From heuermh at acm.org Wed May 7 01:18:57 2008 From: heuermh at acm.org (Michael Heuer) Date: Wed, 7 May 2008 01:18:57 -0400 (EDT) Subject: [Biojava-dev] BOSC 2008 Announcement and Call For Submissions In-Reply-To: <200804291648.m3TGmXk7020802@tenero.duhs.duke.edu> Message-ID: All, The BOSC abstract submission deadline is near. Is there interest in giving a "Bio* Open Source Project Updates" presentation? Or perhaps just a lightning talk? I am willing to help with the abstract and should be at BOSC to give the presentation if no one else can make it. michael On Tue, 29 Apr 2008 darin.london at duke.edu wrote: > > BOSC 2008 Call for Abstracts Reminder > > The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). > > This is a reminder to submit your proposals for talks to the BOSC submission system before May 11. > > Submission Process: > All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). > The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) > Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t > > Important Dates: > May 11: Abstract submission deadline. > June 2: Notification of accepted talks. > June 4: Early registration discount cut-off. > July 18-19: BOSC 2008! > > We hope to see you at BOSC 2008! > > Kam Dahlquist and Darin London > BOSC 2008 Co-organizers > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From ap3 at sanger.ac.uk Wed May 7 06:01:25 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 7 May 2008 11:01:25 +0100 Subject: [Biojava-dev] BOSC 2008 Announcement and Call For Submissions In-Reply-To: References: Message-ID: Hi Michael, It would be great to have a biojava presentation at BOSC. I am not aware of anybody else preparing for this, so please go ahead! Let me know if you need any help with the abstract. I won't be able to attend ISMB this year... Cheers, Andreas On 7 May 2008, at 06:18, Michael Heuer wrote: > All, > > The BOSC abstract submission deadline is near. Is there interest in > giving a "Bio* Open Source Project Updates" presentation? Or > perhaps just > a lightning talk? > > I am willing to help with the abstract and should be at BOSC to > give the > presentation if no one else can make it. > > michael > > > On Tue, 29 Apr 2008 darin.london at duke.edu wrote: > >> >> BOSC 2008 Call for Abstracts Reminder >> >> The 9th annual Bioinformatics Open Source Conference (BOSC 2008) >> will take place in Toronto, Ontario, Canada, as one of several >> Special Interest Group (SIG) meetings occurring in conjunction >> with the 16th annual Intelligent Systems for Molecular Biology >> Conference (ISMB 2008). >> >> This is a reminder to submit your proposals for talks to the BOSC >> submission system before May 11. >> >> Submission Process: >> All abstracts must be submitted through our Open Conference >> Systems site (http://events.open-bio.org/BOSC2008/openconf.php). >> The form will ask for a small Abstract Text to be pasted into it, >> and a full paper. The small Abstract text should be a summary, >> while the longer abstract (should provide more details, including >> the open-source license requirement details) >> Full-length abstracts are limited to one page with one inch (2.5 >> cm) margins on the top, sides, and bottom. The full-length >> abstract should include the title, authors, and affiliations. We >> prefer your abstract to be in PDF format, although plain t >> >> Important Dates: >> May 11: Abstract submission deadline. >> June 2: Notification of accepted talks. >> June 4: Early registration discount cut-off. >> July 18-19: BOSC 2008! >> >> We hope to see you at BOSC 2008! >> >> Kam Dahlquist and Darin London >> BOSC 2008 Co-organizers >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From gcappuccilli at protelix.com Wed May 7 12:55:09 2008 From: gcappuccilli at protelix.com (Guido Cappuccilli) Date: Wed, 7 May 2008 09:55:09 -0700 Subject: [Biojava-dev] BioEntryRelationship problem Message-ID: First of all, I am new here so I apologize in advance if I am discussing something obvious. Moreover I am NOT an BioJava nor Hibernate guru. I am