[Biojava-l] BioJava wiki

Dear BioJava users. The biojava wiki website has been up for a few days at http://biojava.open-bio.org/wiki/Main_Page. Thanks to the amazing efforts of a few early volunteers almost all of the content of the old site has been transfered to the new page. I think that the best part is that now

[Biojava-l] BioJava News site

Dear subscribers - BioJava has a new news and blog site based on WordPress. It can be found at http://biojava.open-bio.org/news/ I have copied some of the more recent news items over and added a few new ones. Feel free to subscirbe and or contribute. All major biojava announcements will be pos

Re: [Biojava-l] biojava wikimedia based home page

On Friday 03 February 2006 03:37, [EMAIL PROTECTED] wrote: > The OBF is moving several of it's projects homepages to wikimedia based > systems. There is a possibility that biojava will move to use this system > too. I think this is a great way to establish a community based biojava > web presence.

Re: [Biojava-l] biojava wikimedia based home page

Hi Mark Marvelous idea ;-) We (the Quebec BIoinformatics Network) are in the process of moving our "Bioinformatics KnowledgeBase" (http://apps.bioneq.qc.ca/twiki/bin/view/Knowledgebase/WebHome) from its current TWiki format toward MediaWiki. We are offering to put this (on going) experience to use

[Biojava-l] biojava wikimedia based home page

Hi all - The OBF is moving several of it's projects homepages to wikimedia based systems. There is a possibility that biojava will move to use this system too. I think this is a great way to establish a community based biojava web presence. The current home page suffers from the problem that on

[Biojava-l] biojava workshop

Hi, We are going to apply to one of the research councils for some BioJava funding. There are now some grants available for supporting tools that support research. The plan would be to apply for: Funding for a workshop: Bring together people who use and develop BioJava (and other Bio* projects

RE: [Biojava-l] BioJava with BioSQL schema on Oracle database

[EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On > Behalf Of > > Duangdaow Kanhasiri > > Sent: Friday, October 07, 2005 4:28 PM > > To: [email protected] > > Subject: [Biojava-l] BioJava with BioSQL schema on > Oracle database > > > > > > H

[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

[Biojava-l] [Biojava-dev] Java 1.5 (final chance to object)

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

[Biojava-l] biojava and matlab

Hello all - I stumbled across this today, it might be of interest to people who use matlab and want to call biojava functions from it. http://www.mathworks.com/company/newsletters/digest/2005/july/integrate_matlab.html - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Instit

Re: [Biojava-l] BioJava libraries for cell modelling wanted?

t;Cor Lieftink" <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 06/07/2005 02:36 AM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] BioJava libraries for cell modelling wanted? Hi all, Is anyone working on cell

[Biojava-l] BioJava libraries for cell modelling wanted?

Hi all, Is anyone working on cell modelling as for example described in the article below (1)? And if so, is she (also) using bioJava for this and/or other open source projects? And if so, what kind of libraries would be helpfull for you? Myself, I am a Java-programmer, in daily life workin

[Biojava-l] BioJava/BioSQL on Oracle

I've committed some changes to biojava-live which make BioJava compatible with BioSQL when the latter is running on Oracle 9i or greater and using the official schema as per the biosql-schema CVS. This involved adding an autodetect function to detect whether Clobs were used in biosequence or not

Re: [Biojava-l] BioJava and DAS

On 18 Mar 2005, at 09:20, Joel Björkman wrote: Hello! I'm new to org.biojava.bio.program.das and I have a couple of questions regarding fetching features and sequences from dazzle servers... At the moment I'm only interested in getting the sequence and annotations from ensembl's database, which sho

[Biojava-l] BioJava and DAS

Hello! I'm new to org.biojava.bio.program.das and I have a couple of questions regarding fetching features and sequences from dazzle servers... At the moment I'm only interested in getting the sequence and annotations from ensembl's database, which should make the problem easier. It's quite obvi

