From rostokec at cs.ubc.ca Fri Jun 3 17:55:40 2005 From: rostokec at cs.ubc.ca (Camilo Rostoker) Date: Fri Jun 3 17:47:36 2005 Subject: [Biojava-dev] newbie HOWTO question Message-ID: <42A0D1DC.5030209@cs.ubc.ca> Hi, I'm new to BioJava, and relatively new to Bioinformatics, so please excuse my ignorance if I'm looking in the wrong spot altogether... Is there a way to connect to a remote database and access details about specific genes (i.e. description, annotation information, etc)? For example, I have a small Java-based data mining application that performs some gene expression analysis using a basic data file that contains just the gene name (ie. something like YCR004C -- the systematic name) and I would like to be able to pull up as much information as possible about that gene from a central repository... Any help/advice is most appreciated. Cheers, Camilo -- ----------------------------------------------------------- Camilo Rostoker www.cs.ubc.ca/~rostokec Department of Computer Science www.cs.ubc.ca University of British Columbia www.ubc.ca From mark.schreiber at novartis.com Sun Jun 5 21:11:39 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Sun Jun 5 21:06:11 2005 Subject: [Biojava-dev] newbie HOWTO question Message-ID: Hello - You could connect to databases that offer webservices such as NCBI or EMBL. For the NCBI look into the eutils link. You can also connect to lots of DAS servers for the 'higher' eukaryotes at Ensembl. There is lots of stuff really. It mostly depends which organism and what type of data you want. - Mark Camilo Rostoker Sent by: biojava-dev-bounces@portal.open-bio.org 06/04/2005 05:55 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] newbie HOWTO question Hi, I'm new to BioJava, and relatively new to Bioinformatics, so please excuse my ignorance if I'm looking in the wrong spot altogether... Is there a way to connect to a remote database and access details about specific genes (i.e. description, annotation information, etc)? For example, I have a small Java-based data mining application that performs some gene expression analysis using a basic data file that contains just the gene name (ie. something like YCR004C -- the systematic name) and I would like to be able to pull up as much information as possible about that gene from a central repository... Any help/advice is most appreciated. Cheers, Camilo -- ----------------------------------------------------------- Camilo Rostoker www.cs.ubc.ca/~rostokec Department of Computer Science www.cs.ubc.ca University of British Columbia www.ubc.ca _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From heuermh at acm.org Mon Jun 6 14:28:59 2005 From: heuermh at acm.org (Michael Heuer) Date: Mon Jun 6 14:39:02 2005 Subject: [Biojava-dev] 1.3 -> 1.4 binary compatibility repor Message-ID: In preparation for a 1.4 release, I've been looking at documenting properly the changes made between the 1.3 release and the current cvs HEAD. Following the documentation on API changes at > http://eclipse.org/eclipse/development/java-api-evolution.html a tool called clirr was developed > http://clirr.sourceforge.net I've run clirr for release-1_3-branch vs. HEAD and posted the results to > http://shore.net/~heuermh/binary-compatibility-report.txt Reference Manual (explanations for message codes) > http://clirr.sourceforge.net/clirr-core/exegesis.html michael From mark.schreiber at novartis.com Mon Jun 6 21:30:58 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Jun 6 21:24:30 2005 Subject: [Biojava-dev] 1.3 -> 1.4 binary compatibility repor Message-ID: Wow, thats an impressive list of additions! And an unfortunately large list of incompatibilities, we are not getting much better at keeping the rules of backwards compatability : ( Michael Heuer Sent by: biojava-dev-bounces@portal.open-bio.org 06/07/2005 02:28 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] 1.3 -> 1.4 binary compatibility repor In preparation for a 1.4 release, I've been looking at documenting properly the changes made between the 1.3 release and the current cvs HEAD. Following the documentation on API changes at > http://eclipse.org/eclipse/development/java-api-evolution.html a tool called clirr was developed > http://clirr.sourceforge.net I've run clirr for release-1_3-branch vs. HEAD and posted the results to > http://shore.net/~heuermh/binary-compatibility-report.txt Reference Manual (explanations for message codes) > http://clirr.sourceforge.net/clirr-core/exegesis.html michael _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From michael.barton1 at ncl.ac.uk Thu Jun 9 08:27:48 2005 From: michael.barton1 at ncl.ac.uk (Michael Barton) Date: Thu Jun 9 07:28:59 2005 Subject: [Biojava-dev] Local binary execution Message-ID: <1118320068.2958.10.camel@barrel07.ncl.ac.uk> Hi, I'm Bioinformatics MRes student at Newcastle. I've been messing around with some java code to execute bioinformatics