getSequenceID() is not recognized, but I dont think > thats due to the version change. Also, I have noticed many API calls > to certain BLAST file features missing i.e. getQueryID, getGaps, > getQuerySequence, getSubjectSequence, and more. Are these really > missing or does the programmer (me) need to define them from the APIs > existing structure? Has anyone else been able to obtain these > features with the missing APIs? Can anyone offer any advise, > suggestions, explanations, etc, to these issues? > > Thanks > > Brian Staats > Bioinformatics Programmer Analyst > NIH/NCI/Core Genotyping Facility > staatsb@mail.nih.gov > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Tue Jan 28 12:05:43 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Mon Jan 27 17:57:19 2003 Subject: [Biojava-dev] CrossProductAlphabet index breaking Serialization Message-ID: Hi - The recent changes to Alphabet indexing are breaking the serialization of crossproduct alphabets like the phred alphabet. Specifically, in line 131 of the AlphabetSerializationTest. It used to work really well! Can someone fix this or roll back the changes please? - Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From RPark at lexgen.com Mon Jan 27 18:01:10 2003 From: RPark at lexgen.com (Park, Roy) Date: Mon Jan 27 18:52:56 2003 Subject: [Biojava-dev] Feature parsing error throwing nasty BioException Message-ID: <80A38867B1DBD511A8C9009027764C8C6D557F@lexchange.lexgen.com> Could we do something about this - sometimes I don't need to parse the Features at all, and by throwing BioException, my entire sequence is thrown out. Any suggestions? Roy *************************************************************************** The contents of this communication are intended only for the addressee and may contain confidential and/or privileged material. If you are not the intended recipient, please do not read, copy, use or disclose this communication and notify the sender. Opinions, conclusions and other information in this communication that do not relate to the official business of my company shall be understood as neither given nor endorsed by it. *************************************************************************** From kalle.naslund at genpat.uu.se Tue Jan 28 01:03:23 2003 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Mon Jan 27 18:54:05 2003 Subject: [Biojava-dev] CrossProductAlphabet index breaking Serialization In-Reply-To: References: Message-ID: <3E35C8CB.5070809@genpat.uu.se> Schreiber, Mark wrote: >Hi - > >The recent changes to Alphabet indexing are breaking the serialization >of crossproduct alphabets like the phred alphabet. Specifically, in line >131 of the AlphabetSerializationTest. > >It used to work really well! Can someone fix this or roll back the >changes please? > > > Hi! I might be the culprit responsible for this :/ I recently commited a class called CrossProductAlphabetIndex, but, i havent touched any other code at all. So i am a bit baffled on how this resulted in serialization breaking for other classes. You got any clues on how me adding a single class, with no changes whatsoever to other code might result in this ? I wil try to figure this out tommorow though. hope i didnt cause to much trouble mvh Kalle From td2 at sanger.ac.uk Tue Jan 28 10:06:42 2003 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Jan 28 04:58:30 2003 Subject: [Biojava-dev] Re: [Biojava-l] BLAST Parser in Anger! In-Reply-To: References: Message-ID: <20030128100642.GA501562@jabba.sanger.ac.uk> On Tue, Jan 28, 2003 at 09:24:05AM +1300, Schreiber, Mark wrote: > Hi - > > There are some deficiencies in the blast parsing API. I know that there > is some reluctance to add new methods to the interface as things will > break, however blast parsing is a core task and it would be v good if we > could make this more functional. One way to get around the interface > thing is to simlply extend it and then make all the classes we have now > implement the extended interface. > > Another way is to simply break the interface before bj1.3 is released > and make it stable from there on. > > Can we please, please sort this out before bj1.3 is released? Perhaps > the development team could get together over a beer at the hackathon and > nut this one out. It really can't be that hard can it? Am I right in thinking that this is just going to be adding accessors to the interfaces? That's actually a relatively low-risk change, especially since I don't think there are any