Re: [Biojava-l] biojava and STRAP

Hi Christoph! Further it has a very fast PDB and DSSP parsers (30ms per PDB-file). I contributed a PDB parser and data model to biojava - CVS a while ago. The parser mainly parses the coordinate section of the PDB files, so it would be nice to get the header section parsed as well. - though I

Re: [Biojava-l] biojava and STRAP

> >I would like to ask whether my program STRAP could benefit from >BioJava and vice versa. Is it worth to develop converters to exchange >objects like protein objects between both? > >http://www.charite.de/bioinf/strap/ > > >STRAP is a multi purpose multiple sequences alignment tool. It >contains

[Biojava-l] biojava and STRAP

Hi, I would like to ask whether my program STRAP could benefit from BioJava and vice versa. Is it worth to develop converters to exchange objects like protein objects between both? http://www.charite.de/bioinf/strap/ STRAP is a multi purpose multiple sequences alignment tool. It contains wrapp

Re: [Biojava-l] Biojava DB

webpages and mailing list. - Mark Ola Spjuth <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/11/2005 07:52 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Biojava DB Hello, I am thinking of using B

[Biojava-l] Biojava DB

Hello, I am thinking of using BioJava for managing sequences and annotations of sequences. BioJava seems to have database support for storing sequences in relational databases. How developed is the support for storing annotated sequences? Is there any documentation (other than JavaDoc) on working

Re: [Biojava-l] BioJava 1.5

ark Wim Glassee <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/07/2005 11:01 PM To: [email protected] cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] BioJava 1.5 Hi all, anybody have any idea if and when a biojava 1.5 is comin

[Biojava-l] BioJava 1.5

Hi all, anybody have any idea if and when a biojava 1.5 is coming? A java.sun.com article stated late 2004, early 2005. I would personally be interested in a build on top of the 1.5 codebase. Partly because of the internal xml library. Thanks, Wim ___

Re: [Biojava-l] biojava and microArray:::::::::Proget

I'm willing to coordinate efforts to bring gene expression support to biojava. However, I don't think it should be done without proper support for MAGE and the MAGE Ontology, out of respect to those active standards communities. I've set up a wiki to discuss a biojava-expr library at > http://h

[Biojava-l] biojava and microArray:::::::::Proget

hie, biojavatien and microarrayers, I'm trying to developping some Java Classe to manipulate Expression data in fact , these classes are adapted for my use hence, for this moment, more specificly . i ' m not a informatics developpers... just a poor bioinformatist but i would like i

Re: [Biojava-l] biojava and Xcode

On Nov 13, 2004, at 3:13 PM, Thomas Down wrote: To follow up on this, it's working now. The trick is to create an "Ant-based Application Jar" project in Xcode (1.5), and copy all the code from the src directory in biojava-1.4pre1 plus my own code into the project. I did have to comment out a cou

Re: [Biojava-l] biojava and Xcode

On 13 Nov 2004, at 19:47, Koen van der Drift wrote: On Nov 10, 2004, at 4:35 AM, Koen van der Drift wrote: So far I was treating biojava and my own code as 2 different targets in the same project. I will try to make just one target and post here if it worked. Thanks all for the comments, To foll

Re: [Biojava-l] biojava and Xcode

On Nov 10, 2004, at 4:35 AM, Koen van der Drift wrote: So far I was treating biojava and my own code as 2 different targets in the same project. I will try to make just one target and post here if it worked. Thanks all for the comments, To follow up on this, it's working now. The trick is to c

Re: [Biojava-l] biojava and Xcode

On Nov 10, 2004, at 3:32 AM, Thomas Down wrote: If that doesn't help, I agree that adding BioJava to the same project is probably the next logical step. Why isn't that working? So far I was treating biojava and my own code as 2 different targets in the same project. I will try to make just one

Re: [Biojava-l] biojava and Xcode

On 10 Nov 2004, at 00:17, Koen van der Drift wrote: Hi, I have been able to build biojava using Apple's Xcode 1.5. I also was able to make a separate small Xcode project and run some code that uses biojava. What I would like to be able to do is, is to debug my code including the code it uses from

