From mark.schreiber at novartis.com Mon Oct 3 01:51:45 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Oct 3 01:58:28 2005 Subject: [Biojava-l] Graph library Message-ID: Hello - Does anyone know of a good java graph library that is LGPL, Apache license or similar? Not data graphing but graph as in the mathematical construct. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From bader at cbio.mskcc.org Mon Oct 3 02:23:08 2005 From: bader at cbio.mskcc.org (Gary Bader) Date: Mon Oct 3 02:53:05 2005 Subject: [Biojava-l] Graph library In-Reply-To: References: Message-ID: <4340CE4C.10204@cbio.mskcc.org> Hi Mark, My favorite is Cytoscape (www.cytoscape.org), which includes a graph library (full disclosure - I'm involved in the project). It is LGPL. You can also look at JUNG (http://jung.sourceforge.net/). It is BSD. Cytoscape is better suited to biological problems than JUNG and I use it with Biojava on a regular basis. Gary mark.schreiber@novartis.com wrote: > Hello - > > Does anyone know of a good java graph library that is LGPL, Apache license > or similar? Not data graphing but graph as in the mathematical construct. > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Mon Oct 3 02:54:35 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Oct 3 02:54:17 2005 Subject: [Biojava-l] Graph library Message-ID: Looks interesting. What is the relationship between cytoscape and GINY? - Mark Gary Bader 10/03/2005 02:23 PM To: Mark Schreiber/GP/Novartis@PH cc: biojava-l@biojava.org Subject: Re: [Biojava-l] Graph library Hi Mark, My favorite is Cytoscape (www.cytoscape.org), which includes a graph library (full disclosure - I'm involved in the project). It is LGPL. You can also look at JUNG (http://jung.sourceforge.net/). It is BSD. Cytoscape is better suited to biological problems than JUNG and I use it with Biojava on a regular basis. Gary mark.schreiber@novartis.com wrote: > Hello - > > Does anyone know of a good java graph library that is LGPL, Apache license > or similar? Not data graphing but graph as in the mathematical construct. > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From bader at cbio.mskcc.org Mon Oct 3 09:58:24 2005 From: bader at cbio.mskcc.org (Gary Bader) Date: Mon Oct 3 09:58:14 2005 Subject: [Biojava-l] Graph library In-Reply-To: References: Message-ID: <43413900.1080006@cbio.mskcc.org> Hi Mark, GINY is the open source graph library underlying Cytoscape - it is a separate project on sourceforge for modularity reasons at http://csbi.sourceforge.net/ This has recently been reimplemented and named FING in the context of Cytoscape. I'm not sure if the GINY sourceforge site is completely up to date with the current Cytoscape - so if you're just interested in the graph library by itself, it would be good to send a message to the cytoscape-discuss@googlegroups.com mailing list asking about it and I can get the main developer to let you know if the sourceforge package is up to date. Gary mark.schreiber@novartis.com wrote: > Looks interesting. What is the relationship between cytoscape and GINY? > > - Mark > > > > > > Gary Bader > 10/03/2005 02:23 PM > > > To: Mark Schreiber/GP/Novartis@PH > cc: biojava-l@biojava.org > Subject: Re: [Biojava-l] Graph library > > > Hi Mark, > My favorite is Cytoscape (www.cytoscape.org), which > includes a graph > library (full disclosure - I'm involved in the project). It is LGPL. > You can also look at JUNG (http://jung.sourceforge.net/). It is BSD. > Cytoscape is better suited to biological problems than JUNG and I use it > with Biojava on a regular basis. > > Gary > > mark.schreiber@novartis.com wrote: > >>Hello - >> >>Does anyone know of a good java graph library that is LGPL, Apache > > license > >>or similar? Not data graphing but graph as in the mathematical > > construct. > >>- Mark >> >>Mark Schreiber >>Principal Scientist (Bioinformatics) >> >>Novartis Institute for Tropical Diseases (NITD) >>10 Biopolis Road >>#05-01 Chromos >>Singapore 138670 >>www.nitd.novartis.com >> >>phone +65 6722 2973 >>fax +65 6722 2910 >> >>_______________________________________________ >>Biojava-l mailing list - Biojava-l@biojava.org >>http://biojava.org/mailman/listinfo/biojava-l > > > > From d.lapointe at comcast.net Mon Oct 3 11:41:40 2005 From: d.lapointe at comcast.net (d.lapointe@comcast.net) Date: Mon Oct 3 11:50:04 2005 Subject: [Biojava-l] Building from CVS Message-ID: <100320051541.11058.43415134000BDF8400002B3222007621940A9B0207019F0E04D20B@comcast.net> I encountered problems building the javadocs from source. The taglets would not compile. I'm using Java 1.4.2. Is it necessary to use 1.5 to compile biojava-live? Other than the JavaDoc taglets problem, the only problem with compiling bijava-live with 1.4.2 was in UniProtFormat.java where the build coughed on Integer.valueOf(taxid) where taxid is an int . A String is required