binaries. It was originally intended for blast but has also been extended for genewise. It takes the hassle out of using process / process builder a little bit. Use goes along the lines of something like this //Search factory for creating searches SearchFactory bsf; bsf = new BlastSearchFactory(); //Paramterise with search specific variables bsf.setSearchBinaryLocation(test_data + "/blast/binary"); bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType,"blastn"); bsf.setSearchParameter(BlastSearchFactory.Parameter.database, test_data + "/blast/db/sargasso"); //Create immutable search object which can be used to run mutiple searches on the same database Search blastSearch = bsf.getSearch(); Simple search result object which returns inputstream SearchResult sr = blastSearch.execute(new File(test_data + "/blast/query/query")); InputStream is = sr.getResultStream(); It's seems to work okay on linux, I haven't tested it on windows. There's a little bit of JavaDoc I started work on but it's a little bit messed up from where I've been changing things around. The source/jar/doc are all here. There's test cases too. http://www.students.ncl.ac.uk/michael.barton1/ Mike From heuermh at acm.org Thu Jun 9 11:54:47 2005 From: heuermh at acm.org (Michael Heuer) Date: Thu Jun 9 11:49:16 2005 Subject: [Biojava-dev] Local binary execution In-Reply-To: <1118320068.2958.10.camel@barrel07.ncl.ac.uk> Message-ID: Hello Michael, Personally I think this kind of code might be better suited in a more general library, say in an Apache Jakarta Commons project for example. In fact, there was just a proposal to pull the exec code out of ant into a separate self-contained library to the commonds-dev mailing list a couple of days ago: > http://tinyurl.com/9culs That said, this comes up quite frequently here, so perhaps we should just bite the bullet and do it up right. michael On Thu, 9 Jun 2005, Michael Barton wrote: > > Hi, > > I'm Bioinformatics MRes student at Newcastle. I've been messing around > with some java code to execute bioinformatics binaries. It was > originally intended for blast but has also been extended for genewise. > It takes the hassle out of using process / process builder a little bit. > > Use goes along the lines of something like this > > //Search factory for creating searches > SearchFactory bsf; > bsf = new BlastSearchFactory(); > > //Paramterise with search specific variables > bsf.setSearchBinaryLocation(test_data + "/blast/binary"); > bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType,"blastn"); > bsf.setSearchParameter(BlastSearchFactory.Parameter.database, > test_data + "/blast/db/sargasso"); > > //Create immutable search object which can be used to run mutiple > searches on the same database > Search blastSearch = bsf.getSearch(); > > Simple search result object which returns inputstream > SearchResult sr = blastSearch.execute(new File(test_data + > "/blast/query/query")); > > InputStream is = sr.getResultStream(); > > It's seems to work okay on linux, I haven't tested it on windows. > > There's a little bit of JavaDoc I started work on but it's a little bit > messed up from where I've been changing things around. > > The source/jar/doc are all here. There's test cases too. > > http://www.students.ncl.ac.uk/michael.barton1/ > > Mike > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From pac at lifeformulae.com Wed Jun 1 13:16:36 2005 From: pac at lifeformulae.com (Pamela Culpepper) Date: Mon Jun 13 13:23:32 2005 Subject: [Biojava-dev] NCBI ASN.1 Sequence Road Message-ID: <1117646196.5258.5.camel@d139.hbnet.edu> We've just published a "road map" guide to the ASN.1 data structures that NCBI uses for its genomic sequence data in Word-97, PostScript and PDF formats. Download for free at http://www.lifeformulae.com under Free Goodies. You can freely duplicate the document or its contents, just be sure to cite the source. Pam Culpepper From Russell.Smithies at agresearch.co.nz Mon Jun 13 21:51:26 2005 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon Jun 13 21:43:11 2005 Subject: [Biojava-dev] OT: JTest Message-ID: Hi all, Sorry about the off-topic question but has anyone tried JTest from ParaSoft? We're thinking of buying it and all the reviews I've read seem OK but I'd like to hear comments from someone who actually uses it. Thanx, Russell Smithies Bioinformatics Software Developer Invermay Research Centre Puddle Alley, Mosgiel, New Zealand www.agresearch.co.nz ======================================================================= 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 michael.barton1 at ncl.ac.uk Tue Jun 14 14:26:45 2005 From: michael.barton1 at ncl.ac.uk (Michael Barton) Date: Tue Jun 14 13:20:42 2005 Subject: [Biojava-dev] Local binary execution In-Reply-To: References: Message-ID: <1118773606.14537.7.camel@barrel07.ncl.ac.uk> I had a look at the post you were refering to. In terms of