working on a small project using BioJava (1.6) + BioSQL (1.0) (mysql 4.1.22 on Mac OS X server 10.4.11). I want to persist relationships between BioEntry objects. Storing objects to DB didn't give any problems. Sample code: Transaction tx=s.beginTransaction(); try { ComparableTerm term=RichObjectFactory.getDefaultOntology ().getOrCreateTerm("TestTerm"); Namespace ns=RichObjectFactory.getDefaultNamespace(); BioEntry parent=new SimpleBioEntry(ns, "parentbe", "pACCESSION",0); BioEntry child=new SimpleBioEntry(ns, "childbe", "cACCESSION",0); BioEntryRelationship rel=new SimpleBioEntryRelationship (parent, child, term, null); parent.addRelationship(rel); s.saveOrUpdate("BioEntry",parent ); tx.commit(); } catch (Exception ex) { tx.rollback(); } When I started to query the db I got errors from hibernate (see below). After digging a little I found out that hibernate couldn't query the Bioentry_relationship table. Even a simple "from BioEntryRelationship" query was giving me these errors. 09:43:19,088 ERROR BasicPropertyAccessor:94 - IllegalArgumentException in class: org.biojavax.bio.SimpleBioEntryRelationship, setter method of property: object 09:43:19,089 ERROR BasicPropertyAccessor:98 - expected type: org.biojavax.bio.BioEntry, actual value: org.biojavax.bio.seq.SimpleRichFeature$$EnhancerByCGLIB$$91b34b44 Checking the mapping files I found the following line in the BioEntryRelationship.hbm.xml: It looked strange to me. So I've changed to Now I can query relationships without problems. Did I do the right thing or I am messing up the mapping and I am breaking something else? If this has been already discussed I apologize and I would appreciate a link to the original thread. Thank you in advance G. From markjschreiber at gmail.com Fri May 9 01:22:02 2008 From: markjschreiber at gmail.com (Mark Schreiber) Date: Fri, 9 May 2008 13:22:02 +0800 Subject: [Biojava-dev] BioEntryRelationship problem In-Reply-To: References: Message-ID: <93b45ca50805082222p19a8ee13nd590bec0c148d84@mail.gmail.com> Hi - The change you propose does seem to make sense. Richard, can you comment on this? Best regards, - Mark On Thu, May 8, 2008 at 12:55 AM, Guido Cappuccilli wrote: > > First of all, I am new here so I apologize in advance if I am discussing something obvious. > Moreover I am NOT an BioJava nor Hibernate guru. > > I am working on a small project using BioJava (1.6) + BioSQL (1.0) (mysql 4.1.22 on Mac OS X server 10.4.11). > I want to persist relationships between BioEntry objects. > Storing objects to DB didn't give any problems. > > Sample code: > > Transaction tx=s.beginTransaction(); > try { > ComparableTerm term=RichObjectFactory.getDefaultOntology().getOrCreateTerm("TestTerm"); > Namespace ns=RichObjectFactory.getDefaultNamespace(); > BioEntry parent=new SimpleBioEntry(ns, "parentbe", "pACCESSION",0); > BioEntry child=new SimpleBioEntry(ns, "childbe", "cACCESSION",0); > BioEntryRelationship rel=new SimpleBioEntryRelationship(parent, child, term, null); > parent.addRelationship(rel); > s.saveOrUpdate("BioEntry",parent ); > tx.commit(); > } catch (Exception ex) { > tx.rollback(); > } > > When I started to query the db I got errors from hibernate (see below). > After digging a little I found out that hibernate couldn't query the Bioentry_relationship table. > Even a simple "from BioEntryRelationship" query was giving me these errors. > > 09:43:19,088 ERROR BasicPropertyAccessor:94 - IllegalArgumentException in class: org.biojavax.bio.SimpleBioEntryRelationship, setter method of property: object > 09:43:19,089 ERROR BasicPropertyAccessor:98 - expected type: org.biojavax.bio.BioEntry, actual value: org.biojavax.bio.seq.SimpleRichFeature$$EnhancerByCGLIB$$91b34b44 > > > Checking the mapping files I found the following line in the BioEntryRelationship.hbm.xml: > > > > It looked strange to me. > So I've changed to > > > > Now I can query relationships without problems. > Did I do the right thing or I am messing up the mapping and I am breaking something else? > If this has been already discussed I apologize and I would appreciate