[Biojava-dev] Reply:biojava-dev Digest, Vol 54, Issue 1

Wed Aug 8 01:24:37 UTC 2007

 Dear sir,         Thank you for your message for biojava. I am very interested in it.        I am a graduate student of China Agriculture University and my major is bioinformatics. I would like to know that if I can join in developing biojava ?                                                                           student simple  
在2007-08-07，biojava-dev-request at lists.open-bio.org 写道：
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. phylo code (Thasso Griebel) 2. Re: phylo code (Richard Holland) 3. Re: phylo code (Thasso Griebel) 4. Re: phylo code (Richard Holland) 5. Re: phylo code (Thasso Griebel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Aug 2007 19:19:01 +0200 From: Thasso Griebel <thasso at minet.uni-jena.de> Subject: [Biojava-dev] phylo code To: biojava-dev at biojava.org Message-ID: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed hi, i recently explored the phylogeny code base in biojava. I am currently working on a phylogeny framework similar to mesquite (http://www.bio.informatik.uni-jena.de/epos) and i would like to add some functionality using biojava (the sequence stuff and the nexus parser). I saw the PhyloSOC07 page ( http://biojava.org/wiki/ BioJava:PhyloSOC07 ) and i might be able to help out with some of the methods, so is there a way to contribute ? Or is this closed to participants of the google summer of code ? I have code for n-consensus and adams consensus methods and some possible extensions for UPGMA (provide other distance computations, i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and rooting support ). As our research groups has a focus on supertree construction, we have java implementations for several graph based supertree methods (aho's build, mincut, modified mincut, ranked tree, ancestral build). Regards, Thasso -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ Message: 2 Date: Wed, 1 Aug 2007 19:03:29 +0100 (BST) From: "Richard Holland" <holland at ebi.ac.uk> Subject: Re: [Biojava-dev] phylo code To: "Thasso Griebel" <thasso at minet.uni-jena.de> Cc: biojava-dev at biojava.org Message-ID: <48008.80.42.98.32.1185991409.squirrel at webmail.ebi.ac.uk> Content-Type: text/plain;charset=iso-8859-1 Hi Thasso. Thanks for your interest! We always welcome all contributions of code and documentation to the BioJava project. Our GSOC project is well under way and has a plan as you have already noticed. The items on that plan are what was agreed with our student, Boh Yun Lee, and will be implemented by the time that GSOC is over (early September) - or at least, most of them will, and any that aren't will be flagged as such. If you have suggestions to make about code already committed, we would welcome them. Such feedback is a necessary part of the development cycle. Likewise we would welcome contributions of code not already mentioned as being planned on the GSOC pages. However, if your existing code implements something that is on the to-do list on the GSOC page, then the best thing would be to hang on till the end of the GSOC project then contribute any items that did not get implemented. cheers, Richard On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: > hi, > > i recently explored the phylogeny code base in biojava. I am > currently working on a phylogeny framework similar to mesquite > (http://www.bio.informatik.uni-jena.de/epos) and i would like to add > some functionality using biojava (the sequence stuff and the nexus > parser). > > I saw the PhyloSOC07 page ( http://biojava.org/wiki/ > BioJava:PhyloSOC07 ) and i might be able to help out with some of the > methods, so is there a way to contribute ? Or is this closed to > participants of the google summer of code ? > > I have code for n-consensus and adams consensus methods and some > possible extensions for UPGMA (provide other distance computations, > i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and > rooting support ). As our research groups has a focus on supertree > construction, we have java implementations for several graph based > supertree methods (aho's build, mincut, modified mincut, ranked tree, > ancestral build). > > > Regards, > > Thasso > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK ------------------------------ Message: 3 Date: Mon, 6 Aug 2007 18:45:35 +0200 From: Thasso Griebel <thasso at minet.uni-jena.de> Subject: Re: [Biojava-dev] phylo code To: Richard Holland <holland at ebi.ac.uk> Cc: biojava-dev at biojava.org Message-ID: <846222BD-73C8-4CE7-8CB1-E2249A25256D at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, thanks for the fast answer. So, I would really like to contribute to the BioJava Phylogeny Package, but I will wait until the GSOC project is finished and I am back from my vacation ;) For now, I just took a look on the io package, especially the three classes concerning phylip io. Some personal feeling about the naming. I wouldn't mention "fire" and "events" in the documentation and rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. For me, this was irritating. I started looking for a fireXXX method immediately and automatically started thinking about the EventDispatchingThread and synchronization. As far as I see, this is a direct handler delegate, the parser delegates some method calls to a given handler callback method, no events are fired (there is not even an Event class that could be fired) and no event dispatching is involved. Also, the io seem to