Re: [Biojava-l] biojava and Xcode

also a good discipline. - Mark Francois Pepin <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 11/10/2004 12:00 PM To: Koen van der Drift <[EMAIL PROTECTED]> cc: biojava-list <[EMAIL PROTECTED]>, (bcc: Mark Schreiber/GP/Novartis) Subject

Re: [Biojava-l] biojava and Xcode

hanks, > > - Koen. > > _______ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] biojava and Xcode

ks, > > - Koen. > > _______ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] biojava and Xcode

Hi, I have been able to build biojava using Apple's Xcode 1.5. I also was able to make a separate small Xcode project and run some code that uses biojava. What I would like to be able to do is, is to debug my code including the code it uses from biojava. I can step through my own code, but as so

[Biojava-l] biojava presentation

Hello all - I have made a few updates to the Biojava in Anger web page. Firstly I have added a link to a powerpoint presentation I have used a few times that describes the core API and some of the phylosophy behind it (~700KB download). I have also updated the link to the new japanese translati

[Biojava-l] biojava article

from the "blowing our own trumpet" department: Take a look at java.sun.com today - there's an article about BioJava and os and genomics. Matthew ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

RE: [Biojava-l] BioJava, BioSQL versions

bject: Re: [Biojava-l] BioJava, BioSQL versions "Gang Wu" <[EMAIL PROTECTED]> wrote: > I got the following exceptions: > Exception in thread "main" org.biojava.bio.BioException: Error accessing > ontologies > Caused by: java.sql.SQLException: Base table or vie

Re: [Biojava-l] BioJava, BioSQL versions

"Gang Wu" <[EMAIL PROTECTED]> wrote: > I got the following exceptions: > Exception in thread "main" org.biojava.bio.BioException: Error accessing > ontologies > Caused by: java.sql.SQLException: Base table or view not found, message > from server: "Table 'biosqldb.term_relationship_term' doesn't e

RE: [Biojava-l] BioJava, BioSQL versions

eciated. Gang -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 9:27 PM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [Biojava-l] BioJava, BioSQL versions My understanding is that biojava 1.3.x is not compatable w

Re: [Biojava-l] BioJava, BioSQL versions

TECTED]> cc: Subject: [Biojava-l] BioJava, BioSQL versions Can anybody tell me what versions of BioJava work with what versions of BioSQL? Thanks Gang ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mail

[Biojava-l] BioJava, BioSQL versions

Can anybody tell me what versions of BioJava work with what versions of BioSQL? Thanks Gang ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

RE: [Biojava-l] Biojava uses which BioSQL shema version ?

PROTECTED] Sent: Tue 6/1/2004 9:05 AM To: Alexandre Dionne Laporte Cc: [EMAIL PROTECTED] Subject:Re: [Biojava-l] Biojava uses which BioSQL shema version ? Hi Alexandre, That version of biosql schema should work fine with the biojava snapshot you have. To load a Genbank file

[Biojava-l] BioJava 1.4pre1

Hi, There's now a biojava 1.4pre1 release available for download and testing: http://www.biojava.org/download14.html BioJava 1.4 includes many new features, including regular expressions on SymbolLists and macromolecular structure APIs, plus the usual bug-fixes and performance improvement

[Biojava-l] Biojava uses which BioSQL shema version ?

Hi, First of all, here are the softwares I use: 1) Biojava snapshot 'biojava-20040528' 2) latest biosql shema : biosqldb-mysql.sql v. 1.38 3) Some of Bioperl 1.4 and bioperl-db projects I would like to store entries from a Genbank file from the NCBI to the BioSQL schema using biojava. That I c

[Biojava-l] Biojava goes 3D

Hi everybody! I am working at the Sanger Centre to extend the DAS protocol toward protein structures. Biojava so far did not contain many tools for protein structure bioinformatics, so I am trying to commit a few things... Biojava now contains a PDB file parser and a few classes to represent t

[Biojava-l] biojava survey

Hi guys, I have put together a short survey about BioJava. If you have a minute, could you pop over to http://polwarth.ncl.ac.uk/ and fill it out? Any/all sudgestions welcome. Thanks, Matthew ___ Biojava-l mailing list - [EMAIL PROTECTED] http://bi

[Biojava-l] biojava script?

