[EMBOSS] EMBOSS Digest, Vol 48, Issue 2

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> Today's Topics:
>
>    1. Re: [emboss-dev] EMBOSS Funding and New developments (Peter Rice)
>    2. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio)
>    3. Re: EMBOSS Funding and New developments (Peter Rice)
>    4. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio)
>    5. Re: EMBOSS Funding and New developments (Guy Bottu)
>    6. Packaging EMBOSS for Fedora (Julian Sikorski)
>    7. Re: Packaging EMBOSS for Fedora (Mahmut Uludag)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 09 Jun 2009 16:11:58 +0100
> From: Peter Rice <pmr at ebi.ac.uk>
> Subject: Re: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments
> To: George Magklaras <georgios at biotek.uio.no>
> Cc: emboss <emboss at emboss.open-bio.org>
> Message-ID: <4A2E7BBE.8030500 at ebi.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
>
> George Magklaras wrote:
>> That's very good news Peter.
>>
>> I would add to the list the production of documentation for the EMBOSS
>> admins. In terms of improving the indexing, may node managers (including
>> myself) have created scripts to automate the formatting of large
>> databases. Maybe it might be an idea to include them in some sort of
>> add-on section, so that people can have error-free formatted dbs with
>> the click of a button or a script call.
>
> Documentation is on the way in the form of an Administrators Guide ...
> long promised but we are now adding the final touches to the text.
>
> The book will be open source and the text will also appear on the EMBOSS
> website.
>
> As to the scripts ... yes, and excellent suggestion. We could make a
> directory adminscripts in the distribution for these.
>
> Please contribute useful scripts for use to include. We would like to
> include some documentation on what the script is intended to do and how
> to modify it. As the target users are administrators, we can expect them
> to be able to make their own modifications.
>
> regards,
>
> Peter Rice
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 9 Jun 2009 17:44:54 +0200
> From: "Giovanni Marco Dall'Olio" <dalloliogm at gmail.com>
> Subject: Re: [EMBOSS] EMBOSS Funding and New developments
> To: Peter Rice <pmr at ebi.ac.uk>
> Cc: emboss-announce at emboss.open-bio.org,
> 	emboss-dev at emboss.open-bio.org,	emboss <emboss at emboss.open-bio.org>
> Message-ID:
> 	<5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Jun 8, 2009 at 3:41 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
>> Dear EMBOSS Users and Developers
>>
>
>
>>   Suggestions for new applications are very welcome.
>>
>
> I think EMBOSS is highly effective when combined with Makefiles or tools
> to
> describe pipelines.
> Maybe in the future you could add some recipe or example in the
> documentation, it would be useful. In any case, it would be good to add to
> the tutorials some references on methods to describe pipelines.
>
> Another need that people have asked me several times (I am administrator
> of
> a web forum on bioinformatics) is to have a standard and official web
> interface to the emboss tools, since the list at
> http://emboss.sourceforge.net/interfaces/#web is outdated and google
> doesn't
> return clear results.
>
>
>
>
>>
>>
>> We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of
>> this month, We will arrange a lunchtime "Birds of a Feather" session
>> at ISMB to discuss the needs of users over the next 3 years.
>>
>> regards,
>>
>> Peter Rice
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>
>
>
> --
> Giovanni Dall'Olio, phd student
> Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
>
> My blog on bioinformatics: http://bioinfoblog.it
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 09 Jun 2009 16:59:45 +0100
> From: Peter Rice <pmr at ebi.ac.uk>
> Subject: Re: [EMBOSS] EMBOSS Funding and New developments
> To: dalloliogm at gmail.com
> Cc: emboss-dev at emboss.open-bio.org, emboss
> 	<emboss at emboss.open-bio.org>
> Message-ID: <4A2E86F1.2050507 at ebi.ac.uk>
> Content-Type: text/plain; charset=UTF-8
>
> Giovanni Marco Dall'Olio wrote:
>> I think EMBOSS is highly effective when combined with Makefiles or tools
>> to
>> describe pipelines.