the ant support for local binary execution I think it is very similar to the newly implemented ProcessBuilder in Java 1.5. This class has a similar way way of adding command line arguments to that of ant . The classes I'm suggesting have an enum of arguments specific to the application which may convienient for suppling different switch/argument pairs, as it it means that only arguments for which the binary allows can be supplied. Any errors should therefore come from incorrent argument values rather than incorrect arguments. If that makes sense. In addition the class throws an exception if the essential arguments required to run the search are not supplied. This means however that the classes are written in Java 1.5. Would this be a problem? On Thu, 2005-06-09 at 11:54 -0400, Michael Heuer wrote: > Hello Michael, > > Personally I think this kind of code might be better suited in a more > general library, say in an Apache Jakarta Commons project for example. > > In fact, there was just a proposal to pull the exec code out of ant into a > separate self-contained library to the commonds-dev mailing list a couple > of days ago: > > > http://tinyurl.com/9culs > > That said, this comes up quite frequently here, so perhaps we should just > bite the bullet and do it up right. > > michael > > > On Thu, 9 Jun 2005, Michael Barton wrote: > > > > > Hi, > > > > I'm Bioinformatics MRes student at Newcastle. I've been messing around > > with some java code to execute bioinformatics binaries. It was > > originally intended for blast but has also been extended for genewise. > > It takes the hassle out of using process / process builder a little bit. > > > > Use goes along the lines of something like this > > > > //Search factory for creating searches > > SearchFactory bsf; > > bsf = new BlastSearchFactory(); > > > > //Paramterise with search specific variables > > bsf.setSearchBinaryLocation(test_data + "/blast/binary"); > > bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType,"blastn"); > > bsf.setSearchParameter(BlastSearchFactory.Parameter.database, > > test_data + "/blast/db/sargasso"); > > > > //Create immutable search object which can be used to run mutiple > > searches on the same database > > Search blastSearch = bsf.getSearch(); > > > > Simple search result object which returns inputstream > > SearchResult sr = blastSearch.execute(new File(test_data + > > "/blast/query/query")); > > > > InputStream is = sr.getResultStream(); > > > > It's seems to work okay on linux, I haven't tested it on windows. > > > > There's a little bit of JavaDoc I started work on but it's a little bit > > messed up from where I've been changing things around. > > > > The source/jar/doc are all here. There's test cases too. > > > > http://www.students.ncl.ac.uk/michael.barton1/ > > > > Mike > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev@biojava.org > > http://biojava.org/mailman/listinfo/biojava-dev > > > From mark.schreiber at novartis.com Tue Jun 14 21:09:18 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue Jun 14 21:01:01 2005 Subject: [Biojava-dev] Local binary execution Message-ID: We would normally not like to use a new JDK in biojava unless it is well supported on all the OS's people are using. Having said that there are several attractive features which would make it nice to use. Is anyones current OS not supporting java 1.5? - Mark Michael Barton Sent by: biojava-dev-bounces@portal.open-bio.org 06/15/2005 02:26 AM To: BioJava-dev cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-dev] Local binary execution I had a look at the post you were refering to. In terms of the ant support for local binary execution I think it is very similar to the newly implemented ProcessBuilder in Java 1.5. This class has a similar way way of adding command line arguments to that of ant . The classes I'm suggesting have an enum of arguments specific to the application which may convienient for suppling different switch/argument pairs, as it it means that only arguments for which the binary allows can be supplied. Any errors should therefore come from incorrent argument values rather than incorrect arguments. If that makes sense. In addition the class throws an exception if the essential arguments required to run the search are not supplied. This means however that the classes are written in Java 1.5. Would this be a problem? On Thu, 2005-06-09 at 11:54 -0400, Michael Heuer wrote: > Hello Michael, > > Personally I think this kind of code might be better suited in a more > general library, say in an Apache Jakarta Commons project for example. > > In fact, there was just a proposal to pull the exec code out of ant into a > separate self-contained library to the commonds-dev mailing list a couple > of days ago: > > > http://tinyurl.com/9culs > > That said, this comes up quite frequently here, so perhaps we should just > bite the bullet and do it up