From mark.schreiber at novartis.com Wed Dec 2 00:55:30 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 2 Dec 2009 13:55:30 +0800 Subject: [Biojava-dev] Fw: [Open-bio-l] Fwd: [Utilities-announce] NCBI E-Utility Policy Change Message-ID: FYI for BioJava developers ... ----- Forwarded by Mark Schreiber/GP/Novartis on 12/02/2009 01:54 PM ----- open-bio-l-bounces at lists.open-bio.org wrote on 12/02/2009 04:00:43 AM: > Hi all, > > I know Biopython and BioPerl are aware of this change, but in case > the other Bio* projects are not please see below. Sign up here: > http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html > > Peter @ Biopython > > ---------- Forwarded message ---------- > From: > Date: Tue, Dec 1, 2009 at 6:59 PM > Subject: [Utilities-announce] NCBI E-Utility Policy Change > To: utilities-announce at ncbi.nlm.nih.gov > > > As part of an ongoing effort to ensure efficient access to the Entrez > Utilities (E-utilities) by all users, NCBI has decided to change the > usage policy for the E-utilities effective June 1, 2010. Effective on > June 1, 2010, all E-utility requests, either using standard URLs or > SOAP, must contain non-null values for both the &tool and &email > parameters. Any E-utility request made after June 1, 2010 that does > not contain values for both parameters will return an error explaining > that these parameters must be included in E-utility requests. > > > > The value of the &tool parameter should be a URI-safe string that is > the name of the software package, script or web page producing the > E-utility request. > > > > The value of the &email parameter should be a valid e-mail address for > the appropriate contact person or group responsible for maintaining > the tool producing the E-utility request. > > > > NCBI uses these parameters to contact users whose use of the > E-utilities violates the standard usage policies described at > http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help. > html#UserSystemRequirements. > These usage policies are designed to prevent excessive requests from a > small group of users from reducing or eliminating the wider > community's access to the E-utilities. NCBI will attempt to contact a > user at the e-mail address provided in the &email parameter prior to > blocking access to the E-utilities. > > > > NCBI realizes that this policy change will require many of our users > to change their code. Based on past experience, we anticipate that > most of our users should be able to make the necessary changes before > the June 1, 2010 deadline. If you have any concerns about making these > changes by that date, or if you have any questions about these > policies, please contact eutilities at ncbi.nlm.nih.gov. > > > > Thank you for your understanding and cooperation in helping us > continue to deliver a reliable and efficient web service. > > > > _______________________________________________ > Utilities-announce mailing list > http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. From holland at eaglegenomics.com Wed Dec 2 06:36:54 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 2 Dec 2009 11:36:54 +0000 Subject: [Biojava-dev] Fw: [Open-bio-l] Fwd: [Utilities-announce] NCBI E-Utility Policy Change In-Reply-To: References: Message-ID: <6D65C618-F05D-4D8D-AB9F-38A35DD9F730@eaglegenomics.com> I've just patched the trunk to take this into account. GenbankRichSequenceDB - two new values accessed via setTool/getTool and setEmail/getEmail with appropriate default values to ensure all current code still works without modification. cheers, Richard On 2 Dec 2009, at 05:55, mark.schreiber at novartis.com wrote: > FYI for BioJava developers ... > > > ----- Forwarded by Mark Schreiber/GP/Novartis on 12/02/2009 01:54 PM ----- > > open-bio-l-bounces at lists.open-bio.org wrote on 12/02/2009 04:00:43 AM: > >> Hi all, >> >> I know Biopython and BioPerl are aware of this change, but in case >> the other Bio* projects are not please see below. Sign up here: >> http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html >> >> Peter @ Biopython >> >> ---------- Forwarded message ---------- >> From: >> Date: Tue, Dec 1, 2009 at 6:59 PM >> Subject: [Utilities-announce] NCBI E-Utility Policy Change >> To: utilities-announce at ncbi.nlm.nih.gov >> >> >> As part of an ongoing effort to ensure efficient access to the Entrez >> Utilities (E-utilities) by all users, NCBI has decided to change the >> usage policy for the E-utilities effective June 1, 2010. Effective on >> June 1, 2010, all E-utility requests, either using standard URLs or >> SOAP, must contain non-null values for both the &tool and &email >> parameters. Any E-utility request made after June 1, 2010 that does >> not contain values for both parameters will return an error explaining >> that these parameters must be included in E-utility requests. >> >> >> >> The value of the &tool parameter should be a URI-safe string that is >> the name of the software package, script or web page producing the >> E-utility request. >> >> >> >> The value of the &email parameter should be a valid e-mail address for >> the appropriate contact person or group responsible for maintaining >> the tool producing the E-utility request. >> >> >> >> NCBI uses these parameters to contact users whose use of the >> E-utilities violates the standard usage policies described at >> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help. >> html#UserSystemRequirements. >> These usage policies are designed to prevent excessive requests from a >> small group of users from reducing or eliminating the wider >> community's access to the E-utilities. NCBI will attempt to contact a >> user at the e-mail address provided in the &email parameter prior to >> blocking access to the E-utilities. >> >> >> >> NCBI realizes that this policy change will require many of our users >> to change their code. Based on past experience, we anticipate that >> most of