From dicknetherlands at gmail.com Mon Aug 4 03:28:12 2008 From: dicknetherlands at gmail.com (Richard Holland) Date: Mon, 4 Aug 2008 08:28:12 +0100 Subject: [Biojava-dev] Error In-Reply-To: <481940.27310.qm@web51103.mail.re2.yahoo.com> References: <481940.27310.qm@web51103.mail.re2.yahoo.com> Message-ID: Could you look in: C:\Program Files\Java\ and see if there is a file called biojava-live.jar. If there is, then modify your classpath to reference that INSTEAD of biojava.jar. Let me know if that fixes it. cheers, Richard 2008/7/22 sudha sadhasivam : > Respected Sir > I am herewith attaching the error report on executing a simple prgm in biojava. I am working as an Asst Prof in CSE dept, PSGCT, INDIA. We are trying to use biojava for sequence alignment examples in ME(CSE) > > Please clarify our doubt at the earliest > > Thanking you > with regards > Dr G Sudha Sadasivam > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- Richard Holland Bioinformatics Software Developer Eagle Genomics http://www.eaglegenomics.com/ From andreas at sdsc.edu Sun Aug 10 11:59:12 2008 From: andreas at sdsc.edu (Andreas Prlic) Date: Sun, 10 Aug 2008 08:59:12 -0700 Subject: [Biojava-dev] biojava paper published Message-ID: <59a41c430808100859k6c8dd460kd2ca8c65de650583@mail.gmail.com> Hi All, I am glad to announce that an Application Note describing BioJava has been accepted for publication in Bioinformatics. The advance access manuscript is available from: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn397v1?ijkey=jIKd6VUGPrgshbv&keytype=ref As alwyas, happy biojava-ing, Andreas From hlapp at gmx.net Sun Aug 10 13:21:57 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 10 Aug 2008 13:21:57 -0400 Subject: [Biojava-dev] [Biojava-l] biojava paper published In-Reply-To: <59a41c430808100859k6c8dd460kd2ca8c65de650583@mail.gmail.com> References: <59a41c430808100859k6c8dd460kd2ca8c65de650583@mail.gmail.com> Message-ID: <7A99248B-DB41-4FCE-AFA2-CE1D0E083827@gmx.net> Congratulations!!! -hilmar On Aug 10, 2008, at 11:59 AM, Andreas Prlic wrote: > Hi All, > > I am glad to announce that an Application Note describing BioJava has > been accepted for publication in Bioinformatics. > The advance access manuscript is available from: > > http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn397v1?ijkey=jIKd6VUGPrgshbv&keytype=ref > > As alwyas, > > happy biojava-ing, > > Andreas > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bugzilla-daemon at portal.open-bio.org Mon Aug 11 22:07:58 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 11 Aug 2008 22:07:58 -0400 Subject: [Biojava-dev] [Bug 2565] New: Cannot parse uniprot P02768 Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2565 Summary: Cannot parse uniprot P02768 Product: BioJava Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: P2 Component: seq.io AssignedTo: biojava-dev at biojava.org ReportedBy: gwaldon at geneinfinity.org Exception thrown during parsing; sequence available at http://www.uniprot.org/uniprot/P02768.txt or http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniprot&id=ALBU_HUMAN&style=raw Problem in reference 62: RN [62] RP VARIANT TYR-73, AND MASS SPECTROMETRY. RC TISSUE=Urine; RX MEDLINE=21537959; PubMed=11680902; RX DOI=10.1002/1615-9861(200101)1:1<93::AID-PROT93>3.3.CO;2-V; RA Spahr C.S., Davis M.T., McGinley M.D., Robinson J.H., Bures E.J., RA Beierle J., Mort J., Courchesne P.L., Chen K., Wahl R.C., Yu W., RA Luethy R., Patterson S.D.; RT "Towards defining the urinary proteome using liquid chromatography- RT tandem mass spectrometry I. Profiling an unfractionated tryptic RT digest."; RL Proteomics 1:93-107(2001). Could not read sequence java.lang.ArrayIndexOutOfBoundsException: 1 at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:486) Caused: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.UniProtFormat Accession=P02768 Id= Comments= Parse_block=RN [61]RP VARIANT TYR-73, AND MASS SPECTROMETRY.RC TISSUE=Urine;RX MEDLINE=21537959; PubMed=11680902; DOI=10.1002/1615-9861(200101)1:1<93::AID-PROT93>3.3.CO;2-V;RA Spahr C.S., Davis M.T., McGinley M.D., Robinson J.H., Bures E.J., Beierle J., Mort J., Courchesne P.L., Chen K., Wahl R.C., Yu W., Luethy R., Patterson S.D.;RT "Towards defining the urinary proteome using liquid chromatography- tandem mass spectrometry I. Profiling an unfractionated tryptic digest.";RL Proteomics 1:93-107(2001). Stack trace follows .... at org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:615) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) Caused: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) -- 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 Tue Aug 12 03:03:07 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Tue, 12 Aug 2008 03:03:07 -0400 Subject: [Biojava-dev] [Bug 2566] New: AbstractSymbolList does not compare alphabets Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=2566 Summary: AbstractSymbolList does not compare alphabets Product: BioJava Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: P2 Component: symbol AssignedTo: biojava-dev at biojava.org ReportedBy: gwaldon at geneinfinity.org in the compare(SymbolList sl1, SymbolList sl2) method and this may result in a false comparison in the particular case where both SymbolList have a length of zero. -- 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 watson at ebi.ac.uk Wed Aug 13 05:00:31 2008 From: watson at ebi.ac.uk (James Watson) Date: Wed, 13 Aug 2008 10:00:31 +0100 Subject: [Biojava-dev] Hands-on course at the European Bioinformatics Institute - Programmatic access in Java: webservices and work flows Message-ID: <48A2A2AF.2@ebi.ac.uk> Dear colleagues, A hands-on course called "Programmatic access in Java: webservices & work flows" will be held on 24-27 November 2008 at the European Bioinformatics Institute in Hinxton, Cambridgeshire, UK. This course will give you the skills to leverage webservice technology to access and manipulate bioinformatics data resources and tools. You will start with simple scripts accessing individual services and then build upon this to create work flows to solve more complex problems in a reusable manner. Participants will be exposed to open standards such as Simple Object Access Protocol (SOAP); the Distributed Annotation System (DAS); REST services and the BioMart web service. Several examples of specific web services will be included, covering programmatic access to both databases and tools at the EBI. The course costs ?75 and interested candidates are encouraged to apply online at the URL below (the training is free, however we need to charge participants an administration fee of ?25 per day to cover food and materials, and participants need to pay their own travel and accommodation): www.ebi.ac.uk/training/handson/course_081124_javawebservices.html This course will have a maximum number of 40 participants on a first come first serve basis, so please register early to avoid disappointment. *The deadline for registering for this event is Monday 27 October 2008.* Best regards, James Watson -- James D Watson Scientific Training Officer EMBL-EBI Wellcome Trust Genome Campus Hinxton Tel: +44(0)1223 492541 http://www.ebi.ac.uk/training/ Upcoming hands on training courses (http://www.ebi.ac.uk/training/handson/): 26-27 August 2008: Interactions and Pathways 1-3 September 2008: Joint EBI?ENFIN workshop - Protein function prediction tools 8-11 September 2008: Programmatic access in Perl: webservices & work flows 6-8 October 2008: 2-day dip into the EBI?s data resources: Understanding your data 24-27 November 2008: Programmatic access in Java: webservices & work flows From bugzilla-daemon at portal.open-bio.org Fri Aug 15 07:09:07 2008 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Fri, 15 Aug 2008 07:09:07 -0400 Subject: [Biojava-dev] [Bug 2566] AbstractSymbolList does not compare alphabets In-Reply-To: Message-ID: <200808151109.m7FB97fb029090@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2566 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #1 from holland at ebi.ac.uk 2008-08-15 07:09 EST ------- Committed fix to subversion. -- 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 talk2ali at gmail.com Tue Aug 19 09:10:19 2008 From: talk2ali at gmail.com (Muhammad Ali) Date: Tue, 19 Aug 2008 09:10:19 -0400 Subject: [Biojava-dev] NCBI Blast XML Parser update Message-ID: Hello, The current version of the BlastXMLParser (used for parsing NCBI BLAST output files) is not handling multiple Iteration entries in the file correctly. It lumps them all together, resulting in a loss of search-specific parameters. The end result is a single SeqSimilaritySearchResult object. The expected output should be one SeqSimilaritySearchResult for each Iteration entry in the file. I've fixed this issue on my locally checked out copy