right. > > michael > > > On Thu, 9 Jun 2005, Michael Barton wrote: > > > > > Hi, > > > > I'm Bioinformatics MRes student at Newcastle. I've been messing around > > with some java code to execute bioinformatics binaries. It was > > originally intended for blast but has also been extended for genewise. > > It takes the hassle out of using process / process builder a little bit. > > > > Use goes along the lines of something like this > > > > //Search factory for creating searches > > SearchFactory bsf; > > bsf = new BlastSearchFactory(); > > > > //Paramterise with search specific variables > > bsf.setSearchBinaryLocation(test_data + "/blast/binary"); > > bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType,"blastn"); > > bsf.setSearchParameter(BlastSearchFactory.Parameter.database, > > test_data + "/blast/db/sargasso"); > > > > //Create immutable search object which can be used to run mutiple > > searches on the same database > > Search blastSearch = bsf.getSearch(); > > > > Simple search result object which returns inputstream > > SearchResult sr = blastSearch.execute(new File(test_data + > > "/blast/query/query")); > > > > InputStream is = sr.getResultStream(); > > > > It's seems to work okay on linux, I haven't tested it on windows. > > > > There's a little bit of JavaDoc I started work on but it's a little bit > > messed up from where I've been changing things around. > > > > The source/jar/doc are all here. There's test cases too. > > > > http://www.students.ncl.ac.uk/michael.barton1/ > > > > Mike > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev@biojava.org > > http://biojava.org/mailman/listinfo/biojava-dev > > > _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at novartis.com Tue Jun 14 23:44:11 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue Jun 14 23:36:09 2005 Subject: [Biojava-dev] Announce: BioJava 1.4pre2 Message-ID: Hello All - A second release candidate for biojava 1.4 is now out. Apart from a years worth of bug fixes and javadoc clean ups the major change over 1.4pre1 is a major work over of the biosql bindings so that BioJava now operates with the upcoming biosql 1.0. Please take this code out for a spin and give your feedback to the list. I hope to make an official release in about a week so we can start working on 1.5. It's certainly been a long time between releases and I would like to reduce this in the near future. Check it out from www.biojava.org or go directly to http://www.biojava.org/download14.html (do not pass Go, do not collect $200). Thanks to Michael Heuer and Richard Holland for helping to squeeze this one out. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From heuermh at acm.org Wed Jun 15 15:51:06 2005 From: heuermh at acm.org (Michael Heuer) Date: Wed Jun 15 15:43:49 2005 Subject: [Biojava-dev] Local binary execution In-Reply-To: <1118773606.14537.7.camel@barrel07.ncl.ac.uk> Message-ID: I guess I would like to see something like the following: A synchronous (blocking) and asynchronous (event-based) interface extending Runnable for each executable Implementations of these interfaces using ProcessBuilder or commons-exec or whatever to call local executables A local executable registry & configuration mechanism Implementations of these interfaces calling web services versions of these executables (e.g. http://rt.bioteam.net:8080/metadot/index.pl?iid=2307) Implementations of these interfaces calling web forms and web-scraping the result pages (e.g. bioperl Bio::Tools::Run::RemoteBlast) Implementations of these interfaces using BioMoby/Semantic Moby/insert your favorite technology du jour here/etc. Hopefully someone from the myGRID/taverna/SOAPLAB folks or elsewhere will respond to this email and tell me that it's been done already and this is where I should go to check it out from cvs/svn... :) michael On Tue, 14 Jun 2005, Michael Barton wrote: > I had a look at the post you were refering to. In terms of the ant > support for local binary execution I think it is very similar to the > newly implemented ProcessBuilder in Java 1.5. > This class has a similar way way of adding command line arguments to > that of ant . > > The classes I'm suggesting have an enum of arguments specific to the > application which may convienient for suppling different switch/argument > pairs, as it it means that only arguments for which the binary allows > can be supplied. > Any errors should therefore come from incorrent argument values rather > than incorrect arguments. If that makes sense. > In addition the class throws an exception if the essential arguments > required to run the search are not supplied. > > This means however that the classes are written in Java 1.5. Would this > be a problem? > > > On Thu, 2005-06-09 at 11:54 -0400, Michael Heuer wrote: > > Hello Michael, > > > > Personally I think this kind of code might be better suited in a more > > general library, say in an