our users should be able to make the necessary changes before >> the June 1, 2010 deadline. If you have any concerns about making these >> changes by that date, or if you have any questions about these >> policies, please contact eutilities at ncbi.nlm.nih.gov. >> >> >> >> Thank you for your understanding and cooperation in helping us >> continue to deliver a reliable and efficient web service. >> >> >> >> _______________________________________________ >> Utilities-announce mailing list >> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce >> _______________________________________________ >> Open-Bio-l mailing list >> Open-Bio-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/open-bio-l > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivery of the > message to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is strictly > prohibited. If you have received this communication in error, please > notify the sender immediately by e-mail and delete the material from any > computer. Thank you. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From holland at eaglegenomics.com Wed Dec 9 07:07:16 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 9 Dec 2009 12:07:16 +0000 Subject: [Biojava-dev] Job vacancies Message-ID: Hi there, Apologies for posting job ads to the lists but I think this one is relevant to the members so please forgive me. If you know of anyone that might be interested, could you forward them this job ad? Also if you have any local resources for posting job ads, it would be great if you could put the ad up there as well. Sorry to intrude - I'll leave you in peace again now. :) thanks! Richard 1. Senior Bioinformatics Software Developer (Perl/Ensembl) 2. Senior Bioinformatics Software Developer (Java/Taverna) Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for TWO top-class developers to work on a wide range of complex projects. Both these roles involve a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had substantial prior experience working in a life science company or research institute. For the Perl/Ensembl role, you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. For the Java/Taverna role you will be an expert Java developer with the ability to rapidly analyse and understand complex systems. Ideally you will have written code or plugins for the Taverna project or written code that makes use of it. For both roles, in addition to your superb technical and customer service skills, you will also: ? be able to communicate clearly and proactively, ? have the ability to quickly translate scientific problems into real software solutions, ? be able to put technical concepts into simple language for end users to understand, ? be able to pick up new skills and techniques in record time, ? work well in a collaborative team environment, ? be creative, innovative, and forward-thinking. You will also have had hands-on experience in at least two of the following: ? SQL query design, ? Open-source bioinformatics toolkits such as BioPerl, BioJava, BioSQL, etc., ? Amazon EC2, ? Workflow/pipeline design, ? System and user documentation, ? Developing user training courses. The successful candidate would be expected to work from our offices near Cambridge, however remote working in the UK/Europe may be considered for exceptional candidates (depending on exact location). We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs @eaglegenomics.com . We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. No agencies please. Closing date: 8th JANUARY 2010. -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From bugzilla-daemon at portal.open-bio.org Thu Dec 17 12:52:38 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 17 Dec 2009 12:52:38 -0500 Subject: [Biojava-dev] [Bug 2971] New: Nexus parser fails to parse internal node names Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2971 Summary: Nexus parser fails to parse internal node names Product: BioJava Version: live (CVS source) Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: tiagoantao at gmail.com The Ancestor1 below is not parsed correctly. Begin TREES; tree test2 = (B:6.0,(A:5.0,C:3.0,E:4.0) Ancestor1:5.0,D:11.0); End; Internal node names (as opposed to leaves) are not correctly processed. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Dec 17 12:53:25 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 17 Dec 2009 12:53:25 -0500 Subject: [Biojava-dev] [Bug 2971] Nexus parser fails to parse internal node names In-Reply-To: Message-ID: <200912171753.nBHHrPsk021176@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2971 tiagoantao at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #1 from tiagoantao at gmail.com 2009-12-17 12:53 EST ------- I will also used this bug to submit a patch to problems with newline parsing. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Dec 18 18:02:09 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 18 Dec 2009 18:02:09 -0500 Subject: [Biojava-dev] [Bug 2971] Nexus parser fails to parse internal node names In-Reply-To: Message-ID: <200912182302.nBIN29mO030812@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2971 ------- Comment #2 from tiagoantao at gmail.com 2009-12-18 18:02 EST ------- Created an attachment (id=1411) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1411&action=view) Patch to naming bug This patch is supplied against the maven style repository. Includes: Patch to code Patch to test code New test file -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From andreas at sdsc.edu Sun Dec 20 23:29:27 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 20 Dec 2009 20:29:27 -0800 Subject: [Biojava-dev] maven and custom jar Message-ID: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> Hi, I am about to commit some major new features to the protein structure modules. For the visualisation of these, the Jmol applet is being used. As such I would like to add the dependency on it to the structure modules. Since I could not find a JmolApplet.jar in maven, I currently install it locally via mvn install:install-file . What is the easiest way to get this set up and installed automatically, if somebody else checks out the code from SVN ? Shall we just document the line that installs Jmol, or should there be a custom target in the pom? Andreas From bugzilla-daemon at portal.open-bio.org Mon Dec 21 10:19:08 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 21 Dec 2009 10:19:08 -0500 Subject: [Biojava-dev] [Bug 2971] Nexus parser fails to parse internal node names In-Reply-To: Message-ID: <200912211519.nBLFJ8bv001831@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2971 holland at eaglegenomics.