focus on the output of alignment. What about trees and distance/character matrices ? And a really important point is the name handling. The method private static String formatSequenceLabel(String label) in PHYLIPFileFormat simply cuts names that are longer than 10 characters. I know that phylip has this stupid limitation. But cutting will not work in a lot of cases. If just two sequence names are identical over the first ten characters, the resulting phylip file is corrupted and can not be used by most of the phylip executables. Maybe the handler can do a renaming and keep track of the map. Then one can use the parser to write some phylip file, start a phylip method on that file, read in the results and do an automatic remapping of the names ? I also wanted to take a look on the tree model. Is this already in the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but it was empty ? regards, thasso On 01.08.2007, at 20:03, Richard Holland wrote: > Hi Thasso. > > Thanks for your interest! We always welcome all contributions of > code and > documentation to the BioJava project. > > Our GSOC project is well under way and has a plan as you have already > noticed. The items on that plan are what was agreed with our > student, Boh > Yun Lee, and will be implemented by the time that GSOC is over (early > September) - or at least, most of them will, and any that aren't > will be > flagged as such. > > If you have suggestions to make about code already committed, we would > welcome them. Such feedback is a necessary part of the development > cycle. > Likewise we would welcome contributions of code not already > mentioned as > being planned on the GSOC pages. > > However, if your existing code implements something that is on the > to-do > list on the GSOC page, then the best thing would be to hang on till > the > end of the GSOC project then contribute any items that did not get > implemented. > > cheers, > Richard > > On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >> hi, >> >> i recently explored the phylogeny code base in biojava. I am >> currently working on a phylogeny framework similar to mesquite >> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >> some functionality using biojava (the sequence stuff and the nexus >> parser). >> >> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >> methods, so is there a way to contribute ? Or is this closed to >> participants of the google summer of code ? >> >> I have code for n-consensus and adams consensus methods and some >> possible extensions for UPGMA (provide other distance computations, >> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >> rooting support ). As our research groups has a focus on supertree >> construction, we have java implementations for several graph based >> supertree methods (aho's build, mincut, modified mincut, ranked tree, >> ancestral build). >> >> >> Regards, >> >> Thasso >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > > -- > Richard Holland > BioMart (http://www.biomart.org/) > EMBL-EBI > Hinxton, Cambridgeshire CB10 1SD, UK -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ Message: 4 Date: Tue, 07 Aug 2007 08:48:05 +0100 From: Richard Holland <holland at ebi.ac.uk> Subject: Re: [Biojava-dev] phylo code To: Thasso Griebel <thasso at minet.uni-jena.de> Cc: biojava-dev at biojava.org Message-ID: <46B823B5.1010401 at ebi.ac.uk> Content-Type: text/plain; charset=ISO-8859-1 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thanks for your feedback Thasso. The fire/events thing is certainly a misnomer - guilty as charged (I wrote the code...) - but I suppose I wasn't expecting the naming to matter much. I'll bear that in mind for future code. We can't really change the existing interfaces now as they've been released and it is not nice to users for us to change public interfaces that might already be in use. The PHYLIP format handler was written by Jim Balhoff. Jim - do you have any responses to Thasso's comments about the output options? I like the sound of your PHYLIP short-name map. You could definitely go ahead and contribute an update which implemented that. (Don't forget to make your code clear the map between one file and the next!) The tree model never materialised in the end. We chose instead to use the external JGraphT package to represent our trees. The exact way in which this is done will be documented by Boh-Yun as part of the GSOC project. cheers, Richard Thasso Griebel wrote: > Hi, > > thanks for the fast answer. > > So, I would really like to contribute to the BioJava Phylogeny > Package, but I will wait until the GSOC project is finished and I am > back from my vacation ;) For now, I just took a look on the io > package, especially the three classes concerning phylip io. > Some personal feeling about the naming. > I wouldn't mention "fire" and "events" in the documentation and > rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. > For me, this was irritating. I started looking for a fireXXX method > immediately and automatically started thinking about the > EventDispatchingThread and synchronization. As far as I see, this is > a direct handler delegate, the parser delegates some method calls to > a given handler callback method, no events are fired (there is not > even an Event class that could be fired) and no event dispatching is > involved. > Also, the io seem to focus on the output of alignment. What about > trees and distance/character matrices ? > And a really important point is the name handling. The