Apache Jakarta Commons project for example. > > > > In fact, there was just a proposal to pull the exec code out of ant into a > > separate self-contained library to the commonds-dev mailing list a couple > > of days ago: > > > > > http://tinyurl.com/9culs > > > > That said, this comes up quite frequently here, so perhaps we should just > > bite the bullet and do it up right. > > > > michael > > > > > > On Thu, 9 Jun 2005, Michael Barton wrote: > > > > > > > > Hi, > > > > > > I'm Bioinformatics MRes student at Newcastle. I've been messing around > > > with some java code to execute bioinformatics binaries. It was > > > originally intended for blast but has also been extended for genewise. > > > It takes the hassle out of using process / process builder a little bit. > > > > > > Use goes along the lines of something like this > > > > > > //Search factory for creating searches > > > SearchFactory bsf; > > > bsf = new BlastSearchFactory(); > > > > > > //Paramterise with search specific variables > > > bsf.setSearchBinaryLocation(test_data + "/blast/binary"); > > > bsf.setSearchParameter(BlastSearchFactory.Parameter.blastType,"blastn"); > > > bsf.setSearchParameter(BlastSearchFactory.Parameter.database, > > > test_data + "/blast/db/sargasso"); > > > > > > //Create immutable search object which can be used to run mutiple > > > searches on the same database > > > Search blastSearch = bsf.getSearch(); > > > > > > Simple search result object which returns inputstream > > > SearchResult sr = blastSearch.execute(new File(test_data + > > > "/blast/query/query")); > > > > > > InputStream is = sr.getResultStream(); > > > > > > It's seems to work okay on linux, I haven't tested it on windows. > > > > > > There's a little bit of JavaDoc I started work on but it's a little bit > > > messed up from where I've been changing things around. > > > > > > The source/jar/doc are all here. There's test cases too. > > > > > > http://www.students.ncl.ac.uk/michael.barton1/ > > > > > > Mike > > > > > > _______________________________________________ > > > biojava-dev mailing list > > > biojava-dev@biojava.org > > > http://biojava.org/mailman/listinfo/biojava-dev > > > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From mark.schreiber at novartis.com Wed Jun 22 01:55:56 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed Jun 22 01:47:28 2005 Subject: [Biojava-dev] searching mailing lists Message-ID: I have found the open-bio search page (http://search.open-bio.org/) you can use this to search mailing lists and webpages for any open-bio project. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From heuermh at acm.org Mon Jun 27 00:36:01 2005 From: heuermh at acm.org (Michael Heuer) Date: Mon Jun 27 00:26:25 2005 Subject: [Biojava-dev] BOSC 2005 lightning talks Message-ID: Hello, The presentations for the lightning talks on biojava and the sourceforge stax I gave at BOSC 2005 are available (temporarily) from > http://shore.net/~heuermh/biojava-24jun2005.ppt and > http://shore.net/~heuermh/stax-24jun2005.ppt respectively. Please let me know if I should make any corrections before making them more widely available. I would like to move them to the public biojava.org and stax.sf.net project websites in a few days. michael From mark.schreiber at novartis.com Tue Jun 28 21:49:19 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue Jun 28 21:40:38 2005 Subject: [Biojava-dev] BLAST functionality Message-ID: There have been a number of requests to the list (and directly to me) for increased functionality for the BLAST parsers (eg capturing more of the information in the report). Originally the design was lightweight and captured what most people wanted but as always there are always people who think different (as Steve Jobs might say) and want different things. The best way for the BLAST parsers to improve is for people to contribute code. There are lots of work arounds that people have made to improve the parsers that have not found there way into biojava. Ideally I'm hoping someone will volunteer to take a look at this and coordinate the effort. The ideal person should be a reasonable Java programmer with a good feel for how the BLAST part of the API works. They would also be someone who uses it a lot and is therefore motivated to improve it. The BLAST API is probably the most used part of biojava so instant fame and adulation await the generous volunteer : ) I know your out there somewhere... - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From chris at bioteam.net Wed Jun 29 19:41:47 2005 From: chris at bioteam.net (Chris Dagdigian) Date: Wed Jun 29 19:35:42 2005 Subject: [Biojava-dev] important notice for open-bio developers - please read Message-ID: Hi folks, Sorry for the mass mailing of all our dev lists but I need to reach developers for whom we currently do not have good contact information for... The O|B|F has 2 brand new colocated