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.
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
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 <[EMAIL PROTECTED]>
wrote:
> Funny you should ask that...
>
> ...for users of biojava-1.4,
It aint biojava. Both of the screen shots look like commercial metabolic
engineering and cell modelling software.
There is a nice open source project called cellware that might be of
interest though. www.bii.a-star.edu.sg/achievements/
applications/cellware/index.asp
- Mark
"Cor Lieftink
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
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
>
>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
Hi -
You would probably want to use something like BioSQL. There is some
documentation under the OBDA section of this page
http://www.biojava.org/docs/bj_in_anger/index.htm
There are some people on the list who are actively working with this. You
would probably aslo want to look at the BioSQL
I'd like to see biojava 1.4 come out first!!
Seriously though, I'm assuming you mean a version that uses java 1.5 (java
5). I think Matthew Pocock is working on something, I think it's called
BioJava2 and represents a major redesign (in which case it probably
shouldn't be called biojava but tha
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
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
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
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
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
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
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
Hi Koen,
I've never tried it, but would it be able to follow the biojava code if
you had both the source and the class files in the jar?
Another way would be to compile biojava without making the jar file and
put the class files with yours. Then there would be no reason why the
debugger can't fol
Hello Koen,
Eclipse (www.eclipse.org) has a pretty slick debugger, can run a build
using ant, and runs well on MacOSX. You can include the biojava jars in
your project and tell Eclipse where the biojava source is and it will step
into the biojava functions where appropriate.
I'd tell you exactly
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
"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
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
My understanding is that biojava 1.3.x is not compatable with the more
recent versions of biosql. To use the current biosql I reccommend getting
one of the nightly snapshots or the pre release version of biojava 1.4
- Mark
Mark Schreiber
Principal Scientist (Bioinformatics)
Novartis Institute
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
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
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
--- Mensaje Original --
De: Matthew Pocock [EMAIL PROTECTED]
Para: [EMAIL PROTECTED] [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED] [EMAIL PROTECTED]
Asunto: Re: [Biojava-l] Biojava GUI and Applets
Fecha: 19/09/2003 06:15:52
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 to be URLs that are relative to your html page that
contains the apple
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
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
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 it looks like the
applet's path is not being searched. What is the tag you are using to
load the applet?
Matthew
[EMAIL PROTECTED] wrote:
Hi,
I updated Java Plugi
Hi,
Are you using the Java Plugin from Sun for the browsers? The default VM
may well be very out of date (the ie one doesn't even support java 1.2).
Matthew
[EMAIL PROTECTED] wrote:
Hi!
I programmed an applet (Swing) and I used several classes from GUI Packages
(FeatureTree, MultiLineRenderer
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 -
]
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
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
Sory for the long delay in answering. You need to delete the seq
package. It never realy worked and is coded to very old BioJava
interfaces. Once you've deleted this package you will be able to use the
socket client.
Matthew
Suman Kanuganti wrote:
Is there any jar for acedb-biojava for runnin
Hi -
BioJava is not a self installing system, you should probably take a look
at the instructions on http://www.biojava.org/docs/started.html
- Mark
> -Original Message-
> From: arun a [mailto:[EMAIL PROTECTED]
> Sent: Thursday, 24 July 2003 10:04 p.m.
> To: [EMAIL PROTECTED]
> Subject:
Hi -
BioJava and Bioperl are both libraries of objects that represent and
manipulate biological information and aid you in the construction of
bioinformatics software and scripts. Bioperl can be found at
www.bioperl.org and BioJava at www.biojava.org both pages have
instructions for downloading an
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
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
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
Cool! Did I realy say that? Let's get that 1.3 release out ASAP (since
it was meant to be out in December ;) ). Anybody who hasn't yet should
pick up the 1.3pre1 from http://www.biojava.org/download/binaries/ and
give it a test-drive.