implementations of those interfaces outside the biojava-live tree (someone please correct me if I'm wrong here). If it meant removing methods or changing their contracts, that's quite a different thing. How long do you think this would take to do? Thomas. From matthew_pocock at yahoo.co.uk Tue Jan 28 09:59:45 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Jan 28 05:09:30 2003 Subject: [Biojava-dev] Re: [Biojava-l] BLAST Parser in Anger! In-Reply-To: References: Message-ID: <3E365491.6070208@yahoo.co.uk> Please, let's get it right b4 1.3 goes live - I know we're meant to be only making small changes now, but blast parsing is so important that it's worth doing properly. Mark, do you have a list of methods you want added/removed/renamed, or are the problems more deep-seated than that? Matthew Schreiber, Mark wrote: > Hi - > > There are some deficiencies in the blast parsing API. I know that there > is some reluctance to add new methods to the interface as things will > break, however blast parsing is a core task and it would be v good if we > could make this more functional. One way to get around the interface > thing is to simlply extend it and then make all the classes we have now > implement the extended interface. > > Another way is to simply break the interface before bj1.3 is released > and make it stable from there on. > > Can we please, please sort this out before bj1.3 is released? Perhaps > the development team could get together over a beer at the hackathon and > nut this one out. It really can't be that hard can it? > > Hear endeth the sermon. > > - Mark > > >>-----Original Message----- >>From: staatsb [mailto:staatsb@mail.nih.gov] >>Sent: Tuesday, 28 January 2003 6:19 a.m. >>To: biojava-l@biojava.org >>Subject: [Biojava-l] BLAST Parser in Anger! >> >> >>I was successful in getting the BLAST parser to work outlined by the >>"BioJava in Anger" doc by changing the version number too >>2.0.11 (thank >>you Mark Schreiber X2). However, a few of the APIs dont seem to >>function i.e. getSequenceID() is not recognized, but I dont think >>thats due to the version change. Also, I have noticed many API calls >>to certain BLAST file features missing i.e. getQueryID, getGaps, >>getQuerySequence, getSubjectSequence, and more. Are these really >>missing or does the programmer (me) need to define them from the APIs >>existing structure? Has anyone else been able to obtain these >>features with the missing APIs? Can anyone offer any advise, >>suggestions, explanations, etc, to these issues? >> >>Thanks >> >>Brian Staats >>Bioinformatics Programmer Analyst >>NIH/NCI/Core Genotyping Facility >>staatsb@mail.nih.gov >> >>_______________________________________________ >>Biojava-l mailing list - Biojava-l@biojava.org >>http://biojava.org/mailman/listinfo/biojava-l >> > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From matthew_pocock at yahoo.co.uk Tue Jan 28 10:37:52 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Tue Jan 28 05:48:31 2003 Subject: [Biojava-dev] CrossProductAlphabet index breaking Serialization In-Reply-To: <3E35C8CB.5070809@genpat.uu.se> References: <3E35C8CB.5070809@genpat.uu.se> Message-ID: <3E365D80.7010501@yahoo.co.uk> Test passes for me now. In CVS. Could you check it works for you? Kalle N?slund wrote: > Schreiber, Mark wrote: > >> Hi - >> >> The recent changes to Alphabet indexing are breaking the serialization >> of crossproduct alphabets like the phred alphabet. Specifically, in line >> 131 of the AlphabetSerializationTest. >> >> It used to work really well! Can someone fix this or roll back the >> changes please? >> >> >> > Hi! > > I might be the culprit responsible for this :/ I recently commited a > class called > CrossProductAlphabetIndex, but, i havent touched any other code at all. > So i am > a bit baffled on how this resulted in serialization breaking for other > classes. You got > any clues on how me adding a single class, with no changes whatsoever to > other code > might result in this ? > > I wil try to figure this out tommorow though. > > hope i didnt cause to much trouble > > mvh Kalle > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From mark.schreiber at agresearch.co.nz Wed Jan 29 10:11:02 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Jan 28 16:02:49 2003 Subject: [Biojava-dev] CrossProductAlphabet index breaking Serialization Message-ID: Hi - I am getting a different error now, very strange one too. Details are below. JDK 1.3.1 on True64, Maybe I need to switch to 