here. (l.274 ) David From heuermh at acm.org Mon Oct 3 12:08:16 2005 From: heuermh at acm.org (Michael Heuer) Date: Mon Oct 3 12:23:29 2005 Subject: [Biojava-l] Graph library In-Reply-To: Message-ID: Mark Schreiber wrote: > Does anyone know of a good java graph library that is LGPL, Apache license > or similar? Not data graphing but graph as in the mathematical construct. Matthew Pocock wrote one in bjv2, package org.bjv2.graph, which he uses for metabolic network support, package org.bjv2.metabolic. In subversion at http://www.derkholm.net/svn/repos/bjv2/trunk/data/src/main/java/org/bjv2/graph/ http://www.derkholm.net/svn/repos/bjv2/trunk/biological/src/main/java/org/bjv2/metabolic/ I wrote another graph library with generics, in cvs at https://dsh-lib.dev.java.net/source/browse/dsh-lib/graph There is an Apache Commons sandbox project called graph2, in subversion at http://svn.apache.org/viewcvs.cgi/jakarta/commons/dormant/graph2/trunk/ michael From mark.schreiber at novartis.com Mon Oct 3 21:06:16 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Oct 3 21:17:19 2005 Subject: [Biojava-l] JDK 1.5 Message-ID: Hello - Biojava is still officially using JDK 1.4.2 I know many people have changed to JDK1.5 While no-one is using generics etc in the code base there have been a number of method calls that have slipped in that rely on JDK 1.5. The most common one is Integer.valueOf(int i) This is only introduced in 1.5 please use the alternative new Integer(i) It even has less typing : ) - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From mark.schreiber at novartis.com Mon Oct 3 22:03:15 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Oct 3 22:03:16 2005 Subject: [Biojava-l] Building from CVS Message-ID: The java code itself should be 1.4.2, some errors have krept in. The taglets problem is a nasty one. Javadoc changed the way it likes to talk to taglets as of java1.5, this may not be backwards compatible, I've been playing with it for a while and I cannot make it work with both. The coders seem to be voting with their feet and a change to 1.5 might be unavoidable. I'm happy with 1.5 but I wonder how many others are stuck with 1.4.2? Which OS's still need a JDK 1.5? Possibly JDK1.5 could begin to be allowed in biojava-live in preparation for biojava1.5?? Anyone protest?? - Mark d.lapointe@comcast.net Sent by: biojava-l-bounces@portal.open-bio.org 10/03/2005 11:41 PM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Building from CVS I encountered problems building the javadocs from source. The taglets would not compile. I'm using Java 1.4.2. Is it necessary to use 1.5 to compile biojava-live? Other than the JavaDoc taglets problem, the only problem with compiling bijava-live with 1.4.2 was in UniProtFormat.java where the build coughed on Integer.valueOf(taxid) where taxid is an int . A String is required here. (l.274 ) David _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Thu Oct 6 01:39:58 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Oct 6 01:39:52 2005 Subject: [Biojava-l] agave, game, game12 Message-ID: Hello - Does anyone still require or make use of the following packages: org.biojava.bio.seq.io.agave org.biojava.bio.seq.io.game org.biojava.bio.seq.io.game12 They represent i/o classes for these now redundant formats. If not then I will mark them as deprecated and probably remove them when we make a 1.5 release. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From mark.schreiber at novartis.com Thu Oct 6 01:47:23 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Oct 6 01:47:37 2005 Subject: [Biojava-l] Java 1.5 (final chance to object) Message-ID: Hello - No one seemed to object to the idea of officially adopting java 1.5 for the biojava-live branch. This would mean ... biojava-live would require java1.5 generics, unboxing and other language features added in 1.5 will start to creep into the codebase. all 'official' and 'preview' releases after biojava1.4 will require JDK1.5 (Java 5). If you plan to use new versions of biojava on a machine for which there is or will be no JDK1.5 then you should protest now! - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From mark.schreiber at novartis.com Thu Oct 6 03:36:05 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Oct 6 03:36:09 2005 Subject: [Biojava-l] Re: [Biojava-dev] Java 1.5 (final chance to object) Message-ID: Does SPICE rely on biojava-live? If it only requires biojava1.4 then this wouldn't be an issue. However, if you are actively building SPICE with biojava-live (possibly not a good idea) we can keep it as 1.4 for a while. - Mark Andreas Prlic 10/06/2005 03:26 PM To: Mark Schreiber/GP/Novartis@PH cc: biojava-dev@biojava.org, biojava-l@biojava.org Subject: Re: [Biojava-dev] Java 1.5 (final chance to object) Hi! I use biojava for the SPICE - protein sequence and structure