Hello, I am hoping to write a script to parse HMMER results and display the results. I know modules to do both these things exist, but has anyone put them together in a script yet? Cheers, Dan. ___ Biojava-l mailing list - [EMAIL PROTECTED] http://b

[Biojava-l] BioJava mentioned in 'on java' article

Thanks to Russell Smithies for passing this on: http://www.onjava.com/pub/a/onjava/2004/03/10/bioinf.html Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 1 Science Park Road #04-14 The Capricorn, Science Park II Singapore 117528 phone +65 6722

[Biojava-l] Biojava development help needed?

Hello, I am a newbie to Biojava and would like to contribute in any way to the project. I am fairly experienced Java architect/developer and can contribute towards development, architecture etc. I would appreciate it if this group could let me know if/how I can help. Thanks Rohini Sulatycki ==

Re: [Biojava-l] biojava doubts and problems

On Tuesday 06 Jan 2004 11:33 am, nandakumar sridharan wrote: > any reference books available for the biojava docs and tutorials. Please look at www.biojava.org for some material. Follow the link there to "Biojava In Anger" for further useful cookbook style materials. > GCContent .java gives exc

[Biojava-l] biojava doubts and problems

any reference books available for the biojava docs and tutorials. GCContent .java gives exception "usage: java GCContent filename.fa" how to solve it - Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes_

[Biojava-l] BioJava and ColdFusion

Has anyone used BioJava and ColdFusion together? I'm playing with the ColdFusion demo and was looking for something useful to do with it. Russell Smithies <>___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] BioJava in the news

Hey - James Gosling knows we exist! http://bio.oreilly.com/news/gosling.html === Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to whic

RE: [Biojava-l] Biojava GUI and applets

I think it might because you have other files that are needed for the applet, put them all in one others.jar file, and put the others.jar file in the archive param. Should work, I did that, it worked. = Haibo Zhang, PhD student Computationa

RE: [Biojava-l] Biojava GUI and applets

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Sat 20/09/2003 2:40 a.m. To: [EMAIL PROTECTED] Cc: Subject: [Biojava-l] Biojava GUI and applets Hi, Thanks Mathew! I

[Biojava-l] Biojava GUI and applets

: [Biojava-l] Biojava GUI and Applets Fecha: 19/09/2003 06:15:52 Mensaje: Ah - I think I see potential problems. Firstly, you should have just one archive attribute with a list of archives seperated by spaces and optional white-space. Secondly, you are using file locations for the jars - they need

Re: [Biojava-l] Biojava GUI and Applets

is Ch. [EMAIL PROTECTED] ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______ Biojava-l mailing list - [EMAIL PROTECTED] http://bioja

Re: Re: [Biojava-l] Biojava GUI and Applets

Hi, Yes, if I remove biojava.jar I get the same error I tried with and Errors remain CLASSPATH is set to C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;. Also there is a copy of .jar files in C:\Archivos de programa\Java\j2re1.4.1_04\lib\applet, without this copy

RE: [Biojava-l] Biojava GUI and Applets

a.m. To: [EMAIL PROTECTED] Cc: biojava-l Subject: Re: [Biojava-l] Biojava GUI and Applets Hi, If you remove biojava.jar either from the web server or from the applet tags, do you get exactly the same error? If so, then

Re: [Biojava-l] Biojava GUI and Applets

One more time, Thanks Luis Ch. [EMAIL PROTECTED] ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______ Biojava-l mailing

[Biojava-l] Biojava GUI and Applets

Hi, I updated Java Plugin, it didn't work. I could notice the following exceptions through Java Console: org.biojava.bio.BioError: Couldn't locate AlphabetManager.xml. This probably means that your biojava.jar file is corrupt or incorrectly built rethrown as org.biojava.bio.BioError: Unable to i