1.4?? Testsuite: org.biojava.bio.symbol.AlphabetSerializationTest Tests run: 6, Failures: 0, Errors: 1, Time elapsed: 1.86 sec ------------- Standard Output --------------- [org.biojava.bio.symbol.LinearAlphabetIndex@8090cc5, org.biojava.bio.symbol.LinearAlphabetIndex@80a0900] ------------- ---------------- --------------- Testcase: testIntegerSerialization took 1.598 sec Testcase: testDoubleSerialization took 0.009 sec Testcase: testSubInt took 0.02 sec Testcase: testDNASerialization took 0.021 sec Testcase: testPhredSerialization took 0.177 sec Caused an ERROR null org.biojava.bio.symbol.IllegalSymbolException: Can't find symbol for [org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol@275, org.biojava.bio.s ymbol.AlphabetManager$WellKnownAtomicSymbol@8076f38] in alphabet (DNA x SubIntegerAlphabet[0..99]) at org.biojava.bio.symbol.SimpleCrossProductAlphabet.getSymbolImpl (SimpleCrossProductAlphabet.java:176) (pc 51) at org.biojava.bio.symbol.AbstractAlphabet.getSymbol (AbstractAlphabet.java:188) (pc 174) at org.biojava.bio.symbol.CrossProductAlphabetIndex.symbolForIndex (CrossProductAlphabetIndex.java:139) (pc 87) rethrown as org.biojava.bio.BioError at org.biojava.bio.symbol.CrossProductAlphabetIndex.symbolForIndex (CrossProductAlphabetIndex.java:142) (pc 99) at org.biojava.bio.symbol.AlphabetSerializationTest.equalSymbols (pc 28) at org.biojava.bio.symbol.AlphabetSerializationTest.testPhredSerialization (pc 60) at java.lang.reflect.Method.invoke (Method.java) Testcase: testPhredSerializationTestcase: testCustom took 0.003 sec > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Tuesday, 28 January 2003 11:38 p.m. > To: Kalle N?slund > Cc: Schreiber, Mark; biojava-dev@biojava.org > Subject: Re: [Biojava-dev] CrossProductAlphabet index > breaking Serialization > > > Test passes for me now. In CVS. Could you check it works for you? > > Kalle N?slund wrote: > > Schreiber, Mark wrote: > > > >> Hi - > >> > >> The recent changes to Alphabet indexing are breaking the > >> serialization of crossproduct alphabets like the phred alphabet. > >> Specifically, in line 131 of the AlphabetSerializationTest. > >> > >> It used to work really well! Can someone fix this or roll back the > >> changes please? > >> > >> > >> > > Hi! > > > > I might be the culprit responsible for this :/ I recently commited a > > class called > > CrossProductAlphabetIndex, but, i havent touched any other > code at all. > > So i am > > a bit baffled on how this resulted in serialization > breaking for other > > classes. You got > > any clues on how me adding a single class, with no changes > whatsoever to > > other code > > might result in this ? > > > > I wil try to figure this out tommorow though. > > > > hope i didnt cause to much trouble > > > > mvh Kalle > > > > > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev@biojava.org > > http://biojava.org/mailman/listinfo/biojava-dev > > > > > -- > BioJava Consulting LTD - Support and training for BioJava > http://www.biojava.co.uk > > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Wed Jan 29 11:08:05 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Jan 28 16:59:49 2003 Subject: [Biojava-dev] RE: [Biojava-l] BLAST Parser in Anger! Message-ID: Hi - The only changes I know of are adding accessors to the interface (or a subinterface if you really want to avoid breakage). As for time, not sure. I'm not very familiar with the internals of the blast parsing API. I suppose as long as the SAXAdapter can produce everything in the BlastLikeDataSetCollection.dtd, It would be great to have methods to access all the info that the dtd supports. - Mark > -----Original Message----- > From: Thomas Down [mailto:td2@sanger.ac.uk] > Sent: Tuesday, 28 January 2003 11:07 p.m. > To: Schreiber, Mark > Cc: biojava-dev@biojava.org > Subject: Re: [Biojava-l] BLAST Parser in Anger! > > > On Tue, Jan 28, 2003 at 09:24:05AM +1300, Schreiber, Mark wrote: > > Hi - > > > > There are some deficiencies in the blast parsing API. I know that > > there is some reluctance to add new methods to the > interface as things > > will break, however blast parsing is a core task and it would be v > > good if we could make this more functional. One way to get > around the > > interface thing is to simlply extend it and then make all > the classes > > we have now implement the extended interface. > > > > Another way is to simply break the interface before bj1.3 > is released > > and make it stable from there on. > > > > Can we