browser. http://www.efamily.org.uk/software/dasclients/spice/ This application is launched from within a browser using Java Web Start. Since many people still are using java 1.4 on their machines I would not want to force them to upgrade and hence I would prefer biojava to stay with 1.4 still for a while. Cheers, Andreas On 6 Oct 2005, at 06:47, mark.schreiber@novartis.com wrote: > Hello - > > No one seemed to object to the idea of officially adopting java 1.5 for > the biojava-live branch. > > This would mean ... > > biojava-live would require java1.5 > generics, unboxing and other language features added in 1.5 will start > to > creep into the codebase. > all 'official' and 'preview' releases after biojava1.4 will require > JDK1.5 > (Java 5). > > If you plan to use new versions of biojava on a machine for which > there is > or will be no JDK1.5 then you should protest now! > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > > ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From ap3 at sanger.ac.uk Thu Oct 6 03:26:24 2005 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu Oct 6 04:16:03 2005 Subject: [Biojava-l] Re: [Biojava-dev] Java 1.5 (final chance to object) In-Reply-To: References: Message-ID: <74ebc3fc158aabd8858638a8160106ab@sanger.ac.uk> Hi! I use biojava for the SPICE - protein sequence and structure browser. http://www.efamily.org.uk/software/dasclients/spice/ This application is launched from within a browser using Java Web Start. Since many people still are using java 1.4 on their machines I would not want to force them to upgrade and hence I would prefer biojava to stay with 1.4 still for a while. Cheers, Andreas On 6 Oct 2005, at 06:47, mark.schreiber@novartis.com wrote: > Hello - > > No one seemed to object to the idea of officially adopting java 1.5 for > the biojava-live branch. > > This would mean ... > > biojava-live would require java1.5 > generics, unboxing and other language features added in 1.5 will start > to > creep into the codebase. > all 'official' and 'preview' releases after biojava1.4 will require > JDK1.5 > (Java 5). > > If you plan to use new versions of biojava on a machine for which > there is > or will be no JDK1.5 then you should protest now! > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > > ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From ady at sanger.ac.uk Thu Oct 6 03:39:10 2005 From: ady at sanger.ac.uk (Andy Yates) Date: Thu Oct 6 04:32:08 2005 Subject: [Biojava-l] Java 1.5 (final chance to object) In-Reply-To: References: Message-ID: <4344D49E.5070409@sanger.ac.uk> Well okay I'll fly the flag for platforms like Alpha where a 1.5 compatible JVM/compiler does not exist nor ever will. I know from the BOF at BOSC there were quite a few people who were reporting a similar situation. Now if no one else objects to the JDK1.5. move then I'm not going to fly the flag for 1.4 since I don't dev any more on Alpha plus I like more reasons to force people who I work with to upgrade :) Andy Y mark.schreiber@novartis.com wrote: > Hello - > > No one seemed to object to the idea of officially adopting java 1.5 for > the biojava-live branch. > > This would mean ... > > biojava-live would require java1.5 > generics, unboxing and other language features added in 1.5 will start to > creep into the codebase. > all 'official' and 'preview' releases after biojava1.4 will require JDK1.5 > (Java 5). > > If you plan to use new versions of biojava on a machine for which there is > or will be no JDK1.5 then you should protest now! > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From wetrull at yahoo.com Thu Oct 6 11:10:01 2005 From: wetrull at yahoo.com (W. Eric Trull) Date: Thu Oct 6 11:19:45 2005 Subject: [Biojava-l] [Biojava-dev] Java 1.5 (final chance to object) Message-ID: <20051006151002.58972.qmail@web81404.mail.yahoo.com> Hello all, I'm new to the list so I have not been following the full discussion and don't know all the issues - excuse my ignorance. I don't have any objections to moving to Java 1.5, except I know that some J2EE application servers (both web tier and business tier (i.e. EJBs)) are slow adopters of the new versions of Java That being said, would BioJava 1.4 be maintained (bug fixes) for those stuck on 1.4.2? I know in my case I'm going to be using BioJava in several web services deploying to pre-existing application servers. The owners of the application servers will balk at the cost of upgrading to Java 1.5 (both the JVM and the application server). Thanks. -Eric Trull From mark.schreiber at novartis.com Thu Oct 6 21:53:12 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Oct 6 21:52:44 2005 Subject: [Biojava-l] Java 1.5 (final chance to object) Message-ID: OK, there seems to have been a few reasonable objections. The consensus seems to be we will wait until the end of the year. I think from then on we will