by modifying a few files in the org.biojava.bio.program.sax.blastxml package. I'm interested in submitting the updated code back to the main repository. Can someone tell me how I can go about doing so? Also the javadocs for the BlastXMLParser seem to be outdated. They mention malformed XML being generated by NCBI, but that doesn't seem to be the case anymore. Thanks, Ali. From TSN at atp.dk Mon Aug 4 05:33:50 2008 From: TSN at atp.dk (TSN at atp.dk) Date: Mon, 04 Aug 2008 09:33:50 -0000 Subject: [Biojava-dev] Vedr.: biojava-dev Digest, Vol 65, Issue 2 In-Reply-To: Message-ID: Hello Sudha Sadhasivam ! I'm just a "plain" member of BioJava and therefore not able to help You about the code. But as a Java Enterprise developer I can certainly give You an advice concerning Java-development. It would definitely decrease development time by using a professional Java-development platform such as SUN-Eclipse , IBM-RAD etc. >From this platform You will later on be able to make setups concerning java versions, getting nice information about errors which directs You to the errorLine. In time this way of Java-development will spare You for a lot of trouble and help other to solve Your problems easier Venlig hilsen Tom Stevns - TSN Direkte nummer: 48 20, e-mail: tsn at atp.dk ATP, Kongens V?nge 8, 3400 Hiller?d Tlf.: 70 11 12 13, Fax: 48 20, www.atp.dk Oplysningerne i denne e-mail kan v?re fortrolige og er udelukkende beregnet til brug for de oven for angivne personer eller virksomheder. Vi g?r opm?rksom p?, at udbredelse, omdeling eller kopiering af oplysningerne efter omst?ndighederne er forbudt. Hvis du har modtaget denne e-mail ved en fejltagelse, bedes du meddele det til afsenderen og derefter slette den. P? forh?nd tak. biojava-dev-request at lists.open-bio.org Sendt af: biojava-dev-bounces at lists.open-bio.org 04-08-2008 00:57 Besvar venligst til biojava-dev at lists.open-bio.org Til biojava-dev at lists.open-bio.org cc Emne biojava-dev Digest, Vol 65, Issue 2 Send biojava-dev mailing list submissions to biojava-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-dev or, via email, send a message with subject or body 'help' to biojava-dev-request at lists.open-bio.org You can reach the person managing the list at biojava-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of biojava-dev digest..." Today's Topics: 1. error (sudha sadhasivam) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Jul 2008 01:39:14 -0700 (PDT) From: sudha sadhasivam Subject: [Biojava-dev] error To: biojava-dev at lists.open-bio.org Message-ID: <702887.88659.qm at web51106.mail.re2.yahoo.com> Content-Type: text/plain; charset="us-ascii" Respected Sir We are herewith attaching the errors when we ran biojava in windows We are not able to identify the mistake. Kindly identify the same Thanking you with regards Dr G Sudha Sadasivam -------------- next part -------------- A non-text attachment was scrubbed... Name: error.doc Type: application/msword Size: 22016 bytes Desc: not available URL: < http://lists.open-bio.org/pipermail/biojava-dev/attachments/20080722/a888a502/attachment.doc > ------------------------------ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev End of biojava-dev Digest, Vol 65, Issue 2 ****************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 554 bytes Desc: not available URL: From andreas at sdsc.edu Tue Aug 19 22:36:51 2008 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 19 Aug 2008 19:36:51 -0700 Subject: [Biojava-dev] NCBI Blast XML Parser update In-Reply-To: References: Message-ID: <59a41c430808191936sb139efcwff92065cffe8f49@mail.gmail.com> Hi Ali, that's good news, can you send your patch to this list, so we can have a look? At this stage it would be also great to provide a new Junit test that makes sure that the parsing works ok and to demonstrate the new feature. If you provide more patches in the future we can also set up write access to the SVN repository. Andreas On Tue, Aug 19, 2008 at 6:10 AM, Muhammad Ali wrote: > Hello, > > The current version of the BlastXMLParser (used for parsing NCBI BLAST > output files) is not handling multiple Iteration entries in the file > correctly. It lumps them all together, resulting in a loss of > search-specific parameters. The end result is a single > SeqSimilaritySearchResult object. The expected output should be one > SeqSimilaritySearchResult for each Iteration entry in the file. > > I've fixed this issue on my locally checked out copy by modifying a > few files in the org.biojava.bio.program.sax.blastxml package. I'm > interested in submitting the updated code back to the main repository. > Can someone tell me how I can go about doing so? > > Also the javadocs for the BlastXMLParser seem to be outdated. They > mention malformed XML being generated by NCBI, but that doesn't seem > to be the case anymore. > > Thanks, > Ali. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From antoine.logean at innoq.com Tue Aug 26 08:49:39 2008 From: antoine.logean at innoq.com (Antoine Logean) Date: Tue, 26 Aug 2008 14:49:39 +0200 (CEST) Subject: [Biojava-dev] Serialization problem Message-ID: <43846.212.117.123.66.1219754979.squirrel@innoq.com> Hi everybody, How can I make a Structure object serializable ? Thanks for your help. Antoine From andreas at sdsc.edu Tue Aug 26 20:46:27 2008 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 26 Aug 2008 17:46:27 -0700 Subject: [Biojava-dev] Serialization problem In-Reply-To: <43846.212.117.123.66.1219754979.squirrel@innoq.com> References: <43846.212.117.123.66.1219754979.squirrel@innoq.com> Message-ID: <59a41c430808261746o1b8866d6te91121bbdebb4619@mail.gmail.com> Hi Antoine, Not 100% sure what your goal is. Serializable is a tagging interface; it does not prescribe methods. If you want to serialize a structure to a database, you can use the Hibernate database mappings to do so. http://biojava.org/wiki/BioJava:CookBook:PDB:hibernate Andreas On Tue, Aug 26, 2008 at 5:49 AM, Antoine Logean wrote: > Hi everybody, > > How can I make a Structure object serializable ? > > Thanks for your help. > > Antoine > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From antoine.logean at innoq.com Tue Aug 26 21:35:31 2008 From: antoine.logean at innoq.com (Antoine Logean) Date: Wed, 27 Aug 2008 03:35:31 +0200 Subject: [Biojava-dev] Serialization problem In-Reply-To: <59a41c430808261746o1b8866d6te91121bbdebb4619@mail.gmail.com> References: <43846.212.117.123.66.1219754979.squirrel@innoq.com> <59a41c430808261746o1b8866d6te91121bbdebb4619@mail.gmail.com> Message-ID: <48B4AF63.9090709@innoq.com> Hi Andreas, Thanks a lot for your very fast answer. It is exactly what I needed. May be I can explain you what I intend to do. The aim of my work is to challenge the performance of a framework/middleware called GigaSpaces (http://www.gigaspaces.com). They provide an implementation of the JavaSpace specification (see http://en.wikipedia.org/wiki/Tuple_space#JavaSpaces). In few words you can see the space as a shared memory where you can write, read and take POJOs. The space can be defined as persistent and asynchronously mirrored in a RDBS via Hibernate. The main idea is to avoid the bottleneck associated with DB accesses and to have all the data and processes in the same JVM. They call this in memory data grid (http://www.gigaspaces.com/wiki/display/OLH/GigaSpaces+for+Hibernate+ORM+Users ). Of course, as for RMI parameters, the objects have to be serializable in order to be written in the space ! I let you know of my progresses. Regards, Antoine Andreas Prlic wrote: > Hi Antoine, > > Not 100% sure what your goal is. Serializable is a tagging interface; > it does not prescribe methods. > If you want to serialize a structure to a database, you can use the > Hibernate database mappings to do so. > > http://biojava.org/wiki/BioJava:CookBook:PDB:hibernate > > Andreas > > > > On Tue, Aug 26, 2008 at 5:49 AM, Antoine Logean > wrote: > >> Hi everybody, >> >> How can I make a Structure object serializable ? >> >> Thanks for your help. >> >> Antoine >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> >> > > From simpleyrx at 163.com Sat Aug 30 10:48:18 2008 From: simpleyrx at 163.com (simpleyrx) Date: Sat, 30 Aug 2008 22:48:18 +0800 (CST) Subject: [Biojava-dev] Does biojava can calculate evalue ? Message-ID: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com> Dear experts, I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced. -- Student From simpleyrx at 163.com Sat Aug 30 10:48:18 2008 From: simpleyrx at 163.com (simpleyrx) Date: Sat, 30 Aug 2008 22:48:18 +0800 (CST) Subject: [Biojava-dev] Does biojava can calculate evalue ? Message-ID: <11620077.684601220107698211.JavaMail.coremail@bj163app60.163.com> Dear experts, I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced. -- Student