Matthew
Schreiber, Mark wrote:
Hi All,
Just noticed a litt
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]
> "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
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
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
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
--
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/
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
> 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
__
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
Patrick McConnell
<[EMAIL PROTECTED]>, [EMAIL PROTECTED]
Subject: Re: [Biojava-l] BioJava discussion board
Does agave allow you to push annotations arround without the sequence?
In a web service environment we may not want to push the dna for chrom I
arround even though we may w
Patrick McConnell <[EMAIL PROTECTED]>
cc:[EMAIL PROTECTED]
Subject: Re: [Biojava-l] BioJava discussion board
> I am quite happy to see web services being applied.
Do you know the other web services for biology?
We receive Web services of other sites and open the WSDL.
> Do
.org on 08/28/2002
> 01:47:53 AM
>
> Sent by:[EMAIL PROTECTED]
>
> To:Brian Gilman <[EMAIL PROTECTED]>
> cc:Thomas Down <[EMAIL PROTECTED]>, [EMAIL PROTECTED]
>
> Subject:Re: [Biojava-l] BioJava discussion board
>
> Hello all,
>
> >
See below...
> -Original Message-
> From: Thomas Down [mailto:[EMAIL PROTECTED]]
> Sent: Wednesday, August 28, 2002 5:56 AM
> To: Brian Gilman
> Cc: Thomas Down; [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] BioJava discussion board
>
> Hi Brian
>
> On W
2002 8:48 a.m.
> To: Thomas Down
> Cc: Brian Gilman; Patrick McConnell; [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] BioJava discussion board
>
>
> Does agave allow you to push annotations arround without the
> sequence?
> In a web service environment we may not want to push th
Does agave allow you to push annotations arround without the sequence?
In a web service environment we may not want to push the dna for chrom I
arround even though we may want to know all features within a region of
it. I am format agnostic. The important things are that:
a) any format can pot
On Wed, Aug 28, 2002 at 09:35:59AM -0400, Brian Gilman wrote:
> I agree with Patrick on that one. Perhaps Agave could be used as the
> serialzation layer here?? It would be a little bit of work to get
> everything munged into Agave or BSML but think about the benefits for we
> poor middleware guys
> -Patrick
>
>
>
>
>
> Thomas Down <[EMAIL PROTECTED]>@biojava.org on 08/28/2002 05:55:42 AM
>
> Sent by:[EMAIL PROTECTED]
>
>
> To:Brian Gilman <[EMAIL PROTECTED]>
> cc: Thomas Down <[EMAIL PROTECTED]>, [EMAIL PROTECTED]
>
wn <[EMAIL PROTECTED]>@biojava.org on 08/28/2002 05:55:42 AM
Sent by:[EMAIL PROTECTED]
To:Brian Gilman <[EMAIL PROTECTED]>
cc:Thomas Down <[EMAIL PROTECTED]>, [EMAIL PROTECTED]
Subject:Re: [Biojava-l] BioJava discussion board
Hi Brian
On Wed, Aug 28, 2002 at 12
002
01:47:53 AM
Sent by:[EMAIL PROTECTED]
To:Brian Gilman <[EMAIL PROTECTED]>
cc:Thomas Down <[EMAIL PROTECTED]>, [EMAIL PROTECTED]
Subject: Re: [Biojava-l] BioJava discussion board
Hello all,
> I'd like to see more services built with biojava. Thin
Hi Brian
On Wed, Aug 28, 2002 at 12:09:05AM -0400, Brian Gilman wrote:
>
> BioJava does not work well in a distributed environment in terms
> of RMI calls or in the "weservices" stack. Custom
> serializers/deserializers need to be made for each and every object that
> exists in the feature
Hello all,
> I'd like to see more services built with biojava. Things like
> performing SSAHA as an RPC/SOAP call would be nice. A deployable app that
> had an installer and set itself up as an "alignment service" would be
> greatI think we could contribute some code to this endeavor.