change over for biojava-live. There was a suggestion of maintaining two branches, one would be a maintenance of biojava1.4 and only use JDK1.4.2, the other would be biojava-live and use JDK1.5. I have done this in the past and have no desire to do it again, it's really not that much fun. I would however like to reserve the option of putting JDK1.5 dependent code into the classes of the org.biojavax package. If this happens I will adjust the ANT build script such that these are not compiled if JDK1.5 is not detected. This should be safe as the biojava packages have no dependencies on the biojavax packages. Bug fixes to biojava would still be in the system. Additionally the org.biojavax packages are undergoing a lot of development right now so you shouldn't be doing any production programming with them anyway. - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From kheeteck at msn.com Fri Oct 7 00:30:11 2005 From: kheeteck at msn.com (Goh khee Teck) Date: Fri Oct 7 00:47:03 2005 Subject: [Biojava-l] Need Help Message-ID: Hi.. Anybody know how to retrieve the annotation property "ORIGIN" My code look like this while(sequences.hasNext()){ try { seq = sequences.nextSequence(); //Annotation Annotation anno = seq.getAnnotation(); //print each key value pair for (Iterator i = anno.keys().iterator(); i.hasNext(); ) { Object key = i.next(); System.out.println(key +" : "+ anno.getProperty(key)); }//for }//while It print out the value for each annotation key but for ORIGIN, there is nothing. ORIGIN FOR A typical genbank file SCU49845 looks like ORIGIN 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg 241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa 301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa 361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat 421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga 481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc 541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga 601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta 661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag 721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa Regards KheeTeck _________________________________________________________________ Download MSN Messenger emoticons and display pictures. http://ilovemessenger.msn.com/?mkt=en-sg From mark.schreiber at novartis.com Fri Oct 7 01:25:27 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Fri Oct 7 01:25:30 2005 Subject: [Biojava-l] Need Help Message-ID: I don't think we capture that property. Why do you want it? If it is the nucleotide sequence you are after then do something like seq.sublist(from, to); seq.seqString(); seq.symbolAt(index); These are SymbolList methods but a Sequence is an instanceof a SymbolList. See also the section on sequence manipulation on this webpage http://www.biojava.org/docs/bj_in_anger/index.htm - Mark "Goh khee Teck" Sent by: biojava-l-bounces@portal.open-bio.org 10/07/2005 12:30 PM To: Biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Need Help Hi.. Anybody know how to retrieve the annotation property "ORIGIN" My code look like this while(sequences.hasNext()){ try { seq = sequences.nextSequence(); //Annotation Annotation anno = seq.getAnnotation(); //print each key value pair for (Iterator i = anno.keys().iterator(); i.hasNext(); ) { Object key = i.next(); System.out.println(key +" : "+ anno.getProperty(key)); }//for }//while It print out the value for each annotation key but for ORIGIN, there is nothing. ORIGIN FOR A typical genbank file SCU49845 looks like ORIGIN 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg 241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa 301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa 361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat 421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga 481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc 541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga 601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta 661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag 721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa Regards KheeTeck _________________________________________________________________ Download MSN Messenger emoticons and display pictures. http://ilovemessenger.msn.com/?mkt=en-sg _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From dbastar at yahoo.com Fri Oct 7 04:27:50 2005 From: dbastar at yahoo.com (Duangdaow Kanhasiri) Date: Fri Oct 7 04:35:00 2005 Subject: [Biojava-l] BioJava with BioSQL schema on Oracle database Message-ID: <20051007082750.93766.qmail@web34701.mail.mud.yahoo.com> Hi, I wonder if there's any one BioJava community has ever used Biojava with BioSQL schema on Oracle database? I really do need some advices... Is there any BioJava program to load the whole genome sequence