a link to the original thread. > Thank you in advance > G. > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From dicknetherlands at gmail.com Fri May 9 04:36:49 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Fri, 9 May 2008 09:36:49 +0100 Subject: [Biojava-dev] BioEntryRelationship problem In-Reply-To: <93b45ca50805082222p19a8ee13nd590bec0c148d84@mail.gmail.com> References: <93b45ca50805082222p19a8ee13nd590bec0c148d84@mail.gmail.com> Message-ID: Guido you are absolutely right - that appears to have been a typo on my behalf when I wrote the files. The change you suggest is correct. Mark - can you make the change in Subversion? I am not quite set up again yet to be able to do it myself.... cheers, Richard 2008/5/9 Mark Schreiber : > Hi - > > The change you propose does seem to make sense. Richard, can you > comment on this? > > Best regards, > > - Mark > > On Thu, May 8, 2008 at 12:55 AM, Guido Cappuccilli > wrote: >> >> First of all, I am new here so I apologize in advance if I am discussing something obvious. >> Moreover I am NOT an BioJava nor Hibernate guru. >> >> I am working on a small project using BioJava (1.6) + BioSQL (1.0) (mysql 4.1.22 on Mac OS X server 10.4.11). >> I want to persist relationships between BioEntry objects. >> Storing objects to DB didn't give any problems. >> >> Sample code: >> >> Transaction tx=s.beginTransaction(); >> try { >> ComparableTerm term=RichObjectFactory.getDefaultOntology().getOrCreateTerm("TestTerm"); >> Namespace ns=RichObjectFactory.getDefaultNamespace(); >> BioEntry parent=new SimpleBioEntry(ns, "parentbe", "pACCESSION",0); >> BioEntry child=new SimpleBioEntry(ns, "childbe", "cACCESSION",0); >> BioEntryRelationship rel=new SimpleBioEntryRelationship(parent, child, term, null); >> parent.addRelationship(rel); >> s.saveOrUpdate("BioEntry",parent ); >> tx.commit(); >> } catch (Exception ex) { >> tx.rollback(); >> } >> >> When I started to query the db I got errors from hibernate (see below). >> After digging a little I found out that hibernate couldn't query the Bioentry_relationship table. >> Even a simple "from BioEntryRelationship" query was giving me these errors. >> >> 09:43:19,088 ERROR BasicPropertyAccessor:94 - IllegalArgumentException in class: org.biojavax.bio.SimpleBioEntryRelationship, setter method of property: object >> 09:43:19,089 ERROR BasicPropertyAccessor:98 - expected type: org.biojavax.bio.BioEntry, actual value: org.biojavax.bio.seq.SimpleRichFeature$$EnhancerByCGLIB$$91b34b44 >> >> >> Checking the mapping files I found the following line in the BioEntryRelationship.hbm.xml: >> >> >> >> It looked strange to me. >> So I've changed to >> >> >> >> Now I can query relationships without problems. >> Did I do the right thing or I am messing up the mapping and I am breaking something else? >> If this has been already discussed I apologize and I would appreciate a link to the original thread. >> Thank you in advance >> G. >> >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > From gcappuccilli at protelix.com Fri May 9 12:05:18 2008 From: gcappuccilli at protelix.com (Guido Cappuccilli) Date: Fri, 9 May 2008 09:05:18 -0700 Subject: [Biojava-dev] BioEntryRelationship problem Message-ID: <01616963-21E6-47A7-B2D5-B7F1F55108B1@protelix.com> Thank you for your replies! Best, Guido From heuermh at acm.org Fri May 9 19:26:35 2008 From: heuermh at acm.org (Michael Heuer) Date: Fri, 9 May 2008 19:26:35 -0400 (EDT) Subject: [Biojava-dev] BOSC 2008 Announcement and Call For Submissions In-Reply-To: Message-ID: Thanks Andreas. I am using > http://biojava.org/wiki/BOSC2008_Abstract as my workspace and will be cribbing from biojava/biojava-paper/BioJavaBioinformatics.odt in SVN unless I hear otherwise. Feel free to jump in, anyone! michael Andreas Prlic wrote: > Hi Michael, > > It would be great to have a biojava presentation at BOSC. I am not > aware of anybody else preparing for this, so please go ahead! > Let me know if you need any help with the abstract. I won't be able > to attend ISMB this year... > > Cheers, > Andreas > > > On 7 