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Comment #3 from holland at eaglegenomics.com 2009-12-21 10:19 EST ------- Committed patch. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mahogny at areta.org Mon Dec 21 10:23:19 2009 From: mahogny at areta.org (Johan Henriksson) Date: Mon, 21 Dec 2009 16:23:19 +0100 Subject: [Biojava-dev] biojava hackathon Message-ID: Hello, has anyone done their homework and figured out which hotels are the best. maybe someone working there knows the "standard" ones? it seems I can join in. have not decided exactly what I will work on but surely not the protein stuff. either improving the core or the algorithms/data structures. I have experimented a bit with alternative ways of dealing with annotation and sequence data, maybe it can be of use. /Johan -- ----------------------------------------------------------- Johan Henriksson PhD student, Karolinska Institutet http://mahogny.areta.org http://www.endrov.net From holland at eaglegenomics.com Mon Dec 21 10:33:25 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 21 Dec 2009 15:33:25 +0000 Subject: [Biojava-dev] biojava hackathon In-Reply-To: References: Message-ID: <603A6F8A-087D-4003-92A0-1EEF5EE136FA@eaglegenomics.com> It used to be that you could get fairly cheap rooms at the Travelodge in central Cambridge, but I no longer live in Cambridge so I'll leave the job of answering correctly to someone who knows better than me. :) Looking forward to seeing you at the hackathon. On 21 Dec 2009, at 15:23, Johan Henriksson wrote: > Hello, > has anyone done their homework and figured out which hotels are the best. > maybe someone working there knows the "standard" ones? > > it seems I can join in. have not decided exactly what I will work on but > surely not the protein stuff. either improving the core or the > algorithms/data structures. I have experimented a bit with alternative ways > of dealing with annotation and sequence data, maybe it can be of use. > > /Johan > > -- > ----------------------------------------------------------- > Johan Henriksson > PhD student, Karolinska Institutet > http://mahogny.areta.org http://www.endrov.net > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Mon Dec 21 11:20:09 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 21 Dec 2009 08:20:09 -0800 Subject: [Biojava-dev] biojava hackathon In-Reply-To: References: Message-ID: <59a41c430912210820p59ae6b46wa239ae78328098d8@mail.gmail.com> A few people asked me where to stay and I suggested to book the Travelodge in Hills road. It is a plain and cheap hotel (for Cambridge), walking distance to the train station, town center (20 min) and close to one of the stops of the Genome Campus bus routes. Andreas On Mon, Dec 21, 2009 at 7:23 AM, Johan Henriksson wrote: > Hello, > has anyone done their homework and figured out which hotels are the best. > maybe someone working there knows the "standard" ones? > > it seems I can join in. have not decided exactly what I will work on but > surely not the protein stuff. either improving the core or the > algorithms/data structures. I have experimented a bit with alternative ways > of dealing with annotation and sequence data, maybe it can be of use. > > /Johan > > -- > ----------------------------------------------------------- > Johan Henriksson > PhD student, Karolinska Institutet > http://mahogny.areta.org ?http://www.endrov.net > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From raphael.andre.bauer at gmail.com Tue Dec 22 16:35:13 2009 From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=) Date: Tue, 22 Dec 2009 22:35:13 +0100 Subject: [Biojava-dev] maven and custom jar In-Reply-To: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> References: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> Message-ID: <9b46aa30912221335i1be5386ataec6008f23fb7ec@mail.gmail.com> On Mon, Dec 21, 2009 at 5:29 AM, Andreas Prlic wrote: > Hi, > > I am about to commit some major new features to the protein structure > modules. For the visualisation of these, the Jmol applet is being cool :) > used. As such I would like to add the dependency on it to the > structure modules. Since I could not find a JmolApplet.jar in maven, I > currently install it locally via mvn install:install-file . ?What is > the easiest way to get this set up and installed automatically, if > somebody else checks out the code from SVN ? Shall we just document > the line that installs Jmol, or should there be a custom target in the Hi Andreas, a quick scan gave me this (unofficial imho) repository: http://wwmm.ch.cam.ac.uk/maven2/net/sourceforge/jmol/jmol/ ready to be referenced by your pom.xml. A second idea is to set up a biojava jmol repository (depending on the license of Jmol) right at the biojava servers that you reference in your pom.xml. A third (and maybe the best idea) is to ask the Jmol team to set up a maven repository, or to upload artifacts to the central repository. The people behind Jmol are really helpful and I am pretty sure they are willing to help. But maybe there are more clever ideas how to work around that problem... Raphael maybe this helps: > pom? > > Andreas > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Sun