method > > private static String formatSequenceLabel(String label) > > in PHYLIPFileFormat simply cuts names that are longer than 10 > characters. I know that phylip has this stupid limitation. But > cutting will not work in a lot of cases. If just two sequence names > are identical over the first ten characters, the resulting phylip > file is corrupted and can not be used by most of the phylip > executables. Maybe the handler can do a renaming and keep track of > the map. Then one can use the parser to write some phylip file, start > a phylip method on that file, read in the results and do an automatic > remapping of the names ? > > I also wanted to take a look on the tree model. Is this already in > the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but > it was empty ? > > regards, > > thasso > > > > On 01.08.2007, at 20:03, Richard Holland wrote: > >> Hi Thasso. >> >> Thanks for your interest! We always welcome all contributions of >> code and >> documentation to the BioJava project. >> >> Our GSOC project is well under way and has a plan as you have already >> noticed. The items on that plan are what was agreed with our >> student, Boh >> Yun Lee, and will be implemented by the time that GSOC is over (early >> September) - or at least, most of them will, and any that aren't >> will be >> flagged as such. >> >> If you have suggestions to make about code already committed, we would >> welcome them. Such feedback is a necessary part of the development >> cycle. >> Likewise we would welcome contributions of code not already >> mentioned as >> being planned on the GSOC pages. >> >> However, if your existing code implements something that is on the >> to-do >> list on the GSOC page, then the best thing would be to hang on till >> the >> end of the GSOC project then contribute any items that did not get >> implemented. >> >> cheers, >> Richard >> >> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>> hi, >>> >>> i recently explored the phylogeny code base in biojava. I am >>> currently working on a phylogeny framework similar to mesquite >>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >>> some functionality using biojava (the sequence stuff and the nexus >>> parser). >>> >>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >>> methods, so is there a way to contribute ? Or is this closed to >>> participants of the google summer of code ? >>> >>> I have code for n-consensus and adams consensus methods and some >>> possible extensions for UPGMA (provide other distance computations, >>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >>> rooting support ). As our research groups has a focus on supertree >>> construction, we have java implementations for several graph based >>> supertree methods (aho's build, mincut, modified mincut, ranked tree, >>> ancestral build). >>> >>> >>> Regards, >>> >>> Thasso >>> >>> -- >>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>> Bioinformatik >>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>> Informatik >>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>> Universitaet Jena >>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>> Germany >>> >>> >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> >> -- >> Richard Holland >> BioMart (http://www.biomart.org/) >> EMBL-EBI >> Hinxton, Cambridgeshire CB10 1SD, UK > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU Hbne6alMOuzmr8CxX/hqsfs= =U4gJ -----END PGP SIGNATURE----- ------------------------------ Message: 5 Date: Tue, 7 Aug 2007 10:29:08 +0200 From: Thasso Griebel <thasso at minet.uni-jena.de> Subject: Re: [Biojava-dev] phylo code To: Richard Holland <holland at ebi.ac.uk> Cc: biojava-dev at biojava.org Message-ID: <CC512170-7C9F-4B71-97EA-2DDA2AA615FF at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, On the fire/event thing. You are right, it is not a good idea to change this if the code is already released. But maybe a little helper class with some static methods ( like IOTools ) would help. Something like PhylipIO.readTree(File) or PhylipIO.readAlignment (File) might do the job, the interfaces do not have to change and when it avoids direct contact with the parser implementation as long as standard phylip dataypes are concerned. And, as far as I see, this would follow the main path IO is done in BioJava. I can ( and will ) definitely work on the short-name map, but this has to wait at least 5 week as I am going on vacation ( yeah, 5 weeks without a computer nearby !!!). But currently I am really interested in a good phylip parser, so I will work on that. One thing about JGraphT. I used and use that a lot when doing phylogenetics, and its a great library. But you might consider adding a little interface structure on top at some point to decouple the the usage from the library. This would allow BioJava compatible tree implementations without the need of JGraphT. JGraphT is great for all the simple, and even the complex jobs, but for me there is one little drawback. You can fill in every Object as a graph vertex, which is great, but this makes the underlying implementation rather complex. I do not remember exactly, but I think they use a large set of HashMap structures and some complex mapping mechanism to build up a graph. There are situations where this makes it hard to extend. For example, for one of our supertree algorithm implementations we needed a MultiGraph, a graph with different edge types, and it was a real pain to add that to the library without reimplementing JGraphT's Graph