Shakuntala Baichoo | 18 Apr 12:08 2014

Re: Biojava-l Digest, Vol 134, Issue 2

Can anyone tell me which method is used by Alignments.getAllPairsScorers to
find the pairwise distance for global alignments? Is it the method
described by Kimura et al?



On Tue, Apr 15, 2014 at 8:00 PM, <biojava-l-request <at>>wrote:

> Send Biojava-l mailing list submissions to
>         biojava-l <at>
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> or, via email, send a message with subject or body 'help' to
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> You can reach the person managing the list at
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biojava-l digest..."
> Today's Topics:
>    1. doubt about version... (Kelvin Vieira Kredens)
>    2. Re: doubt about version... (Andreas Prlic)
(Continue reading)

Kelvin Vieira Kredens | 14 Apr 21:11 2014

doubt about version...

Hi, I'm a brazilian doctoral student in computer sciences.... I'm in the
very beginning of my studies...

I will work with DNA datasets... with some data mining questions...

I found this API BioJava and I want to use it... But I've a doubt about
what version I should use.

the version 3 is new, but have little information about... and version 1 is
older but I found lots of information...

I'm thinking about use version 1... what will be the greatest problems I
will need to deal about this choice?

Is there any source of information about version 3?



Kelvin Vieira Kredens
“Não seria ciência se tivesse garantias, e, francamente, seria um pouco
chato. Mas não buscaríamos algo se fosse uma causa perdida” - Rick
Gaitskell (físico procurando evidências de matéria escura)

Biojava-l mailing list  -  Biojava-l <at>
Michael Heuer | 3 Apr 07:56 2014

BioJava Legacy 1.8.5 released

== BioJava Legacy 1.8.5 released ==

BioJava Legacy 1.8.5 was released on April 2nd 2014 and is available from as well as from the
BioJava maven repository at

BioJava Legacy 1.8.5 includes a few bug fixes and updated dependency versions.

For a detailed comparison see here:

About BioJava:

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming

On behalf of all the BioJava developers,

Biojava-l mailing list  -  Biojava-l <at>

Rose, Peter | 26 Mar 01:08 2014

[Job] Senior Java Web Developer at RCSB PDB

Help define the future of the RCSB Protein Data Bank (
as the Senior Java Web Developer. With over 300,000 unique users from over
160 countries around the world, the RCSB PDB is one of the worldwide
leading Biological Databases. As the Senior Java Web Developer, you will
be able to demonstrate your abilities at both web development and database
design. You will not only help define and meet new goals, but guarantee
the site continues to meet its 24/7/365 uptime requirements.

As a Senior Java Web Developer you will provide senior-level expertise and
leadership in enhancing the RCSB PDB website, data access layer, and data
warehouse. You will help set standards for project management and software
engineering practices.  You will ensure cutting-edge web development and
database design and architectures are employed. You will help translate
new and emergent requirements for the website into actionable strategic
plans as well as aid in selecting the best web technologies and
architectures for the RCSB PDB site. You will be a part of, and help
sustain, the RCSB¹s established history of bringing high quality
information in a reliable and dependable way to our large user community.


* MS degree in Computer Science or comparable combination of education and
experience with considerable focus in web development and software
* Established demonstrated work experience in the role of a developer and
architect on medium to large size database-driven web applications and web
services using Java EE technology and standards.
* Advanced experience with RDBMS such as MySQL and NoSQL databases,
including experience in data modeling and object-relational mapping with
tools such as Hibernate or EJB3.
(Continue reading)

Andreas Prlic | 25 Mar 23:34 2014

BioJava 3.0.8 released

== BioJava 3.0.8 released ==

BioJava 3.0.8 was released on March 25th 2014 and is available from as well as from the
BioJava maven repository at

This release would not have been possible without contributions from
13 developers, thanks to all for their support!

BioJava 3.0.8 includes a lot of new features as well as numerous bug fixes
and improvements.

New Features:

 - new Genbank writer
 - new parser for Karyotype file from UCSC
 - new parser for Gene locations from UCSC
 - new parser for Gene names file from
 - new module for Cox regression code for survival analysis
 - new calculation of accessible surface area (ASA)
 - new module for parsing .OBO files (ontologies)
 - improved representation of SCOP and Berkeley-SCOP classifications

For a detailed comparison see here:

For the next release we are planning some refactoring and removal of code
that has been deprecated for a long time. As such the next release will be
named 3.1.0.

(Continue reading)

Andreas Prlic | 20 Mar 01:41 2014

BioJava release plans


The BioJava code base has made a lot of progress lately on github and it is
time for a new release. I suggest that we release the current 3.0.8 code
base next Tuesday (March 25th). Please commit all outstanding commits by
Monday midnight. The code base will be frozen after that until the release
has been made.