Dec 27 23:41:22 2009 From: heuermh at acm.org (Michael Heuer) Date: Sun, 27 Dec 2009 23:41:22 -0500 (EST) Subject: [Biojava-dev] FASTQ support on release-1_7-branch, prepare for 1.7.1? Message-ID: All, I have copied FASTQ-format support from the biojava3 branch to the release-1_7-branch branch, with some modification to match the older project structure. I'd like to cut a version 1.7.1 release soon, since this code is referred to in the open-bio FASTQ paper recently published in NAR. Might someone review the release-1_7-branch? I could also use a hand with the actual release process. Thank you, michael From andreas at sdsc.edu Mon Dec 28 10:31:48 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 28 Dec 2009 07:31:48 -0800 Subject: [Biojava-dev] FASTQ support on release-1_7-branch, prepare for 1.7.1? In-Reply-To: References: Message-ID: <59a41c430912280731r2d961501w4f1602b9667633f3@mail.gmail.com> Hi Michael, In principle the BioJava 3.0 release is scheduled for early next year, but I assume you don't want to wait so long, due to the FASTQ paper? I will try to automatize the biojava 3.0 release procedure using Maven as much as possible. As such I would not want to spend the time for a minor version update now, but if you want to go for it, fine with me. Building a release is straightforward, I documented the release procedure of 1.7 on this page: http://biojava.org/wiki/BioJava:Make_release Probably you should add a page about the new FASTQ parser to the Cookbook as well, particularly if this is going to be the main new feature of 1.7.1 ... Let us know how it goes... Andreas On Sun, Dec 27, 2009 at 8:41 PM, Michael Heuer wrote: > All, > > I have copied FASTQ-format support from the biojava3 branch to the > release-1_7-branch branch, with some modification to match the older > project structure. > > I'd like to cut a version 1.7.1 release soon, since this code is referred > to in the open-bio FASTQ paper recently published in NAR. ?Might someone > review the release-1_7-branch? ?I could also use a hand with the actual > release process. > > Thank you, > > ? michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andreas at sdsc.edu Mon Dec 28 10:46:19 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 28 Dec 2009 07:46:19 -0800 Subject: [Biojava-dev] maven and custom jar In-Reply-To: <9b46aa30912221335i1be5386ataec6008f23fb7ec@mail.gmail.com> References: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> <9b46aa30912221335i1be5386ataec6008f23fb7ec@mail.gmail.com> Message-ID: <59a41c430912280746w784d2639q21a607f434a3f11e@mail.gmail.com> Hi Raphael, Thanks for the link to the Jmol maven. Problem is it is a bit out of date and the latest release version is already two increments higher. I will post to the Jmol list about getting a more up to date version and if that does not work out, I will do something via the BioJava servers... Thanks, Andreas On Tue, Dec 22, 2009 at 1:35 PM, Raphael Andr? Bauer wrote: > On Mon, Dec 21, 2009 at 5:29 AM, Andreas Prlic wrote: >> Hi, >> >> I am about to commit some major new features to the protein structure >> modules. For the visualisation of these, the Jmol applet is being > cool :) >> used. As such I would like to add the dependency on it to the >> structure modules. Since I could not find a JmolApplet.jar in maven, I >> currently install it locally via mvn install:install-file . ?What is >> the easiest way to get this set up and installed automatically, if >> somebody else checks out the code from SVN ? Shall we just document >> the line that installs Jmol, or should there be a custom target in the > > Hi Andreas, > > > a quick scan gave me this (unofficial imho) repository: > http://wwmm.ch.cam.ac.uk/maven2/net/sourceforge/jmol/jmol/ ready to be > referenced by your pom.xml. A second idea is to set up a biojava jmol > repository (depending on the license of Jmol) right at the biojava > servers that you reference in your pom.xml. A third (and maybe the > best idea) is to ask the Jmol team to set up a maven repository, or to > upload artifacts to the central repository. The people behind Jmol are > really helpful and I am pretty sure they are willing to help. > > > But maybe there are more clever ideas how to work around that problem... > > Raphael > > > > maybe this helps: > > > > >> pom? >> >> Andreas >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > From heuermh at acm.org Mon Dec 28 23:19:56 2009 From: heuermh at acm.org (Michael Heuer) Date: Mon, 28 Dec 2009 23:19:56 -0500 (EST) Subject: [Biojava-dev] FASTQ support on release-1_7-branch, prepare for 1.7.1? In-Reply-To: <59a41c430912280731r2d961501w4f1602b9667633f3@mail.gmail.com> Message-ID: Andreas Prlic wrote: > In principle the BioJava 3.0 release is scheduled for early next year, > but I assume you don't want to wait so long, due to the FASTQ paper? Right. The paper explicitly mentions a version 1.7.1, so that needs to exist sometime soon. :) > I will try to automatize the biojava 3.0 release procedure using Maven > as much as possible. As such I would not want to spend the time for a > minor version update now, but if you want to go for it, fine with me. I'm in the midst of cutting a release for some other maven-based projects, and it's not as straightforward as one might expect. > Building a release is straightforward, I documented the release > procedure of 1.7 on this page: > > http://biojava.org/wiki/BioJava:Make_release Whew, that's a lot to do! Very nice job documenting the process. > Probably you should add a page about the new FASTQ parser to the > Cookbook as well, particularly if this is going to be the main new > feature of 1.7.1 ... Will do. Thanks, michael From mark.schreiber at novartis.com Wed Dec 2 05:55:30 2009 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Wed, 2 Dec 2009 13:55:30 +0800 Subject: [Biojava-dev] Fw: [Open-bio-l] Fwd: [Utilities-announce] NCBI E-Utility Policy Change Message-ID: FYI for BioJava developers ... ----- Forwarded by Mark Schreiber/GP/Novartis on 12/02/2009 01:54 PM ----- open-bio-l-bounces at lists.open-bio.org wrote on 12/02/2009 04:00:43 AM: > Hi all, > > I know Biopython and BioPerl are aware of this change, but in case > the other Bio* projects are not please see below. Sign up here: > http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html > > Peter @ Biopython > > ---------- Forwarded message ---------- > From: > Date: Tue, Dec 1, 2009 at 6:59 PM > Subject: [Utilities-announce] NCBI E-Utility Policy Change > To: utilities-announce at ncbi.nlm.nih.gov > > > As part of an ongoing effort to ensure efficient access to the Entrez > Utilities (E-utilities) by all users, NCBI has decided to change the > usage policy for the E-utilities effective June 1, 2010. Effective on > June 1, 2010, all E-utility requests, either using standard URLs or > SOAP, must contain non-null values for both the &tool and &email > parameters. Any E-utility request made after June 1, 2010 that does > not contain values for both parameters will return an error explaining > that these parameters must be included in E-utility requests. > > > > The value of the &tool parameter should be a URI-safe string that is > the name of the software package, script or web page producing the > E-utility request. > > > > The value of the &email parameter should be a valid e-mail address for > the appropriate contact person or group responsible for maintaining > the tool producing the E-utility request. > > > > NCBI uses these parameters to contact users whose use of the > E-utilities violates the standard usage policies described at > http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help. > html#UserSystemRequirements. > These usage policies are designed to prevent excessive requests from a > small group of users from reducing or eliminating the wider > community's access to the E-utilities. NCBI will attempt to contact a > user at the e-mail address provided in the &email parameter prior to > blocking access to the E-utilities. > > > > NCBI realizes that this policy change will require many of our users > to change their code. Based on past experience, we anticipate that > most of our users should be able to make the necessary changes before > the June 1, 2010 deadline. If you have any concerns about making these > changes by that date, or if you have any questions about these > policies, please contact eutilities at ncbi.nlm.nih.gov. > > > > Thank you for your understanding and cooperation in helping us > continue to deliver a reliable and efficient web service. > > > > _______________________________________________ > Utilities-announce mailing list > http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. From holland at eaglegenomics.com Wed Dec 2 11:36:54 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 2 Dec 2009 11:36:54 +0000 Subject: [Biojava-dev] Fw: [Open-bio-l] Fwd: [Utilities-announce] NCBI E-Utility Policy Change In-Reply-To: References: Message-ID: <6D65C618-F05D-4D8D-AB9F-38A35DD9F730@eaglegenomics.com> I've just patched the trunk to take this into account. GenbankRichSequenceDB - two new values accessed via setTool/getTool and setEmail/getEmail with appropriate default values to ensure all current code still works without modification. cheers, Richard On 2 Dec 2009, at 05:55, mark.schreiber at novartis.com wrote: > FYI for BioJava developers ... > > > ----- Forwarded by Mark Schreiber/GP/Novartis on 12/02/2009 01:54 PM ----- > > open-bio-l-bounces at lists.open-bio.org wrote on 12/02/2009 04:00:43 AM: > >> Hi all, >> >> I know Biopython and BioPerl are aware of this change, but in case >> the other Bio* projects are not please see below. Sign up here: >> http://www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html >> >> Peter @ Biopython >> >> ---------- Forwarded message ---------- >> From: >> Date: Tue, Dec 1, 2009 at 6:59 PM >> Subject: [Utilities-announce] NCBI E-Utility Policy Change >> To: utilities-announce at ncbi.nlm.nih.gov >> >> >> As part of an ongoing effort to ensure efficient access to the Entrez >> Utilities (E-utilities) by all users, NCBI has decided to change the >> usage policy for the E-utilities effective June 1, 2010. Effective on >> June 1, 2010, all E-utility requests, either using standard URLs or >> SOAP, must contain non-null values for both the &tool and &email >> parameters. Any E-utility request made after June 1, 2010 that does >> not contain values for both parameters will return an error explaining >> that these parameters must be included in E-utility requests. >> >> >> >> The value of the &tool parameter should be a URI-safe string that is >> the name of the software package, script or web page producing the >> E-utility request. >> >> >> >> The value of the &email parameter should be a valid e-mail address for >> the appropriate contact person or group responsible for maintaining >> the tool producing the E-utility request. >> >> >> >> NCBI uses these parameters to contact users whose use of the >> E-utilities violates the standard usage policies described at >> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help. >> html#UserSystemRequirements. >> These usage policies are designed to prevent excessive requests from a >> small group of users from reducing or eliminating the wider >> community's access to the E-utilities. NCBI will attempt to contact a >> user at the e-mail address provided in the &email parameter prior to >> blocking access to the E-utilities. >> >> >> >> NCBI realizes that this policy change will require many of our users >> to change their code. Based on past experience, we anticipate that >> most of our users should be able to make the necessary changes before >> the June 1, 2010 deadline. If you have any concerns about making these >> changes by that date, or if you have any questions about these >> policies, please contact eutilities at ncbi.nlm.nih.gov. >> >> >> >> Thank you for your understanding and cooperation in helping us >> continue to deliver a reliable and efficient web service. >> >> >> >> _______________________________________________ >> Utilities-announce mailing list >> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce >> _______________________________________________ >> Open-Bio-l mailing list >> Open-Bio-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/open-bio-l > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivery of the > message to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is strictly > prohibited. If you have received this communication in error, please > notify the sender immediately by e-mail and delete the material from any > computer. Thank you. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From holland at eaglegenomics.com Wed Dec 9 12:07:16 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Wed, 9 Dec 2009 12:07:16 +0000 Subject: [Biojava-dev] Job vacancies Message-ID: Hi there, Apologies for posting job ads to the lists but I think this one is relevant to the members so please forgive me. If you know of anyone that might be interested, could you forward them this job ad? Also if you have any local resources for posting job ads, it would be great if you could put the ad up there as well. Sorry to intrude - I'll leave you in peace again now. :) thanks! Richard 1. Senior Bioinformatics Software Developer (Perl/Ensembl) 2. Senior Bioinformatics Software Developer (Java/Taverna) Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for TWO top-class developers to work on a wide range of complex projects. Both these roles involve a large element of customer support and so you'll need to be friendly, communicative, and happy to work face-to-face with our customers on a daily basis. You will have had substantial prior experience working in a life science company or research institute. For the Perl/Ensembl role, you will have had extensive experience as a Perl developer and ideally you will have written code or plugins for the Ensembl Genome Browser or used its APIs in your own progams. For the Java/Taverna role you will be an expert Java developer with the ability to rapidly analyse and understand complex systems. Ideally you will have written code or plugins for the Taverna project or written code that makes use of it. For both roles, in addition to your superb technical and customer service skills, you will also: ? be able to communicate clearly and proactively, ? have the ability to quickly translate scientific problems into real software solutions, ? be able to put technical concepts into simple language for end users to understand, ? be able to pick up new skills and techniques in record time, ? work well in a collaborative team environment, ? be creative, innovative, and forward-thinking. You will also have had hands-on experience in at least two of the following: ? SQL query design, ? Open-source bioinformatics toolkits such as BioPerl, BioJava, BioSQL, etc., ? Amazon EC2, ? Workflow/pipeline design, ? System and user documentation, ? Developing user training courses. The successful candidate would be expected to work from our offices near Cambridge, however remote working in the UK/Europe may be considered for exceptional candidates (depending on exact location). We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs @eaglegenomics.com . We are only able to offer positions to EEA citizens and permanent residents, or existing holders of UK Tier 1 migrant visas. No agencies please. Closing date: 8th JANUARY 2010. -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From bugzilla-daemon at portal.open-bio.org Thu Dec 17 17:52:38 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 17 Dec 2009 12:52:38 -0500 Subject: [Biojava-dev] [Bug 2971] New: Nexus parser fails to parse internal node names Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2971 Summary: Nexus parser fails to parse internal node names Product: BioJava Version: live (CVS source) Platform: All OS/Version: All Status: NEW Severity: normal Priority: P2 Component: Others AssignedTo: biojava-dev at biojava.org ReportedBy: tiagoantao at gmail.com The Ancestor1 below is not parsed correctly. Begin TREES; tree test2 = (B:6.0,(A:5.0,C:3.0,E:4.0) Ancestor1:5.0,D:11.0); End; Internal node names (as opposed to leaves) are not correctly processed. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Thu Dec 17 17:53:25 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Thu, 17 Dec 2009 12:53:25 -0500 Subject: [Biojava-dev] [Bug 2971] Nexus parser fails to parse internal node names In-Reply-To: Message-ID: <200912171753.nBHHrPsk021176@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2971 tiagoantao at gmail.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Comment #1 from tiagoantao at gmail.com 2009-12-17 12:53 EST ------- I will also used this bug to submit a patch to problems with newline parsing. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Dec 18 23:02:09 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 18 Dec 2009 18:02:09 -0500 Subject: [Biojava-dev] [Bug 2971] Nexus parser fails to parse internal node names In-Reply-To: Message-ID: <200912182302.nBIN29mO030812@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2971 ------- Comment #2 from tiagoantao at gmail.com 2009-12-18 18:02 EST ------- Created an attachment (id=1411) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1411&action=view) Patch to naming bug This patch is supplied against the maven style repository. Includes: Patch to code Patch to test code New test file -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From andreas at sdsc.edu Mon Dec 21 04:29:27 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 20 Dec 2009 20:29:27 -0800 Subject: [Biojava-dev] maven and custom jar Message-ID: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> Hi, I