files(e.g. genbank format) in to BioSQL database like in BioPerl has load_ncbi_taxonomy.pl and load_seqdatabase.pl? Or anybody used to do the stuff like this and has some tricks/work around for this? My problem is that I used to use these BioPerl scripts to load my genbank files into BioSQL schema in PostgreSQL database; however, due to the hugh increasing amout of my data (the whole complete bacterial genome genbank files and Blast result files from them), I have to move to Oracle instead of PostgreSQL (in order to use the extra features that don't have in PostgreSQL e.g. table partioning, clustering, etc). When I use the load_seqdatabase.pl BioPerl scripts directly with Oracle database (Oracle version 10.1.3), it can load some genbank files into the database and then it just dead with some STACK error. I don't know if the problem is due to the versions of the code in BioPerl-db that change so fast... I did try to port data from PostgreSQL to Oracle but there're problems with some fields in many tables that has LOB type that I couldn't load these tables. By the way, I know some java but I'm just the newbie with BioJava, any help would be very grateful... Regards, Duangdaow __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From christoph.gille at charite.de Fri Oct 7 04:44:05 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri Oct 7 04:57:59 2005 Subject: [Biojava-l] moving to java 1.5 Message-ID: <60923.192.168.220.203.1128674645.squirrel@webmail.charite.de> Hi everyone, I followed the discussion on java 1.5. Is 1.5 installable on all MacOSX systems? There might be a problem with early OSX systems but I do not have a Mac to check it. It would be bad to break platform independence by moving to 1.5. By googling I found retroweaver, a converter of 1.5 to 1.4 which might be the solution to all problems. One can compile to 1.5 bytecode and after compilation one can convert the 1.5 bytecode to 1.4 bytecode. I have checked some of the included examples and it works indeed. Does anyone has experiences with converting larger projects ? Why not give it a try for BioJava ciao Christoph From dbastar at yahoo.com Fri Oct 7 05:21:12 2005 From: dbastar at yahoo.com (Duangdaow Kanhasiri) Date: Fri Oct 7 05:30:54 2005 Subject: [Biojava-l] BioJava with BioSQL schema on Oracle database In-Reply-To: <6D9E9B9DF347EF4385F6271C64FB8D5602428BE7@BIONIC.biopolis.one-north.com> Message-ID: <20051007092112.24663.qmail@web34713.mail.mud.yahoo.com> Thanks a lot Richard ... While I'm waiting for your new improvement, in the mean time, I'll look at the example you said and try to do some work around with it... Cheers, Duangdaow --- Richard HOLLAND wrote: > Funny you should ask that... > > ...for users of biojava-1.4, there is an FAQ on this > at the BioJava in > Anger website: > http://www.biojava.org/docs/bj_in_anger/ - scroll > down > the page to the section on sequence databases and > you'll find a page to > help you out there... > > ...but neither the file parsers nor the BioSQL > interface are perfect, > and they do strange things with the fields they > load. > > If you can bear to wait a while, we are currently > rewriting the file > parsers and BioSQL interfaces as part of the > biojavax project. Once > these are finished we will announce them here, and > provide tutorials on > how to use them. However they will be not-at-all > compatible with the > current contents of BioSQL databases loaded using > biojava-1.4, so if a > lot of data is involved and this is a new and > not-urgent project, it may > pay to wait a little while. > > cheers, > Richard > > Richard Holland > Bioinformatics Specialist > GIS extension 8199 > --------------------------------------------- > This email is confidential and may be privileged. If > you are not the > intended recipient, please delete it and notify us > immediately. Please > do not copy or use it for any purpose, or disclose > its content to any > other person. Thank you. > --------------------------------------------- > > > > -----Original Message----- > > From: biojava-l-bounces@portal.open-bio.org > > [mailto:biojava-l-bounces@portal.open-bio.org] On > Behalf Of > > Duangdaow Kanhasiri > > Sent: Friday, October 07, 2005 4:28 PM > > To: biojava-l@biojava.org > > Subject: [Biojava-l] BioJava with BioSQL schema on > Oracle database > > > > > > Hi, > > > > I wonder if there's any one BioJava community has > ever > > used Biojava with BioSQL schema on Oracle > database? I > > really do need some advices... > > > > Is there any BioJava program to load the whole > genome > > sequence files(e.g. genbank format) in to BioSQL > > database like in BioPerl has load_ncbi_taxonomy.pl > and > > load_seqdatabase.pl? Or anybody used to do the > stuff > > like this and has some tricks/work around for > this? > > > > My problem is that I used to use these BioPerl > scripts > > to load my genbank files into BioSQL schema in > > PostgreSQL database; however, due to the hugh > > increasing amout of my data (the whole complete > > bacterial genome genbank files and Blast result > files > > from them), I have to move to Oracle instead of > > PostgreSQL (in order to use the extra features > that > > don't have in PostgreSQL e.g. table partioning, > > clustering, etc). > > > > When I use the load_seqdatabase.pl BioPerl scripts > > directly with Oracle database (Oracle version > 10.1.3), > > it can load some genbank files into the database > and > > then it just dead with some STACK error. I don't > know > > if the problem is due to the versions of the code > in > > BioPerl-db that change so fast... > > > > I did try to port data from PostgreSQL to Oracle > but > > there're problems with some fields in many tables > that > > has LOB type that I couldn't load these tables. > > > > By the way, I know some java but I'm just the > newbie > > with BioJava, any help would be very grateful... > > > > Regards, > > > > Duangdaow > > > > > > > > > > > > > > __________________________________ > > Yahoo! Mail - PC Magazine Editors' Choice 2005 > > http://mail.yahoo.com > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From duze at gmx.de Fri Oct 7 11:14:41 2005 From: duze at gmx.de (=?ISO-8859-1?Q?=22Andreas_Dr=E4ger=22?=) Date: Fri Oct 7 11:22:10 2005 Subject: [Biojava-l] Another problem with TaxonFactories Message-ID: <11445.1128698081@www4.gmx.net> Hello, every monday NCBI releases a new version of taxon names, merged nodes etc. A scientific name of a taxon might be changed someday. If a TaxonFactory only allowes to search for a taxon by scientific name which is the case at the moment at least for SimpleTaxonFactory, we might lose information, if we want to perform a database update for example. I would like to suggest to extend this for the NCBI-Taxon ID so that we can consider changed names properties. By the way, one does not easily understand that the parameter called 'String id' is the 'scientific name' in reality. I would like to suggest to change that. Andreas -- Highspeed-Freiheit. Bei GMX supergünstig, z.B. GMX DSL_Cityflat, DSL-Flatrate für nur 4,99 Euro/Monat* http://www.gmx.net/de/go/dsl From hollandr at gis.a-star.edu.sg Sat Oct 8 00:22:16 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Sat Oct 8 00:34:36 2005 Subject: [Biojava-l] Another problem with TaxonFactories Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D5601E87200@BIONIC.biopolis.one-north.com> biojavax should circumvent this. have a look in the org.biojavax.bio packages in biojava-live for a sneak preview. Basically we have adopted the BioSQL conventions, and created a new NCBITaxon class to represent the table from the database. The code is written to work with Hibernate for database access, so that you can search the taxa any way you wish - no need for a TaxonFactory in this new version. Docs and HowTos will be provided when this biojavax thing is finished. Mark won't set a date but personally I'd like to see it out by the end of the year. cheers, Richard -----Original Message----- From: biojava-l-bounces@portal.open-bio.org on behalf of "Andreas Dr?ger" Sent: Fri 10/7/2005 11:14 PM To: biojava-l@biojava.org Cc: Subject: [Biojava-l] Another problem with TaxonFactories Hello, every monday NCBI releases a new version of taxon names, merged nodes etc. A scientific name of a taxon might be changed someday. If a TaxonFactory only allowes to search for a taxon by scientific name which is the case at the moment at least for SimpleTaxonFactory, we might lose information, if we want to perform a database update for example. I would like to suggest to extend this for the NCBI-Taxon ID so that we can consider changed names properties. By the way, one does not easily understand that the parameter called 'String id' is the 'scientific name' in reality. I would like to suggest to change that. Andreas -- Highspeed-Freiheit. Bei GMX superg?nstig, z.B. GMX DSL_Cityflat, DSL-Flatrate f?r nur 4,99 Euro/Monat* http://www.gmx.net/de/go/dsl _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From joel.pitt at gmail.com Wed Oct 12 21:46:27 2005 From: joel.pitt at gmail.com (Joel Peter William Pitt) Date: Thu Oct 13 07:38:35 2005 Subject: [Biojava-l] Disabling SequencePanel updates Message-ID: Hi All, I'm trying to develop a GUI based sequence analysis tool. I have a SequencePanel displaying features that are found by a seperate thread. Within this thread are calls to Sequence.createFeature when an appropriate match is found - my problem is that SequencePanel listens for all changes to a sequence and there is no way (that I know of) to disable this. The reason this is annoying is because I would like allow a user to still view the sequence while waiting for the search to complete. I can push events