Re: [Biojava-l] BioJava GUI and applets question

/mailman/listinfo/biojava-l _______ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] BioJava GUI and applets question

Hi! I programmed an applet (Swing) and I used several classes from GUI Packages (FeatureTree, MultiLineRenderer, SequencePanel, etc.). All Applet's components works properly with AppletViewer but not in any Browser. The most calls to BioJava methods apparently are ignored when applet is loaded fro

RE: [Biojava-l] Biojava in Artemis

Sorry but i am at the end of a very high latency link and i can't make any meaningful reply until I return to Cambridge. The stuff is intended to provide codon usage data from standard tables for various species. rgds, dh ___ Biojava-l mailing list -

RE: [Biojava-l] Biojava in Artemis

] Sent: Tue 26/08/2003 9:04 p.m. To: Derek Gatherer Cc: [EMAIL PROTECTED] Subject: Re: [Biojava-l] Biojava in Artemis Once upon a time, Derek Gatherer wrote: > Hi > > I have a couple of questions regarding c

Re: [Biojava-l] Biojava in Artemis

Once upon a time, Derek Gatherer wrote: > Hi > > I have a couple of questions regarding codon bias measurements. > > 1) Is there a codon usage object in Biojava? > 2) How easy would it be to integrate it into Artemis (to add things to the > Graph menu)? > > I've seen references to > CrossProduc

[Biojava-l] Biojava in Artemis

Hi I have a couple of questions regarding codon bias measurements. 1) Is there a codon usage object in Biojava? 2) How easy would it be to integrate it into Artemis (to add things to the Graph menu)? I've seen references to CrossProductAlphabet codonAlphabet = AlphabetManager in the archive, so

Re: [Biojava-l] biojava-acedb

http://sitebuilder.yahoo.com ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] biojava-acedb

Is there any jar for acedb-biojava for running its programs. I downloaded biojava-acedb.tar but couldnt figure how to build corresponding .jar to add it in my path. Could any one tell me about this? Suman K __ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use

[Biojava-l] BioJava in Anger in French

Hi - For all you francophiles out there there is now a translation of the BioJava in anger pages in French. Just follow the link of the main page http://www.biojava.org/docs/bj_in_anger/index.htm Thanks to Sylvain Foisy for doing this good dead. - Mark ===

RE: [Biojava-l] Biojava Perl

D] > Subject: [Biojava-l] Biojava Perl > > > Dear Friends >I am having solaries 6.0 and I tried to download the > BioJava in that system. It got downloaded. But it is not > installing. Any one help me how to install. Is it a need to > have Java for Biojava installati

[Biojava-l] Biojava Perl

Dear Friends I am having solaries 6.0 and I tried to download the BioJava in that system. It got downloaded. But it is not installing. Any one help me how to install. Is it a need to have Java for Biojava installation. Kindly help me Thanks in advance -- ___

RE: [Biojava-l] BIOJava

same thing. - Mark > -Original Message- > From: arun a [mailto:[EMAIL PROTECTED] > Sent: Tuesday, 22 July 2003 2:11 a.m. > To: [EMAIL PROTECTED] > Subject: [Biojava-l] BIOJava > > > Dear friends, >I am very new to Bioinformatics. Can any one guide me wha

[Biojava-l] BIOJava

Dear friends, I am very new to Bioinformatics. Can any one guide me what is BioJava and BioPerl. What is the difference between these two with the original Java and Perl and how to get these two. If you could give me the details, then it will be great. Awaiting for your response. Thanks in

[Biojava-l] BioJava Boot Camp

Where and where will be the next BioJava bootcamp in th UK? [EMAIL PROTECTED] wrote: > > Send Biojava-l mailing list submissions to > [EMAIL PROTECTED] > > To subscribe or unsubscribe via the World Wide Web, visit > http://biojava.org/mailman/listinfo/biojava-l > or, via email, s