am about to commit some major new features to the protein structure modules. For the visualisation of these, the Jmol applet is being used. As such I would like to add the dependency on it to the structure modules. Since I could not find a JmolApplet.jar in maven, I currently install it locally via mvn install:install-file . What is the easiest way to get this set up and installed automatically, if somebody else checks out the code from SVN ? Shall we just document the line that installs Jmol, or should there be a custom target in the pom? Andreas From bugzilla-daemon at portal.open-bio.org Mon Dec 21 15:19:08 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 21 Dec 2009 10:19:08 -0500 Subject: [Biojava-dev] [Bug 2971] Nexus parser fails to parse internal node names In-Reply-To: Message-ID: <200912211519.nBLFJ8bv001831@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2971 holland at eaglegenomics.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Comment #3 from holland at eaglegenomics.com 2009-12-21 10:19 EST ------- Committed patch. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From mahogny at areta.org Mon Dec 21 15:23:19 2009 From: mahogny at areta.org (Johan Henriksson) Date: Mon, 21 Dec 2009 16:23:19 +0100 Subject: [Biojava-dev] biojava hackathon Message-ID: Hello, has anyone done their homework and figured out which hotels are the best. maybe someone working there knows the "standard" ones? it seems I can join in. have not decided exactly what I will work on but surely not the protein stuff. either improving the core or the algorithms/data structures. I have experimented a bit with alternative ways of dealing with annotation and sequence data, maybe it can be of use. /Johan -- ----------------------------------------------------------- Johan Henriksson PhD student, Karolinska Institutet http://mahogny.areta.org http://www.endrov.net From holland at eaglegenomics.com Mon Dec 21 15:33:25 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 21 Dec 2009 15:33:25 +0000 Subject: [Biojava-dev] biojava hackathon In-Reply-To: References: Message-ID: <603A6F8A-087D-4003-92A0-1EEF5EE136FA@eaglegenomics.com> It used to be that you could get fairly cheap rooms at the Travelodge in central Cambridge, but I no longer live in Cambridge so I'll leave the job of answering correctly to someone who knows better than me. :) Looking forward to seeing you at the hackathon. On 21 Dec 2009, at 15:23, Johan Henriksson wrote: > Hello, > has anyone done their homework and figured out which hotels are the best. > maybe someone working there knows the "standard" ones? > > it seems I can join in. have not decided exactly what I will work on but > surely not the protein stuff. either improving the core or the > algorithms/data structures. I have experimented a bit with alternative ways > of dealing with annotation and sequence data, maybe it can be of use. > > /Johan > > -- > ----------------------------------------------------------- > Johan Henriksson > PhD student, Karolinska Institutet > http://mahogny.areta.org http://www.endrov.net > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Mon Dec 21 16:20:09 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 21 Dec 2009 08:20:09 -0800 Subject: [Biojava-dev] biojava hackathon In-Reply-To: References: Message-ID: <59a41c430912210820p59ae6b46wa239ae78328098d8@mail.gmail.com> A few people asked me where to stay and I suggested to book the Travelodge in Hills road. It is a plain and cheap hotel (for Cambridge), walking distance to the train station, town center (20 min) and close to one of the stops of the Genome Campus bus routes. Andreas On Mon, Dec 21, 2009 at 7:23 AM, Johan Henriksson wrote: > Hello, > has anyone done their homework and figured out which hotels are the best. > maybe someone working there knows the "standard" ones? > > it seems I can join in. have not decided exactly what I will work on but > surely not the protein stuff. either improving the core or the > algorithms/data structures. I have experimented a bit with alternative ways > of dealing with annotation and sequence data, maybe it can be of use. > > /Johan > > -- > ----------------------------------------------------------- > Johan Henriksson > PhD student, Karolinska Institutet > http://mahogny.areta.org ?http://www.endrov.net > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From raphael.andre.bauer at gmail.com Tue Dec 22 21:35:13 2009 From: raphael.andre.bauer at gmail.com (=?UTF-8?Q?Raphael_Andr=C3=A9_Bauer?=) Date: Tue, 22 Dec 2009 22:35:13 +0100 Subject: [Biojava-dev] maven and custom jar In-Reply-To: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> References: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> Message-ID: <9b46aa30912221335i1be5386ataec6008f23fb7ec@mail.gmail.com> On Mon, Dec 21, 2009 at 5:29 AM, Andreas Prlic wrote: > Hi, > > I am about to commit some major new features to the protein structure > modules. For the visualisation of these, the Jmol applet is being cool :) > used. As such I would like to add the dependency on it to the > structure modules. Since I could not find a JmolApplet.jar in maven, I > currently install it locally via mvn install:install-file . ?What is > the easiest way to get this set up and installed automatically, if > somebody else checks out the code from SVN ? Shall we just document > the line that installs Jmol, or should there be a custom target in the Hi Andreas, a quick scan gave me this (unofficial imho) repository: http://wwmm.ch.cam.ac.uk/maven2/net/sourceforge/jmol/jmol/ ready to be referenced by your pom.xml. A second idea is to set up a biojava jmol repository (depending on the license of Jmol) right at the biojava servers that you reference in your pom.xml. A third (and maybe the best idea) is to ask the Jmol team to set up a maven repository, or to upload artifacts to the central repository. The people behind Jmol are really helpful and