to the Swing EventQueue that add features, but this drastically slows down the search due to the number of matches found - I would rather just fire a ChangeEvent once the search has completed. I thought I could override the setSequence method in a subclass of SequencePanel and not assign changeListeners, but then the other methods of SequencePanel won't have access to the sequence. Alternatively I could make a copy of the sequence for viewing and one for searching on. Can anyone suggest the best way to go about this? Thanks, Joel From mark.schreiber at novartis.com Thu Oct 13 21:12:18 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Oct 13 21:11:36 2005 Subject: [Biojava-l] Disabling SequencePanel updates Message-ID: I'm no expert on the GUI classes but your last suggestion sounds reasonable. Set the sequence and let people view it while running a search on a copy of the sequence and then when the features have all been added you can swap the sequences and update the display. It's not elegant and there may be a better way. - Mark Joel Peter William Pitt Sent by: biojava-l-bounces@portal.open-bio.org 10/13/2005 09:46 AM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Disabling SequencePanel updates Hi All, I'm trying to develop a GUI based sequence analysis tool. I have a SequencePanel displaying features that are found by a seperate thread. Within this thread are calls to Sequence.createFeature when an appropriate match is found - my problem is that SequencePanel listens for all changes to a sequence and there is no way (that I know of) to disable this. The reason this is annoying is because I would like allow a user to still view the sequence while waiting for the search to complete. I can push events to the Swing EventQueue that add features, but this drastically slows down the search due to the number of matches found - I would rather just fire a ChangeEvent once the search has completed. I thought I could override the setSequence method in a subclass of SequencePanel and not assign changeListeners, but then the other methods of SequencePanel won't have access to the sequence. Alternatively I could make a copy of the sequence for viewing and one for searching on. Can anyone suggest the best way to go about this? Thanks, Joel _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From mark.schreiber at novartis.com Thu Oct 20 03:29:19 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Oct 20 03:28:34 2005 Subject: [Biojava-l] substitution matrices and probability Message-ID: Hello - A while back someone posted a question about how you could simulate a substitution matrix in an HMM pairwise alignment (relating to the example http://www.biojava.org/docs/bj_in_anger/PairAlign.htm). I gave a pretty poor answer but have since rediscovered the full explanation. The procedure is outlined on page 118 of Durbin et al, Biological Sequence Analysis and in much more detail in Altschul 1991 (J Mol Biol 219: 555-65) - Mark From crackeur at comcast.net Wed Oct 26 02:26:02 2005 From: crackeur at comcast.net (Jimmy zhang) Date: Wed Oct 26 02:30:14 2005 Subject: [Biojava-l] [ANN]: VTD-XML 1.0 released Message-ID: <002801c5d9f6$26c00db0$0202a8c0@ximplewa9u1u8q> I am pleased to announce that both Java and C version 1.0 of VTD-XML -- an open-source, high-performance and non-extractive XML processing API -- is freely available on sourceforge.net. For source code, documentation, detailed description of API and code examples, please visit http://vtd-xml.sourceforge.net New in VTD-XML 1.0 is the integrated support of XPath that also features a easy-to-use interface that further enhances VTD-XML's inherent benefits, such as CPU/memory efficiency, random access, and incremental update. A demo of the XPath capability is available at http://vtd-xml.sourceforge.net/demo.html For further reading, please refer to the following articles about VTD-XML * Process SOAP with VTD-XML http://xml.sys-con.com/read/48764.htm * Better, faster XML processing with VTD-XML http://www.devx.com/xml/Article/22219?trk=DXRSS_XML * XML on a chip http://www.xml.com/pub/a/2005/03/09/chip.html * Improve XML processing with VTD-XML http://www.intel.com/cd/ids/developer/asmo-na/eng/dc/xeon/multicore/211657.htm From russ at kepler-eng.com Wed Oct 26 16:39:04 2005 From: russ at kepler-eng.com (Russ Kepler) Date: Wed Oct 26 17:06:13 2005 Subject: [Biojava-l] ABITrace and quality values Message-ID: <200510261439.04481.russ@kepler-eng.com> Anyone modify ABITrace to fetch and return the quality calls now available in AB1 files? From hollandr at gis.a-star.edu.sg Mon Oct 31 04:28:09 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Tue Nov 1 16:46:00 2005 Subject: [Biojava-l] BioJavaX ready for testing Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560265652E@BIONIC.biopolis.one-north.com> Hello people! Mark is away