Re: [Biojava-l] biojava-db

Once upon a time, Juguang Xiao wrote: > HI guys, > > I may miss or ignore some relevant emails before, sorry about that. I > am just keen to know whether there is any biojava API equivalent to > bioperl-db? Thanks Yes there is. Better still, it uses the same SQL schema, and should in princip

[Biojava-l] biojava-db

HI guys, I may miss or ignore some relevant emails before, sorry about that. I am just keen to know whether there is any biojava API equivalent to bioperl-db? Thanks Cheers. Juguang ATGCCGAGCTTCT-- Juguang Xiao Temasek Life Sciences Laboratory, National University

[Biojava-l] BioJava in Anger updated

Hi all, The tutorial site BioJava in Anger has been updated so the code examples reflect the new APIs in the upcomming BioJava 1.3 release. Take a peek at http://bioconf.otago.ac.nz/biojava - Mark Mark Schreiber PhD AgResearch Joint Bioinformatics Institute School of Biological Sciences Univers

Re: [Biojava-l] BioJava Speaker

On Friday 07 Mar 2003 9:21 pm, Ryan Cuprak wrote: > Hello, > I head the Connecticut Java Users Group (www.cooug.org/java) and was > just curious if there are any speakers out there who would be interested > in doing an intro presentation on bioinformatics/biojava? Having > recently taken over the

[Biojava-l] BioJava Speaker

Hello,   I head the Connecticut Java Users Group (www.cooug.org/java) and was just curious if there are any speakers out there who would be interested in doing an intro presentation on bioinformatics/biojava? Having recently taken over the SIG I am now trying to line up speakers for the rest of the

[Biojava-l] BioJava DAS Examples/Tutorial?

Hi Everybody: Can anyone point me to any BioJava DAS examples / tutorials? I found the examples in the demos/das directory, but I was hoping for some more documentation. Any help is appreciated. Thanks, Ethan __ Do you Yahoo!? Yahoo! Tax Center

Re: [Biojava-l] Biojava-db?

On Tuesday 18 Feb 2003 6:22 am, Xiao Juguang wrote: > Hi guys, > > I can find schema for biosql in [biosql] / biosql-schema and perl api in > [bioperl] / bioperl-db, but where are the java APIs for biosql?? thanks > All Biojava APIs are documented in the API Javadocs. In the case of biosql, these

[Biojava-l] Biojava-db?

Hi guys, I can find schema for biosql in [biosql] / biosql-schema and perl api in [bioperl] / bioperl-db, but where are the java APIs for biosql?? thanks Juguang ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/bio

[Biojava-l] biojava workshop

check out the photo of Mark Schreiber's workshop at the NZ Bioinformatics Conference :-) http://bioconf.otago.ac.nz/ ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

Re: [Biojava-l] Biojava in the news

imited. If you have received this message in error, please notify the sender immediately. === ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo

[Biojava-l] Biojava in the news

Hi All, Just noticed a little snippit about biojava in the latest issue of the scientist http://www.the-scientist.com/yr2003/jan/labcon_030127.html (free registration required to view the article) Hmm, that logo looks to be derived from a very familiar piece of code ;-) - Mark Mark Schreiber P

RE: [Biojava-l] BioJava 1.3pre1

handeled now and even work! And Believe it or not the Javadocs are a lot better. - Mark > -Original Message- > From: Keith James [mailto:[EMAIL PROTECTED]] > Sent: Tuesday, 14 January 2003 11:58 p.m. > To: Thomas Down; [EMAIL PROTECTED] > Subject: Re: [Biojava-l]

Re: [Biojava-l] BioJava 1.3pre1

> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes: Thomas> - Improvements to the handler code for building object Thomas> models from search results (Keith?). BlastXML support. Mostly fixes in the search result arena, I think (aside from now using StAX). Also - KMP and re

Re: [Biojava-l] BioJava 1.3pre1

On Mon, Jan 13, 2003 at 08:10:21PM -0500, Brian Gilman wrote: > On 1/13/03 6:31 PM, "Thomas Down" <[EMAIL PROTECTED]> wrote: > > Hey Thomas, > > Do you have a doc that describes the functionality in this release?? > Something like a feature matrix would be nice to see. Now, there's a questio