Hello Thomas,
I'd be interested in this. You've asked me for a gripes list about
BioJava in general. I'm still thinking about this but, some things that
come to mind are:
BioJava does not work well in a distributed environment in terms
of RMI calls or in the "weservices" stack. C
On Mon, Jul 08, 2002 at 10:05:05AM -0700, Tim Burcham wrote:
> I realize that this has probably been discussed before, but I have looked at
> the docs & the list archives...
>
> BioJava 1.21 expects BioSQL running on MySQL version 4.0 or higher correct?
> MySQL version 3 does not support the DELE
add a note to the source or docs that says which versions
of which DBMS this code works with?
Thanks - Tim
-Original Message-
From: Thomas Down [mailto:[EMAIL PROTECTED]]
Sent: Monday, July 08, 2002 3:43 PM
To: Tim Burcham
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Biojava 1.21 & Bi
first, as someone who was fortunate enough to have attented
one of the biojava bootcamps, those materials are an
excellent starting point. i can't personally provide any assistance
on the warm-blooded instructor front (i've just LEFT a pleasant
stay in berlin and am afraid i can't come back for
forgot to include the link:
http://www-cse.ucsd.edu/~rik/compbio/hmm.html
rik
--
Richard K. Belew [EMAIL PROTECTED]
http://www.cs.ucsd.edu/~rik
Computer Science & Engr. Dept.
Univ. California -- San Diego 858 / 5
On Tuesday 18 Jun 2002 12:56 pm, Witold Eryk Wolski wrote:
> Hi!
>
> I am a student of bioinformatic on the free University of Berlin. I
> started to work with the biojava API. I found biojava quite interesting
> and usefull. Also the idea of open source tools in science is quite
> important. Ther
>It will be great if some of the core developers will be
> interested in
> visiting Berlin this Summer and give for example a broad
> overview to all
> parts of biojava during one weekend as a start of this course
> and help
> to work out a schedule for such an course.
>I already ta
I am not sure about the binary download. For CVS checkout, the file is
under biojava-live/demos/eventbasedparsing/. With all the jar files
(biojava.jar and bytecode.jar) in your CLASSPATH, you only need to do
(assuming your current directory is biojava-live/demos/) :
1. javac eventbasedparsi
Yes.
It works for 90% + of all entries in swissprot40.
SeqIOTools.readSwissprot() should do the trick. You will get back a
normal SequenceIterator object over all the swissprot entries in the
file. The entries it fails on tend to have a domain at coordinate 0
which is an initiations site. The
Hello Keith,
The jakarta apache projects use several different implementations of
xml/stylesheet-based formats and systems to generate web and paper
versions of documentation, but at this point it's probably best just to
stick with DocBook. If we want to move to something else at a later
date,
Then again maybe XFF will do the trick?
How did I not notice that package before :-)
> -Original Message-
> From: Emig, Robin [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, 7 May 2002 4:04 a.m.
> To: Schreiber, Mark; [EMAIL PROTECTED]
> Subject: RE: [Biojava-l] Biojava XM
4:04 a.m.
> To: Schreiber, Mark; [EMAIL PROTECTED]
> Subject: RE: [Biojava-l] Biojava XML Binding (BJXB)
>
>
> Although we have had similiar problems, I'd like to know what
> information you need is lost exporting to the mentioned file
> formats? For the most part you can re
Although we have had similiar problems, I'd like to know what information you need is
lost exporting to the mentioned file formats? For the most part you can recover what
you need. Esp if you REALLY mean you don't want to be held to biojava/java on either
end of the process. I'd just hate to cr
> "Tanya" == Tanya Vavouri <[EMAIL PROTECTED]> writes:
[...]