please, please sort this out before bj1.3 is > released? Perhaps > > the development team could get together over a beer at the > hackathon > > and nut this one out. It really can't be that hard can it? > > Am I right in thinking that this is just going to be adding > accessors to the interfaces? That's actually a relatively > low-risk change, especially since I don't think there are any > implementations of those interfaces outside the biojava-live > tree (someone please correct me if I'm wrong here). If it > meant removing methods or changing their contracts, that's > quite a different thing. > > How long do you think this would take to do? > > Thomas. > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From mark.schreiber at agresearch.co.nz Wed Jan 29 11:11:56 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Tue Jan 28 17:03:46 2003 Subject: [Biojava-dev] RE: [Biojava-l] BLAST Parser in Anger! Message-ID: Hi - I don't think the problems are deepseated. Actually the BlastParsing API is really good. Basically if we can add appropriate accessor methods for all the info available in the BlastLikeDataCollection.dtd then the API will pretty much do everything you could want. The other option would be to write a SAX parser for the new NCBI blast dtd. This might be a bit of a major overhaul but it could be a nice standardization. I think it would be worth delaying 1.3 till we get this fully functional. - Mark > -----Original Message----- > From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] > Sent: Tuesday, 28 January 2003 11:00 p.m. > To: Schreiber, Mark > Cc: staatsb; biojava-l@biojava.org; biojava-dev@biojava.org > Subject: Re: [Biojava-l] BLAST Parser in Anger! > > > Please, let's get it right b4 1.3 goes live - I know we're > meant to be > only making small changes now, but blast parsing is so important that > it's worth doing properly. > > Mark, do you have a list of methods you want > added/removed/renamed, or > are the problems more deep-seated than that? > > Matthew > > Schreiber, Mark wrote: > > Hi - > > > > There are some deficiencies in the blast parsing API. I know that > > there is some reluctance to add new methods to the > interface as things > > will break, however blast parsing is a core task and it would be v > > good if we could make this more functional. One way to get > around the > > interface thing is to simlply extend it and then make all > the classes > > we have now implement the extended interface. > > > > Another way is to simply break the interface before bj1.3 > is released > > and make it stable from there on. > > > > Can we please, please sort this out before bj1.3 is > released? Perhaps > > the development team could get together over a beer at the > hackathon > > and nut this one out. It really can't be that hard can it? > > > > Hear endeth the sermon. > > > > - Mark > > > > > >>-----Original Message----- > >>From: staatsb [mailto:staatsb@mail.nih.gov] > >>Sent: Tuesday, 28 January 2003 6:19 a.m. > >>To: biojava-l@biojava.org > >>Subject: [Biojava-l] BLAST Parser in Anger! > >> > >> > >>I was successful in getting the BLAST parser to work outlined by the > >>"BioJava in Anger" doc by changing the version number too > >>2.0.11 (thank > >>you Mark Schreiber X2). However, a few of the APIs dont seem to > >>function i.e. getSequenceID() is not recognized, but I dont think > >>thats due to the version change. Also, I have noticed many > API calls > >>to certain BLAST file features missing i.e. getQueryID, getGaps, > >>getQuerySequence, getSubjectSequence, and more. Are these really > >>missing or does the programmer (me) need to define them > from the APIs > >>existing structure? Has anyone else been able to obtain these > >>features with the missing APIs? Can anyone offer any advise, > >>suggestions, explanations, etc, to these issues? > >> > >>Thanks > >> > >>Brian Staats > >>Bioinformatics Programmer Analyst > >>NIH/NCI/Core Genotyping Facility > >>staatsb@mail.nih.gov > >> > >>_______________________________________________ > >>Biojava-l mailing list - Biojava-l@biojava.org > >>http://biojava.org/mailman/listinfo/biojava-l > >> > > > > > ====================================================================== > > = > > Attention: The information contained in this message and/or > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential > and/or privileged > > material. Any review, retransmission, dissemination or > other use of, or > > taking of any action in reliance upon, this