servers sitting on fast links to the internet here in Boston - and we really want to begin using them! We are slowing beginning the process of moving our developers and code repositories to one machine while moving websites and mailing lists to the second machine. We are going to move the CVS repositories and user accounts first. However, before we make the switch we need to be make sure all the folks with user accounts on the pub.open-bio.org system know what is happening and for that to happen we need to know how to contact them. I've been testing the new code server and we are ready to make the switch very soon now. If you have a user account on pub.open-bio.org please login via SSH and run "finger " -- please verify that a good email address for you is listed within one of the fields. If your email address needs to be changed you can run the command "chfn " to reset the information. If you do that make sure your full name, project affiliation and email address are all stored there. Project leaders or people who are very familiar with their project - we have tons of accounts on the system from long gone or inactive developers. *please* make my life easier by logging into the system and taking a look at /etc/password or the userdirs in /home/ -- contact me and let me know which user accounts can be disabled or removed. This is the last time we are going to do a public mailing. At some point within the next 2 weeks we are going to collect the email addresses from the finger information and use that to build a one-off mailing list to coordinate the server move (existing devs with good email addresses probably saw the obf-developers unsubscription notice today as we purged the old address in preparation for rebuilding the list with fresh data...) . Anyone who does not have a valid email address collected at that time will be left out and his/her user account will be disabled. We will still relocate the user accounts and files but the password will be locked and the user will have to contact the sysadmin team before gaining login or CVS commit access. Please use our new helpdesk support system to contact me with any questions or information about long-gone accounts we can disable: support@helpdesk.open-bio.org Regards, Chris PS - for the hardware geeks out there, the 2 servers are Rackable C1000 boxes running Centos4 Linux. A bad picture of them is online here: http://bioteam.net/gallery/bioteamBDC/DSCN1627 From ady at sanger.ac.uk Thu Jun 30 15:15:37 2005 From: ady at sanger.ac.uk (Andrew Yates) Date: Thu Jun 30 15:06:28 2005 Subject: [Biojava-dev] SCF Issues and leading up to 1.4 release Message-ID: <42C444D9.1030805@sanger.ac.uk> Hi guys, First post on the dev list here but with talk of a 1.4 release coming up soon at BOSC it reminded me that there are certain bugs in the SCF parser code. The bug is with the wrapping of byte/short values into the int[] output. I've seen cases where the current parser generates trace files with an intensity of 65000 (slightly over the range ABI machines can handle by about 30000) when dealing with byte centric files (SCF can write values in byte if the delta delta values do not exceed unsigned byte boundries). I've developed a fix for it and have the new source available for it (and this code has been tested & running flawlessly in our program for about 6 months) but I thought it best to try to shoehorn it in before a 1.4 release hopefully and if not get it in so it gets into any update release. What's the best way around this? I don't mind editing the CVS entry but since this is my contribution to biojava I know I wouldn't be happy from an admin point of view. Cheers, Andy Yates ~~~~~~~~~~ Computer Biologist Cancer Genome Project Wellcome Trust Sanger Institute P.S. Good conference guys From heuermh at acm.org Thu Jun 23 18:32:49 2005 From: heuermh at acm.org (Michael Heuer) Date: Fri Jul 8 16:37:09 2005 Subject: [Biojava-dev] Region & Junction Message-ID: Hello, Just floating an idea that's been in my head for a bit. What if for a "biojava next" we replace Sequence and typed Features etc. with classes extending the two basic SOFA classes _region_ and _junction_. A region is a length of symbols and a junction is the space between two symbols [1, 2]. At the API level Region would look something like a SymbolList but with interbase (zero-based) coordinates. Subclasses of _region_, such as _exon_ and _transposable_element_, and of _junction_, like _insertion_site_, might be generated as java classes from SOFA itself (or maybe an OWL representation thereof). Methods could be generated between these classes representing the various SOFA relationship types (_kind_of_, _derives_from_, _part_of_). Of course, in java land these class names would take on proper JavaClassNameCapitalization instead of lowercase_with_underscores. michael [1] > http://song.sf.net [2] > http://genomebiology.com/2005/6/5/R44