>> Maybe in the future you could add some recipe or example in the
>> documentation, it would be useful. In any case, it would be good to add
>> to
>> the tutorials some references on methods to describe pipelines.
>
> What pipelines so users prefer?
>
> We have experience with Taverna and with SoapLab web services. We have
> also worked with Accelrys/Scitegic's Pipeline Pilot. These all include
> EMBOSS examples in their documentation.
>
>> Another need that people have asked me several times (I am administrator
>> of
>> a web forum on bioinformatics) is to have a standard and official web
>> interface to the emboss tools, since the list at
>> http://emboss.sourceforge.net/interfaces/#web is outdated and google
>> doesn't
>> return clear results.
>
> We have long hoped that one interface would become the standard. Our
> usual recommendation for web-based users is the wEMBOSS interface but
> when ever we ask which interfaces users prefer we get many different
> replies.
>
> So, please let us know which interfaces you like best and we will try to
> work with the developers to make sure it keeps up with changes to EMBOSS
> ... and we can try to help them by adding new features or by
> automatically building their interface to a new EMBOSS release.
>
> regards,
>
> Peter Rice
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 9 Jun 2009 19:11:11 +0200
> From: "Giovanni Marco Dall'Olio" <dalloliogm at gmail.com>
> Subject: Re: [EMBOSS] EMBOSS Funding and New developments
> To: Peter Rice <pmr at ebi.ac.uk>
> Cc: emboss-dev at emboss.open-bio.org, emboss
> 	<emboss at emboss.open-bio.org>
> Message-ID:
> 	<5aa3b3570906091011v16ea5f89h55c14928e4b4361d at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
>> Giovanni Marco Dall'Olio wrote:
>> > I think EMBOSS is highly effective when combined with Makefiles or
>> tools
>> to
>> > describe pipelines.
>> > Maybe in the future you could add some recipe or example in the
>> > documentation, it would be useful. In any case, it would be good to
>> add
>> to
>> > the tutorials some references on methods to describe pipelines.
>>
>> What pipelines so users prefer?
>>
>> We have experience with Taverna and with SoapLab web services. We have
>> also worked with Accelrys/Scitegic's Pipeline Pilot. These all include
>> EMBOSS examples in their documentation.
>
>
> Yes, taverna and soaplab services are very good but they are more oriented
> to write applications that connect to Internet and execute tools which are
> also web services.
>
> Sometimes you need much simpler tools, e.g. organize a workflow of command
> line tools to be run in local on an unix shell, and this is something for
> which emboss is very good, since it resembles many unix tools like grep
> and
> similar.
>
> My favorite introduction to Makefiles is the one on the Software Carpentry
> manual:
> - http://swc.scipy.org/lec/build.html
>
> I could write some example for you if you want, but actually I haven't
> been
> using emboss for a while, so.. let me re-read the documentation first :-)
>
>
>
>  > Another need that people have asked me several times (I am
> administrator
>> of
>> > a web forum on bioinformatics) is to have a standard and official web
>> > interface to the emboss tools, since the list at
>> > http://emboss.sourceforge.net/interfaces/#web is outdated and google
>> doesn't
>> > return clear results.
>>
>> We have long hoped that one interface would become the standard. Our
>> usual recommendation for web-based users is the wEMBOSS interface but
>> when ever we ask which interfaces users prefer we get many different
>> replies.
>>
>> So, please let us know which interfaces you like best and we will try to
>> work with the developers to make sure it keeps up with changes to EMBOSS
>> ... and we can try to help them by adding new features or by
>> automatically building their interface to a new EMBOSS release.
>>
>
> the web forum is this one (in Italian):
> - http://www.molecularlab.it/forum/default.asp
> usually, people ask questions like 'how to I translate a sequence to
> protein?', 'how to create a dotplot', etc.. - there is not always a good
> answer to these questions, but in the past I have suggested the emboss
> tools
> because they seemed a kind of standard.