information by > persons or > > entities other than the intended recipients is prohibited > by AgResearch > > Limited. If you have received this message in error, please > notify the > > sender immediately. > > > ============================================================== > ========= > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > > -- > BioJava Consulting LTD - Support and training for BioJava > http://www.biojava.co.uk > > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From support at biotaq.com Tue Jan 28 23:32:08 2003 From: support at biotaq.com (support@biotaq.com) Date: Tue Jan 28 23:23:53 2003 Subject: [Biojava-dev] IBC LIFE SCIENCES 10TH ANNUAL ANTIBODY PRODUCTION & DOWNSTREAM PROCESSING EVENT Message-ID: <001f90832041d13VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net> KEITH WEBBER, Ph.D., OF CBER, FDA TO PRESENT AT IBC LIFE SCIENCES 10TH ANNUAL ANTIBODY PRODUCTION & DOWNSTREAM PROCESSING EVENT IBC's Antibody Production & Downstream Processing is celebrating 10 years of providing superior content and networking to the Biopharmaceutical industry. It has announced that Keith Webber, of CBER and FDA will present the Keynote Address at this meeting to be held on March 5-7, 2003 at the Hilton La Jolla Torrey Pines in La Jolla, CA. Co-Located with Process Validation for Biologicals and Antibody Partnering & Collaboration both held March 3-4, 2003, this 10 year celebration will provide the top notch presenters a venue to discuss the essentials for producing therapeutic antibodies and learn how to maximize production efficiency. The meeting is expected to surpass its previous year's attendance of over 500 attendees and over 40 exhibit booths. Keith Webber, Director, Division of Monoclonal Antibodies, Office of Therapeutic Research and Review, CBER, FDA will present the Keynote Address on FDA Regulation of Biologics Produced in Bioengineered Plants. Dr. Webber is Chair of the FDA/USDA Interagency Working Group that has recently published a draft Guidance for Industry on drugs, biologics, and medical devices derived from bioengineered plants for use in humans and animals. The content of the meeting focuses primarily on the most relevant aspects of antibody manufacturing. Some of the highlights will include: · Thomas Harnett revealing the design considerations for start-up and operation of Centocor's new Malvern, PA Facility · Greg Blank of Genentech discussing the criteria for what makes a good manufacturing process within the context of high volume production · Brian Hubbard of Amgen divulging the changes implemented to the approved commercial process for manufacture of Enbrel® · Lynn Conley of IDEC Pharmaceuticals detailing the challenges encountered with developing the purification and conjugation process for Zevalin · Reed Harris of Genentech delivering new data about the impact of c glycans on the clearance of XolairTM For more information on attending Antibody Production & Downstream Processing in La Jolla, March 5-7, 2003, visit http://www.lifesciencesinfo.com/antibodyprod Or call 508-616-5550, X1004 ******************************************************** This segmented email list tends to serve the people who are interested in news and product info in Proteomics sector. To edit or change your interest category selections or unsubscribe,simply reply to this email. To distribute your releases to this list, contact sales@biotaq.com. BIOTAQ.COM's email news service is focused exclusively on biotech industry. Welcome to join BIOTAQ.COM at: http://www.biotaq.com/Joinbiotaq.htm ************************************************************************** ** From matthew_pocock at yahoo.co.uk Wed Jan 29 15:29:01 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Jan 29 10:41:45 2003 Subject: [Biojava-dev] CrossProductAlphabet index breaking Serialization In-Reply-To: References: Message-ID: <3E37F33D.3050305@yahoo.co.uk> Schreiber, Mark wrote: > Hi - > > I am getting a different error now, very strange one too. Details are below. JDK 1.3.1 on True64, Maybe I need to switch to 1.4?? > > org.biojava.bio.symbol.IllegalSymbolException: Can't find symbol for [org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol@275, org.biojava.bio.s > ymbol.AlphabetManager$WellKnownAtomicSymbol@8076f38] in alphabet (DNA x SubIntegerAlphabet[0..99]) weird - the symbol is of the form (5,A) but the alphabet is (DNA x [0..99] which presumably likes things of the form (A,5). Found a potential bug that seems to remove