interface completely. I think a Tree interface structure on top would be simple and easy and might be really helpful at some point. regards, thasso On 07.08.2007, at 09:48, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? > > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) > > The tree model never materialised in the end. We chose instead to use > the external JGraphT package to represent our trees. The exact way in > which this is done will be documented by Boh-Yun as part of the GSOC > project. > > cheers, > Richard > > > Thasso Griebel wrote: >> Hi, >> >> thanks for the fast answer. >> >> So, I would really like to contribute to the BioJava Phylogeny >> Package, but I will wait until the GSOC project is finished and I am >> back from my vacation ;) For now, I just took a look on the io >> package, especially the three classes concerning phylip io. >> Some personal feeling about the naming. >> I wouldn't mention "fire" and "events" in the documentation and >> rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. >> For me, this was irritating. I started looking for a fireXXX method >> immediately and automatically started thinking about the >> EventDispatchingThread and synchronization. As far as I see, this is >> a direct handler delegate, the parser delegates some method calls to >> a given handler callback method, no events are fired (there is not >> even an Event class that could be fired) and no event dispatching is >> involved. >> Also, the io seem to focus on the output of alignment. What about >> trees and distance/character matrices ? >> And a really important point is the name handling. The method >> >> private static String formatSequenceLabel(String label) >> >> in PHYLIPFileFormat simply cuts names that are longer than 10 >> characters. I know that phylip has this stupid limitation. But >> cutting will not work in a lot of cases. If just two sequence names >> are identical over the first ten characters, the resulting phylip >> file is corrupted and can not be used by most of the phylip >> executables. Maybe the handler can do a renaming and keep track of >> the map. Then one can use the parser to write some phylip file, start >> a phylip method on that file, read in the results and do an automatic >> remapping of the names ? >> >> I also wanted to take a look on the tree model. Is this already in >> the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but >> it was empty ? >> >> regards, >> >> thasso >> >> >> >> On 01.08.2007, at 20:03, Richard Holland wrote: >> >>> Hi Thasso. >>> >>> Thanks for your interest! We always welcome all contributions of >>> code and >>> documentation to the BioJava project. >>> >>> Our GSOC project is well under way and has a plan as you have >>> already >>> noticed. The items on that plan are what was agreed with our >>> student, Boh >>> Yun Lee, and will be implemented by the time that GSOC is over >>> (early >>> September) - or at least, most of them will, and any that aren't >>> will be >>> flagged as such. >>> >>> If you have suggestions to make about code already committed, we >>> would >>> welcome them. Such feedback is a necessary part of the development >>> cycle. >>> Likewise we would welcome contributions of code not already >>> mentioned as >>> being planned on the GSOC pages. >>> >>> However, if your existing code implements something that is on the >>> to-do >>> list on the GSOC page, then the best thing would be to hang on till >>> the >>> end of the GSOC project then contribute any items that did not get >>> implemented. >>> >>> cheers, >>> Richard >>> >>> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>>> hi, >>>> >>>> i recently explored the phylogeny code base in biojava. I am >>>> currently working on a phylogeny framework similar to mesquite >>>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to >>>> add >>>> some functionality using biojava (the sequence stuff and the nexus >>>> parser). >>>> >>>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>>> BioJava:PhyloSOC07 ) and i might be able to help out with some >>>> of the >>>> methods, so is there a way to contribute ? Or is this closed to >>>> participants of the google summer of code ? >>>> >>>> I have code for n-consensus and adams consensus methods and some >>>> possible extensions for UPGMA (provide other distance computations, >>>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup >>>> and >>>> rooting support ). As our research groups has a focus on supertree >>>> construction, we have java implementations for several graph based >>>> supertree methods (aho's build, mincut, modified mincut, ranked >>>> tree, >>>> ancestral build). >>>> >>>> >>>> Regards, >>>> >>>> Thasso >>>> >>>> -- >>>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>>> Bioinformatik >>>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>>> Informatik >>>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>>> Universitaet Jena >>>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>>> Germany >>>> >>>> >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >>> -- >>> Richard Holland >>> BioMart (http://www.biomart.org/) >>> EMBL-EBI >>> Hinxton, Cambridgeshire CB10 1SD, UK >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU > Hbne6alMOuzmr8CxX/hqsfs= > =U4gJ > -----END PGP SIGNATURE----- -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ _______________________________________________ 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 54, Issue 1 ******************************************