> (by the way, it would be good to know which tests have being applied to
> verify emboss code. I don't like telling people to use a command line
> tool,
> if there is no way to tell that it has been proved to work fine).
>
> I used to like very much this interface:
> - http://embossgui.sourceforge.net/demo/
> which is very clear and has a list of all the tools, but is still running
> the 3.0 version.
>
> I also like the ebi interface, because it is hosted on an well-known
> server
> (people don't like using servers they don't know) but it supports very few
> tools;
>
> galaxy has also a nice web interface to emboss, but sometimes you just
> need
> to link a paste&submit interface to execute simple tasks like translating
> a
> sequence, and I haven't found anything like that yet.
>
>
>
>> regards,
>>
>> Peter Rice
>>
>
>
>
> --
> Giovanni Dall'Olio, phd student
> Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)
>
> My blog on bioinformatics: http://bioinfoblog.it
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 11 Jun 2009 16:41:10 +0200
> From: Guy Bottu <gbottu at vub.ac.be>
> Subject: Re: [EMBOSS] EMBOSS Funding and New developments
> To: Peter Rice <pmr at ebi.ac.uk>
> Cc: emboss-dev at emboss.open-bio.org, emboss
> 	<emboss at emboss.open-bio.org>
> Message-ID: <4A311786.6000504 at vub.ac.be>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Giovanni Marco Dall'Olio wrote:
>> Another need that people have asked me several times (I am administrator
>> of
>> a web forum on bioinformatics) is to have a standard and official web
>> interface to the emboss tools, since the list at
>> http://emboss.sourceforge.net/interfaces/#web is outdated and google
>> doesn't
>> return clear results.
>
> Now that we are at it, could the hyperlink not be changed ? It is
> http://wemboss.sourceforge.net and not anymore http://www.wemboss.org
>
> 	Guy Bottu
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 12 Jun 2009 22:40:08 +0200
> From: Julian Sikorski <belegdol at gmail.com>
> Subject: [EMBOSS] Packaging EMBOSS for Fedora
> To: emboss at emboss.open-bio.org
> Message-ID: <h0uef8$bdu$1 at ger.gmane.org>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> a while ago I made an attempt to create an EMBOSS package for Fedora
> [1]. The progress was stalled for a while due to my MSc having higher
> priority, but I have recently picked up the work again.
> I have one crucial question: is it worth to package jemboss? It seems it
> didn't see development since 2005, and I have experienced some important
> issues when trying to use it (mainly not working with files with spaces
> in filenames). What do you think?
>
> Kind regards,
> Julian
>
> [1] https://bugzilla.redhat.com/show_bug.cgi?id=496133
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sat, 13 Jun 2009 00:49:16 +0100
> From: Mahmut Uludag <uludag at ebi.ac.uk>
> Subject: Re: [EMBOSS] Packaging EMBOSS for Fedora
> To: Julian Sikorski <belegdol at gmail.com>
> Cc: emboss at emboss.open-bio.org
> Message-ID: <1244850556.8999.7.camel at login-svr1.ebi.ac.uk>
> Content-Type: text/plain
>
> Hi Julian,
>
>> I have one crucial question: is it worth to package jemboss? It seems it
>> didn't see development since 2005, and I have experienced some important
>> issues when trying to use it (mainly not working with files with spaces
>> in filenames). What do you think?
>
> I had a quick look into the files with spaces in filenames problem, we
> can include a fix in the coming release (6.1) for this problem. Previous
> release of EMBOSS (6.0) included some fixes of similar nature, as well
> as some small gui improvements. We recently have updated EMBOSS/Jemboss
> make/install machinery to make standalone Jemboss come out of box when
> users install EMBOSS, i think we were successful and this will be a new
> feature in EMBOSS 6.1.
>
> Regards,
> Mahmut
>
>
>
>
> ------------------------------
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
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>
>
> End of EMBOSS Digest, Vol 48, Issue 2
> *************************************
>