For the period after this release we are planning some refactoring in the
structure modules and we will remove some of the deprecated methods that we
have carried along for a long time. That means the release after this
should be a major version increment and the next release will be called

Biojava-l mailing list  -  Biojava-l <at>

Eric Talevich | 15 Mar 06:30 2014

Google Summer of Code 2014: Call for student applications

Hi everyone,

Google Summer of Code is an annual program that funds students all over the
world to work with open-source software projects to develop new code. This
summer, the Open Bioinformatics Foundation (OBF) is taking on students
through the Google Summer of Code program to work with mentors on
established bioinformatics software projects including BioJava.

We invite students to submit applications by Friday, March 21.  Full
details are here:

All the best,
Eric & Raoul
OBF GSoC organization admins
Biojava-l mailing list  -  Biojava-l <at>

Peter Cock | 4 Mar 19:42 2014

Fwd: [OBF Members] BOSC 2014 Call for Abstracts

Dear all,

I hope to see some of you in Boston this summer for BOSC and the Codefest :)


---------- Forwarded message ----------
From: Nomi Harris <nlharris <at>>
Date: Tue, Mar 4, 2014 at 5:40 PM
Subject: [OBF Members] BOSC 2014 Call for Abstracts
To: bosc-announce <at>, members <at>, GMOD
Announcements List <gmod-announce <at>>
Cc: BOSC 2014 <bosc <at>>

Call for Abstracts for the 15th Annual Bioinformatics Open Source
Conference (BOSC 2014)
A Special Interest Group (SIG) of ISMB 2014

Dates: July 11-12, 2014
Location: Boston, MA, USA
Web site:
Email: bosc <at>
BOSC announcements mailing list:

Important Dates:
March 24, 2014: Registration opens for ISMB and BOSC
April 4, 2014: Deadline for submitting BOSC abstracts
(Continue reading)

Eric Talevich | 4 Mar 10:31 2014

Re: [GSoC] gsoc idea interest

Hi Larry,

You can find out some more about JSBML and this project on the JSBML

Try fetching the source code and building it to see how it works. Then, see
our guidelines for preparing your GSoC application:

The core of your application will be the project timeline, ideally a
week-by-week plan of the coding activities for each step of the project.
Feel free to modify the original project idea to suit your own interests.
We can give you feedback on your plan if you share it with us before you
submit your GSoC application to Google.


On Sun, Mar 2, 2014 at 9:09 AM, Larry Akah <larryakah <at>> wrote:

> Hi all, i have developed interest in a project amongst those that were
> proposed. its about
> : "Implement support for the SBML
> Multistate/Multicomponent Species
> package" . I also think that a java implementation for this would work
> just fine. i need to discuss and make sure i get a complete
> understanding of what it requires with those in charge. Thanks and i
> look forward to hearing from you.
> _______________________________________________
(Continue reading)

Eric Talevich | 4 Mar 00:20 2014

Re: [jsbml-team] [GSoC] GSoC 2014 with OBF and JSBML

Hi guys,

Thanks for clarifying this. I've updated the OBF ideas page to reflect this

For GSoC it's not necessary that JSBML be dropped into the BioJava
codebase; there appears to be enough overlap between the developer
communities that any students who take on these projects will be kept on
track with the current arrangement. Once the students begin writing their
project plans it should be more apparent how much BioJava will be directly
involved in the coding portion of the summer. For now, we'll assume that
both mailing lists will be copied on the student's weekly report, and
conversations on development can take off from there.


On Mon, Mar 3, 2014 at 2:15 PM, Andreas Dräger <andraeger <at>>wrote:

> Dear Peter and all,
> Thank you for accepting JSBML and offering that we can participate under
> BioJava :-). The reason why I referred the student to the JSBML-specific
> mailing list was just that I didn't know how many JSBML-specific e-mails
> BioJava developers are willing to receive. We can use both mailing lists
> for GSoC now as you propose.
> BTW, JSBML uses the BioJava package for ontology parsing and there are
> most likely use-cases in which both libraries could be useful within the
(Continue reading)

P. Troshin | 3 Mar 09:19 2014

Re: [GSoC] GSoC 2014 with OBF and JSBML


Hi Guys,

Since JSBML is a pure Java project and it
provides functionality not available in BioJava I do not see why it cannot
be packed as a BioJava module. In that case, yes, I think the project
should be using biojava mailing list as well as any project specific
mailing list the mentors see fit.

Using BioJava section to write down JSBML project idea seems fully
justified. Over the years we have developed parsers for various files
within BioJava community, so its not something totally new to BioJava.

Similarly, if any Bio Scala project idea appears on the horizon, it could
be affiliated with BioJava taking the interoperability of the two languages
into account. We just need to make sure any new project extends BioJava in
some way and provides some bindings into BioJava object model.


On 3 March 2014 07:29, Eric Talevich <eric.talevich <at>> wrote:

> Folks,
> Now that the Open Bioinformatics Foundation is serving as a mentoring org
> for GSoC 2014, we've had some recent discussions on how auxilliary projects
> (i.e. not the Bio* libraries) can participate and how these potential
> projects will be handled administratively for GSoC.
(Continue reading)