the symptom. Writing JUnit regression tests now. Matthew -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From tasan at eecs.cwru.edu Thu Jan 30 16:13:29 2003 From: tasan at eecs.cwru.edu (Murat Tasan) Date: Thu Jan 30 16:04:59 2003 Subject: [Biojava-dev] SequenceDB way too big!!! Message-ID: I've just started using biojava to help in my development of sequence analysis and searching projects, but I have run into a huge (no pun intended) problem. I make a call to SeqIOTools.readFasta(...), to read a FASTA file of approximately 14MB in size. Because the file is only 14MB or so, I figure getting a SequenceDB object from it will AT WORST take up twice that in memory (~30MB) (with all of the extra information associated with sequences... although my FASTA file has just sequence data). Instead, my virtual machine eventually crashes out as I run out of memory. I watched the execution using 'top' and witnessed over 75MB being allocated to the running process. Is there a more efficient implementation of this? Better yet, can anyone tell me why so much space is being taken up for only 14MB of sequence data? Thanks for any help!!!! Murat -- Murat Tasan mxt6@po.cwru.edu tasan@eecs.cwru.edu http://genomics.cwru.edu From mark.schreiber at agresearch.co.nz Fri Jan 31 11:13:15 2003 From: mark.schreiber at agresearch.co.nz (Schreiber, Mark) Date: Thu Jan 30 17:05:28 2003 Subject: [Biojava-dev] SequenceDB way too big!!! Message-ID: Hi - Have you tried using the -XMx option to assign more memory to the VM? - Mark > -----Original Message----- > From: Murat Tasan [mailto:tasan@eecs.cwru.edu] > Sent: Friday, 31 January 2003 10:13 a.m. > To: biojava-dev@biojava.org > Subject: [Biojava-dev] SequenceDB way too big!!! > > > I've just started using biojava to help in my development of > sequence analysis and searching projects, but I have run into > a huge (no pun > intended) problem. I make a call to > SeqIOTools.readFasta(...), to read a FASTA file of > approximately 14MB in size. Because the file is only 14MB or > so, I figure getting a SequenceDB object from it will AT > WORST take up twice that in memory (~30MB) (with all of the > extra information associated with sequences... although my > FASTA file has just sequence data). Instead, my virtual > machine eventually crashes out as I run out of memory. I > watched the execution using 'top' and witnessed over 75MB > being allocated to the running process. > > Is there a more efficient implementation of this? Better > yet, can anyone tell me why so much space is being taken up > for only 14MB of sequence data? > > Thanks for any help!!!! > > Murat > > -- > Murat Tasan > mxt6@po.cwru.edu > tasan@eecs.cwru.edu > http://genomics.cwru.edu > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From matthew_pocock at yahoo.co.uk Fri Jan 31 12:09:27 2003 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Fri Jan 31 07:41:47 2003 Subject: [Biojava-dev] SequenceDB way too big!!! In-Reply-To: References: Message-ID: <3E3A6777.7020501@yahoo.co.uk> Hi Murat, I think (though I may be wrong) that sequences of this sort of size get internaly represented using binary bit-packing. I will investigate for you. On unixy platforms (Tru64 is a bad offender on this), the vm often reserves much more memory than it actualy uses. It tends to grab blocks of memory in case it needs it in the future. If the memory is not used by the VM, then it is available to other applications, even though it shows up on top. Relatively trivial java apps on Tru64 can claim to be using 120M, but you can run loads of these apps, far exceeeding the physical memory of the box without causing it to swap. Having said this, you should not be getting memory-related crashes with this size of file. I'll take a peek. As Mark said, the quick fix is to run java with the "-Xmxmb" switch - replace with some number of megabytes to allocate e.g. 500. It's an upper limit on how far the process can grow before running out of memory, and won't require the vm to use that amount of space. Matthew Murat Tasan wrote: > I've just started using biojava to help in my development of sequence > analysis and searching projects, but I have run into a huge (no pun > intended) problem. I make a call to SeqIOTools.readFasta(...), to read a > FASTA file of approximately 14MB in size. Because the file is only 14MB > or so, I figure getting a SequenceDB object from it will AT WORST take up > twice that in memory (~30MB) (with all of the extra information associated > with sequences... although my FASTA file has just sequence data). > Instead, my virtual machine eventually crashes out as I run out of memory. > I watched the execution using 'top' and witnessed over 75MB being > allocated to the running process. > > Is there a more efficient implementation of this? Better yet, can anyone > tell me why so much space is being taken up for only 14MB of sequence > data? > > Thanks for any help!!!! > > Murat > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk From support at biotaq.com Fri Jan 31 13:06:06 2003 From: support at biotaq.com (support@biotaq.com) Date: Fri Jan 31 12:58:26 2003 Subject: [Biojava-dev] CHI's PepTalk event piques the interest ofproteomics researchers Message-ID: <001970606181f13VIRTUALSCAPE18@VIRTUALSCAPE18.Hostcentric.Net> Cambridge Healthtech Institute's PepTalk event piques the interest ofproteomics researchers This four-day event took place January 13-16, 2003 in San Diego, California and delivered the ideal mix of science, discussion and networking missing from many recent proteomic events. Over 600 protein researchers and biotech business leaders experienced the expanded agenda at PepTalk 2003. The first two days of PepTalk was composed of three concurrent tracks on Protein Arrays, Protein Informatics and Protein Expression. All three of these tracks were busy and attendees showed their enthusiasm by asking many questions during each session panel discussions. Over 60% of those participating in the track sessions stayed on to hear the latest on the Human Proteome Project including updates on HUPO's five initiatives. Attendees at the two days of the Human Proteome Project forum were presented with true insight into the future of proteomics and were active partici- pants in defining the future of the Human Proteome Project. Click here to be receive details on next year’s event: http://www.chi-peptalk.com/info.asp Here's what attendees were saying about the event: "Once again CHI has produced another successful conference. I always find that CHI has a good balance of excellent talks and a comprehensive exhibit hall with all the key people in attendance. PepTalk proved to be successful for us." Russell Wheatcroft, Technology Networks Ltd "I would recommend my colleagues attend the next Peptalk conference. Holding the conference in San Diego in January is the best place and time for us. I really enjoyed the conference and learned a great deal." Rick Chu, Ph.D., Aventis Pharmaceuticals, Inc. The meeting also included great opportunities for networking including receptions, multiple breaks as well as the one of a kind Proteins in 3D keynote. Exhibiting companies exhibiting were thrilled by both the volume and quality of visitors that stopped by their booths. Many exhibitors have already reserved their booth space for next year's event. Read two articles about the event at http:// www.proteomonitor.com: ARTICLE TITLES: Arrays, Expression, and Informatics: Proteins get PepTalk at CHI meeting HUPO, Opening It's Umbrella, Reports Progress on Initiatives, Adds Education CHI is determined to deliver the latest and most exciting proteomic science at PepTalk. We appreciate all those that participated at this year's event. Special thanks to all our 2003 Sponsors: VivaScience Invitrogen NonLinear Physiome Sciences Confirmant Accelrys Cipheragen PEPTALK 2004 January 12-15, 2004 San Diego, California http://www.chi-peptalk.com ******************************************************** This segmented email list tends to serve the people who are interested in news and product info in Proteomics sector. To edit or change your interest category selections or unsubscribe,simply reply to this email. To distribute your releases to this list, contact sales@biotaq.com. BIOTAQ.COM's email news service is focused exclusively on biotech industry. Welcome to join BIOTAQ.COM at: http://www.biotaq.com/Joinbiotaq.htm ************************************************************************** ** From saran123in at yahoo.com Fri Jan 31 23:14:26 2003 From: saran123in at yahoo.com (saravanan saravanan) Date: Sat Feb 1 02:05:49 2003 Subject: [Biojava-dev] Please help me to install Biojava Message-ID: <20030201071426.29040.qmail@web14106.mail.yahoo.com> Dear sir I am failing to install biojava.As per your www.biojava.org I have loaded,after I compiled some files it's giving error.Please send the details for installation. by Saravanan __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com