so I'm taking the liberty of sneaking this one out... :) I've cross-posted this to both BioJava and BioSQL as much of what is new in BioJavaX will probably be of interest to BioSQL users too. We've been doing a lot of work recently on creating some extensions to BioJava called BioJavaX. Primarily the purpose of these extensions is to provide better interaction with BioSQL databases, which has been achieved using Hibernate (www.hibernate.org). You can now fully interact with every column of every table in BioSQL, using Hibernate's own HQL language to construct queries that result in sets of BioJavaX objects. Selects, inserts, updates, primary key assignment, foreign key relations, and deletes are all handled transparently by Hibernate, removing the need for any SQL at all to be included in BioJavaX. As a side effect of constructing a Hibernate-compatible extension to the BioJava object model, we were required to define objects that hold much more detailed information about themselves. For instance, a Sequence object cannot tell you what namespace it lives in in the BioSQL database, but our extension to it, RichSequence, can. As RichSequence extends Sequence and doesn't replace it, this means you can use the new objects with your existing code without any hassle casting them. To be able to load information from files into these new RichSequence objects in a meaningful way, we had to create a more detailed SeqIOListener, called RichSeqIOListener. Then, we had to create new file parsers for the common file formats which were able to extract more detailed information than before in order to satisfy the RichSeqIOListener. It's pretty safe to say that the file parsers in BioJavaX are leagues ahead of the existing ones in BioJava, even if I do say so myself. :P The downside of this extra detail though is that the parsers are much more sensitive and will not play well at all with incomplete or incorrectly formed files. If someone can edit them to be less sensitive whilst still retaining the level of detail required, that'd be great. We've included parsers for FASTA, GenBank, EMBL, UniProt, INSDseq, EMBLxml, UniProtXML, and an extra one for parsing NCBI Taxonomy data. Do note that BioJavaX cannot fully convert sequences created using the old BioJava model into the new BioJavaX model. It'll do its best, but the RichSequence object you'll end up with will have lots of properties set to null and a tonne of annotations instead, pretty much the same as the original Sequence object I suppose. So its best to try to avoid conversions and deal with RichSequence objects from the ground up. This is particularly important to consider when converting a BioSQL database previously used with BioJava into one for use with BioJavaX. You'll also find that if you pass a converted old-style Sequence object to one of the new file parsers for writing it may fail or produce output with lots of missing fields, as it will not find the information it is looking for in the places it expects. The whole lot is specifically designed to mimic and be compatible with BioSQL, but you don't need to have a BioSQL database to use it. Everything is standalone and will work just fine without a backing data source. Also there is no reason why you couldn't create a new set of Hibernate mappings that map the BioJavaX object model to some other relational database schema of your choice. The upshot of it all is the org.biojavax package, which you can find in biojava-live branch on CVS. Development is pretty much complete, and it now needs some serious testing. We need volunteers to: a) test the BioSQL interaction via Hibernate with the various database flavours supported (HSQL, Oracle, MySQL, PostGreSQL) b) test the various file formats, particularly looking for special-case exceptions which the parsers may not be aware of yet c) do some load-testing and help us find ways to improve it if it turns out to be too slow when under pressure Documentation of the new features can be found in DocBook XML format in docs/docbook/BioJavaX.xml in the biojava-live branch of CVS. It's as detailed as I could make it without getting bored to death writing it. I've never been the world's best documentation writer, so if anyone would like to help improve it you're more than welcome. Our plan is to make all this an official part of BioJava come the 1.5 release, whenever that may be. For now though it is very very much a testing-stage thing, not even an alpha release. Questions on a postcard to either Mark or myself. Feedback most welcome. cheers, Richard Richard Holland Bioinformatics Specialist Genome Institute of Singapore 60 Biopolis Street, #02-01 Genome, Singapore 138672 Tel: (65) 6478 8000 DID: (65) 6478 8199 Email: hollandr@gis.a-star.edu.sg --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. ---------------------------------------------