I am pretty sure they are willing to help. But maybe there are more clever ideas how to work around that problem... Raphael maybe this helps: > pom? > > Andreas > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From heuermh at acm.org Mon Dec 28 04:41:22 2009 From: heuermh at acm.org (Michael Heuer) Date: Sun, 27 Dec 2009 23:41:22 -0500 (EST) Subject: [Biojava-dev] FASTQ support on release-1_7-branch, prepare for 1.7.1? Message-ID: All, I have copied FASTQ-format support from the biojava3 branch to the release-1_7-branch branch, with some modification to match the older project structure. I'd like to cut a version 1.7.1 release soon, since this code is referred to in the open-bio FASTQ paper recently published in NAR. Might someone review the release-1_7-branch? I could also use a hand with the actual release process. Thank you, michael From andreas at sdsc.edu Mon Dec 28 15:31:48 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 28 Dec 2009 07:31:48 -0800 Subject: [Biojava-dev] FASTQ support on release-1_7-branch, prepare for 1.7.1? In-Reply-To: References: Message-ID: <59a41c430912280731r2d961501w4f1602b9667633f3@mail.gmail.com> Hi Michael, In principle the BioJava 3.0 release is scheduled for early next year, but I assume you don't want to wait so long, due to the FASTQ paper? I will try to automatize the biojava 3.0 release procedure using Maven as much as possible. As such I would not want to spend the time for a minor version update now, but if you want to go for it, fine with me. Building a release is straightforward, I documented the release procedure of 1.7 on this page: http://biojava.org/wiki/BioJava:Make_release Probably you should add a page about the new FASTQ parser to the Cookbook as well, particularly if this is going to be the main new feature of 1.7.1 ... Let us know how it goes... Andreas On Sun, Dec 27, 2009 at 8:41 PM, Michael Heuer wrote: > All, > > I have copied FASTQ-format support from the biojava3 branch to the > release-1_7-branch branch, with some modification to match the older > project structure. > > I'd like to cut a version 1.7.1 release soon, since this code is referred > to in the open-bio FASTQ paper recently published in NAR. ?Might someone > review the release-1_7-branch? ?I could also use a hand with the actual > release process. > > Thank you, > > ? michael > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From andreas at sdsc.edu Mon Dec 28 15:46:19 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 28 Dec 2009 07:46:19 -0800 Subject: [Biojava-dev] maven and custom jar In-Reply-To: <9b46aa30912221335i1be5386ataec6008f23fb7ec@mail.gmail.com> References: <59a41c430912202029n4920e983r63b455959fb8bc56@mail.gmail.com> <9b46aa30912221335i1be5386ataec6008f23fb7ec@mail.gmail.com> Message-ID: <59a41c430912280746w784d2639q21a607f434a3f11e@mail.gmail.com> Hi Raphael, Thanks for the link to the Jmol maven. Problem is it is a bit out of date and the latest release version is already two increments higher. I will post to the Jmol list about getting a more up to date version and if that does not work out, I will do something via the BioJava servers... Thanks, Andreas On Tue, Dec 22, 2009 at 1:35 PM, Raphael Andr? Bauer wrote: > On Mon, Dec 21, 2009 at 5:29 AM, Andreas Prlic wrote: >> Hi, >> >> I am about to commit some major new features to the protein structure >> modules. For the visualisation of these, the Jmol applet is being > cool :) >> used. As such I would like to add the dependency on it to the >> structure modules. Since I could not find a JmolApplet.jar in maven, I >> currently install it locally via mvn install:install-file . ?What is >> the easiest way to get this set up and installed automatically, if >> somebody else checks out the code from SVN ? Shall we just document >> the line that installs Jmol, or should there be a custom target in the > > Hi Andreas, > > > a quick scan gave me this (unofficial imho) repository: > http://wwmm.ch.cam.ac.uk/maven2/net/sourceforge/jmol/jmol/ ready to be > referenced by your pom.xml. A second idea is to set up a biojava jmol > repository (depending on the license of Jmol) right at the biojava > servers that you reference in your pom.xml. A third (and maybe the > best idea) is to ask the Jmol team to set up a maven repository, or to > upload artifacts to the central repository. The people behind Jmol are > really helpful and I am pretty sure they are willing to help. > > > But maybe there are more clever ideas how to work around that problem... > > Raphael > > > > maybe this helps: > > > > >> pom? >> >> Andreas >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > From heuermh at acm.org Tue Dec 29 04:19:56 2009 From: heuermh at acm.org (Michael Heuer) Date: Mon, 28 Dec 2009 23:19:56 -0500 (EST) Subject: [Biojava-dev] FASTQ support on release-1_7-branch, prepare for 1.7.1? In-Reply-To: <59a41c430912280731r2d961501w4f1602b9667633f3@mail.gmail.com> Message-ID: Andreas Prlic wrote: > In principle the BioJava 3.0 release is scheduled for early next year, > but I assume you don't want to wait so long, due to the FASTQ paper? Right. The paper explicitly mentions a version 1.7.1, so that needs to exist sometime soon. :) > I will try to automatize the biojava 3.0 release procedure using Maven > as much as possible. As such I would not want to spend the time for a > minor version update now, but if you want to go for it, fine with me. I'm in the midst of cutting a release for some other maven-based projects, and it's not as straightforward as one might expect. > Building a release is straightforward, I documented the release > procedure of 1.7 on this page: > > http://biojava.org/wiki/BioJava:Make_release Whew, that's a lot to do! Very nice job documenting the process. > Probably you should add a page about the new FASTQ parser to the > Cookbook as well, particularly if this is going to be the main new > feature of 1.7.1 ... Will do. Thanks, michael