May 2008, at 06:18, Michael Heuer wrote: > > > All, > > > > The BOSC abstract submission deadline is near. Is there interest in > > giving a "Bio* Open Source Project Updates" presentation? Or > > perhaps just > > a lightning talk? > > > > I am willing to help with the abstract and should be at BOSC to > > give the > > presentation if no one else can make it. > > > > michael > > > > > > On Tue, 29 Apr 2008 darin.london at duke.edu wrote: > > > >> > >> BOSC 2008 Call for Abstracts Reminder > >> > >> The 9th annual Bioinformatics Open Source Conference (BOSC 2008) > >> will take place in Toronto, Ontario, Canada, as one of several > >> Special Interest Group (SIG) meetings occurring in conjunction > >> with the 16th annual Intelligent Systems for Molecular Biology > >> Conference (ISMB 2008). > >> > >> This is a reminder to submit your proposals for talks to the BOSC > >> submission system before May 11. > >> > >> Submission Process: > >> All abstracts must be submitted through our Open Conference > >> Systems site (http://events.open-bio.org/BOSC2008/openconf.php). > >> The form will ask for a small Abstract Text to be pasted into it, > >> and a full paper. The small Abstract text should be a summary, > >> while the longer abstract (should provide more details, including > >> the open-source license requirement details) > >> Full-length abstracts are limited to one page with one inch (2.5 > >> cm) margins on the top, sides, and bottom. The full-length > >> abstract should include the title, authors, and affiliations. We > >> prefer your abstract to be in PDF format, although plain t > >> > >> Important Dates: > >> May 11: Abstract submission deadline. > >> June 2: Notification of accepted talks. > >> June 4: Early registration discount cut-off. > >> July 18-19: BOSC 2008! > >> > >> We hope to see you at BOSC 2008! > >> > >> Kam Dahlquist and Darin London > >> BOSC 2008 Co-organizers > >> > >> > >> > >> _______________________________________________ > >> biojava-dev mailing list > >> biojava-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > >> > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > ----------------------------------------------------------------------- > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From cappuccilli at gmail.com Fri May 9 12:04:45 2008 From: cappuccilli at gmail.com (Guido Cappuccilli) Date: Fri, 09 May 2008 16:04:45 -0000 Subject: [Biojava-dev] BioEntryRelationship problem Message-ID: <71FEF98A-E581-474D-9D94-C53835286FA7@gmail.com> Thank you for your replies. Best, Guido From rvincent at asti.dost.gov.ph Wed May 28 21:59:50 2008 From: rvincent at asti.dost.gov.ph (Rey Vincent Babilonia) Date: Thu, 29 May 2008 01:59:50 -0000 Subject: [Biojava-dev] [Fwd: large genbank data] Message-ID: <483E0CA2.4010906@asti.dost.gov.ph> -------- Original Message -------- Subject: large genbank data Date: Wed, 28 May 2008 18:02:48 +0800 From: Rey Vincent Babilonia To: biojava-l at biojava.org hi, anybody tried uploading a large genbank data (e.g. ftp://bio-mirror.net/biomirror/genbank/gbbct1.seq.gz) to biosql? load_seqdatabase.pl of bioperl can do this. i'm switching to biojava and it can't read the sequence (maybe because it has 30000+ sequences). thanks. -- /** * @author Rey Vincent P. Babilonia * @number +63 2 426 9760 local 1302 * @pgp 0x383454CF pgp.mit.edu * @project Philippine Bioinformatics Solutions * @program Philippine e-Science Grid * @division Research and Development Division * @agency Advanced Science and Technology Institute * @url http://www.psigrid.gov.ph */ -- /** * @author Rey Vincent P. Babilonia * @number +63 2 426 9760 local 1302 * @pgp 0x383454CF pgp.mit.edu * @project Philippine Bioinformatics Solutions * @program Philippine e-Science Grid * @division Research and Development Division * @agency Advanced Science and Technology Institute * @url http://www.psigrid.gov.ph */ -------------- next part -------------- No virus found in this outgoing message. Checked by AVG. Version: 8.0.100 / Virus Database: 269.24.2/1471 - Release Date: 5/28/2008 5:33 PM