Tanya> Has biojava been used in any type of sequence
Tanya> browser/viewer applications like that ? I would be
Tanya> interested to have a look at what other people have done
Tanya> using biojava before I start usin
Hi Ben,
I don't think we ever got the ace->sequence bridge working fully. It was
done before the days of the feature projection framework, when life was even
more complicated. The package for retrieving ace objects should all work
fine though. Initialy, you could 'hide' the org.acedb.sequence pac
On 20 Mar 2002, Keith James wrote:
> The material from this bootcamp, including some screenshots will be on
> the web at the end of this week. We realise that some of this
> (especially a sourcecode-only resource) is not very accessible. This
> was emphasised by feedback from the bootcamp today.
> "Mathieu" == Wiepert, Mathieu <[EMAIL PROTECTED]> writes:
Mathieu> Hi Mark, I am not going to answer this well, but the
Mathieu> tutorial at http://www.biojava.org/tutorials/index.html
Mathieu> doesn't seem to have much on it at first glance. I know
Mathieu> that some of th
Dear Mark,
You also might want to check out Apollo, an open source genome browser
application being developed as a joint project between Ensembl
and the Berkeley Drosophila Genome Project.
(see: http://www.fruitfly.org/annot/apollo/)
I don't believe it uses the biojava data models however.
I
Hi Mark,
I am not going to answer this well, but the tutorial at
http://www.biojava.org/tutorials/index.html doesn't seem to have much on it
at first glance. I know that some of this was covered at the biojava
bootcamp last year, I presume it will be again this year. Matthew, Thomas
or Ketih mi
Keith James wrote:
>LOTS of stuff deletet to keep traffic volume down.
>
I think this is a very good idea. I can only see benefits an no real
disadvantages.
___
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes:
[...]
Thomas> However, there's also been a lot of new code gone into the
Thomas> project since 1.20 -- especially some hackathon-related
Thomas> work. I've therefore been wondering if we should look at
Thomas> relaxing th
On Fri, Sep 21, 2001 at 11:45:29PM +0100, David Huen wrote:
> On Fri, 21 Sep 2001, Cox, Greg wrote:
>
> > Has anyone done work with BioJava on very large sequences (i.e. contigs)?
> > The types of issues we're thinking about are keeping a sub-set of the
> > sequence in memory, but ensuring that t
On Fri, 21 Sep 2001, Cox, Greg wrote:
> Has anyone done work with BioJava on very large sequences (i.e. contigs)?
> The types of issues we're thinking about are keeping a sub-set of the
> sequence in memory, but ensuring that the indices of the bases are accurate.
> Has anyone dealt with this?
>
Hi Janis,
Sory for taking a long time to reply. Have you made sure that
biojava.jar is in your CLASSPATH enviroment variable, or listed in the
-classpath option to javac?
All the best,
Matthew
Janis, Michael wrote:
> Hello:
>
> I would much like to use your wonderful package. However, I a
On Tue, 24 Jul 2001, David Huen wrote:
> I've been experiencing problems with both the biojava.org and
> cvs.biojava.org CVS repositories.
>
> With biojava.org, I can see from WebCVS that cvs.biojava.org has been
> updated with new DASSequence.java sources from Thomas Down 28 hours ago
> but a c
Hi Subba,
Take a look at the org.biojava.bio.seq.io package. There are some
interfaces and classes there that allow you to parse the three formats
you mention (and others). You can use the utility methods in SeqIOTools
to get instances of these parsers easily.
Once you have used a parser to m
I saw that a number of the laptops at our bootcamp were running Mac OS
X, and seemed to be functioning fine. I didn't notice any OSX specific
problems. Can somebody post insallation/running instructions for OSX?
Thanks,
Matthew
Yann Le Guen wrote:
> Hi all,
>
> new to this list, i would sim
Hi Jason,
The biojava-biocorba package should be tagged with a 0.1 tag. After
that, we can make it work with the current code-base and IDL. I take it
from your message that you are keen to do *some* of the coding for this.
I can help out a bit, but I am realy doing DAS related stuff at the
mo
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