Re: [Biojava-l] BioJava 1.3pre1

On 1/13/03 6:31 PM, "Thomas Down" <[EMAIL PROTECTED]> wrote: Hey Thomas, Do you have a doc that describes the functionality in this release?? Something like a feature matrix would be nice to see. Best, -B > We've had a number

[Biojava-l] BioJava 1.3pre1

We've had a number of requests recently for a more recent snapshot of the biojava-live code, so I've just put together a biojava-1.3pre1 release. Get source, binaries, and javadocs from: http://www.biojava.org/download/ This isn't absolutely set in stone yet, but should give a reasonable ind

Re: [Biojava-l] biojava cvs

Hiya, biojava-live is the module that contains what everybody thinks of as biojava. Everything else is either exciting or arcane code (read, it may or may work). bytecode contains a java bytecode generator that looks like a macro-assembler and is used to build new bytecode.jar files. Matthew --

[Biojava-l] biojava cvs

Hi guys, I have dev.open-bio.org cvs account. But I am not sure which module I should checkout. Can you explain the following modules? thanks. biodata/ biojava-acedb/ biojava-bsane/ biojava-corba/ biojava-ensembl/ biojava-exptl/ biojava-html/ biojava-lims/ biojava-live/

[Biojava-l] biojava-ensembl 1.3.9 released

Hi... I've just put together a new release of the biojava-ensembl code, which works with the latest BioJava code, and current (schemaVersion 9) Ensembl databases (earlier database versions are still supported). For those who haven't seen it before, biojava-ensembl offers full read-only access to

[Biojava-l] Biojava in Anger

Hi - I have setup some web pages that provide a cookbook, how to, kind of approach to performing basic tasks in biojava. It's available at http://bioconf.otago.ac.nz/biojava/ Comments, suggestions, flames and financial support all welcome. Enjoy Mark Schreiber PhD Bioinformatics AgResearch Inve

Re: [Biojava-l] Biojava demos.

On Fri, Nov 22, 2002 at 02:18:18PM -, Colin Watt wrote: > I am new to Java and can't find the Demo Programs referred to on the Getting > Started page at biojava.com. You need to download the source code distribution. You can either get this from: http://www.biojava.org/download/source/

[Biojava-l] Biojava demos.

I am new to Java and can't find the Demo Programs referred to on the Getting Started page at biojava.com. Can anyone help? Regards Colin ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

RE: [Biojava-l] [Biojava-I] RemoteFeature.Region.isRemote() bugged ?

Given that the returned location refers to the local sequence,I prefer the id of the local sequence. Thanks -Original Message- From: Matthew Pocock [mailto:matthew_pocock@;yahoo.co.uk] Sent: Thursday, October 24, 2002 4:40 PM To: Stephane Marcel; biojava Subject: Re: [Biojava-l

Re: [Biojava-l] [Biojava-I] RemoteFeature.Region.isRemote() bugged ?

> Is it normal or the result should be: > AL123465true[123,567] > nullfalse [363963,367351] > nullfalse [368780,369208] > Also, would you prefer to get the id of the local sequence rather than null for local regions? Matthew __

Re: [Biojava-l] [Biojava-I] RemoteFeature.Region.isRemote() bugged ?

Hi Stephane, Looks like a bug to me. It turns out it's my fault from when first writing the code. Line 200 of RemoteFeature.java has a == that should be a !=. Fixed in cvs. Apologies. Matthew --- Stephane Marcel <[EMAIL PROTECTED]> wrote: > Hi, > > when I read the doc of the Class > RemoteFeat

[Biojava-l] [Biojava-I] RemoteFeature.Region.isRemote() bugged ?

Hi, when I read the doc of the Class RemoteFeature.Region I can see that : isRemote() should return true if the sequence is a remote sequence (a clone for example) and getSeqID() will return the ID of the remote sequence. But if I try this: for(Iterator i = regions.iterator(); i.hasNext(); )

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