Raoul J P Bonnal | 23 Feb 09:51 2015

OBF GSoC Registration

Please all possible mentors,

register yourself

https://www.google-melange.com/gsoc/homepage/google/gsoc2015

and try to connect to the organization Open Bioinformatics Foundation
id: obf

in case you are aware that some mentor can not be reached by this 
message feel free to forward it.

Best,
--
Ra & Fra

On 2/20/15 8:51 PM, Raoul Bonnal wrote:
> Dear All,
> I have created a special section
>
>
> http://www.open-bio.org/wiki/Google_Summer_of_Code#Scientific_Achievements
>
> I think that would be very useful to add all the references where GSoC has been used for doing science.
>
>
> please go ahead and add your project/paper/or whatever you think that google should know about our work.
>
>
> --
(Continue reading)

Raoul J P Bonnal | 16 Feb 17:17 2015

Google Summer of Code 2015, call for project idea and mentors.

Hi All


We have LESS than a week to submit the application for the Google Summer of Code 2015, and complete the application.

20 February:

19:00 UTC

Mentoring organization application deadline.

23 - 27 February:

Google program administrators review organization applications.

2 March:

19:00 UTC

List of accepted mentoring organizations published on the Google Summer of Code 2015 site.



OBF is going to apply to be a mentoring organization for Google Summer of
Code 2015. To make the ideas list more digestible for Google's reviewers,
we consolidated all of the Bio* projects' ideas into a single page on the
OBF wiki:
 http://www.open-bio.org/wiki/Google_Summer_of_Code_2015_Ideas

Me (Raoul J.P. Bonnal) and Francesco Strozzi are the OrgAdmin, thanks to the OBF Board.

We encourage each mentor of an affiliated sub-project to fill in/add project
to the above page. Please report directly to me(bonnal <at> ingm.org) your availability as a mentor
for this year. Student from past years can mentor and propose an idea, if supported by
their community.

Any other communication related to OBF and GSoC must use  gsoc <at> mailman.open-bio.org
Subscribe here: http://lists.open-bio.org/mailman/listinfo/gsoc


Last year we introduced the Cross Projects, i.e.
those involving two or more programming languages or Bio* project
communities and/or can be useful to many languages
( web APIs reusable from any language ). The first 2015 cross project
is http://www.nextflow.io/ and you can find the proposal here:
http://www.open-bio.org/wiki/Google_Summer_of_Code_2015_Ideas#Cross-project_ideas


This page is the one we listed in our application. It is separate from the
OBF wiki page for general GSoC information:
http://www.open-bio.org/wiki/Google_Summer_of_Code

If OBF is accepted for GSoC 2015, it would make sense to point each Bio*
project's GSoC wiki page to this one, instead of duplicating the content.

As another way to interact with potential students, we've created a Google
Plus page for OBF:
https://plus.google.com/115564754756543103019/posts

And a G+ community for OBF's GSoC activities:
https://plus.google.com/communities/103096212020630764091

Feel free to forward this message to your colleagues or other possible orgs that want to join us.

Thanks to Eric Talevich, the GSoC 2014 main OrgAdmin, he did a great work and provide a lot of docs and useful hints.

Best regards,
Raoul & Francesco
OBF GSoC 2015 Org Admins
_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l
Jose Manuel Duarte | 11 Feb 17:54 2015
Picon

Cookbook update

FYI I've updated many of the cookbook pages in www.biojava.org to adapt 
them to Biojava 4. I'm sure there are still a lot of pointers to 3 and 
some other inconsistencies, but it's a first step towards an up-to-date 
Biojava 4 cookbook.

Jose
_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Steve Darnell | 3 Feb 18:19 2015

[Job Posting] Software developer position at DNASTAR (Madison, WI USA)

Greetings,

My company is hiring software developers for our structural biology group in Madison, WI USA. If
interested, please submit applications to resume <at> dnastar.com.

Best regards,
Steve Darnell

--
DNASTAR is a leading developer of desktop computer software for molecular biologists. Established in
1984, our products are used by pharmaceutical, biotech and academic researchers in more than 65
countries. 

Due to company growth, we seek an experienced software developer to join our development team. Five or more
years of experience using Java and C++ in a commercial development environment are required. Bachelor's
or advanced degree in computer science and/or life science domain and experience developing software
for life scientists are preferred. Position is available in our structural biology group, which focuses
on 3D protein structure prediction, protein-protein docking, and computational protein engineering. 

We have a team oriented work environment, along with a competitive health, dental and 401k benefits
package. 

To apply, send resume and salary requirements to resume <at> dnastar.com. No calls please.

--
Steve Darnell, Ph.D.
Senior Scientist
DNASTAR, Inc.
3801 Regent Street
Madison, WI 53705 USA

_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Khalil El Mazouari | 31 Jan 14:40 2015
Picon

file i/o with ArrayList

Hi Stefan,

I recently had a similar problem. Object serialisation was OK. However, deserialization of huge sequence
list may consume a lot of memory => less performance ... 

I highly recommend to take a look at ChronicleMap (CM): A low latency Key Value Store, with consistency,
persistence and performance. Data can be stored and reloaded from disk, in a single file. You can also use
CM as off-heap store.

With CM we managed to persist, load and process 1.000.000 sequences with just 4G RAM.  

Best Regards,

Khalil

On 30 Jan 2015, at 13:00, biojava-l-request <at> mailman.open-bio.org wrote:

> Today's Topics:
> 
>   1. file i/o with ArrayList (stefan harjes)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 30 Jan 2015 11:01:33 +0000 (UTC)
> From: stefan harjes <stefanharjes <at> yahoo.de>
> To: "biojava-l <at> mailman.open-bio.org" <biojava-l <at> mailman.open-bio.org>
> Subject: [Biojava-l] file i/o with ArrayList
> Message-ID:
> 	<1067364125.3039846.1422615693955.JavaMail.yahoo <at> mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi biojava-l
> 
> 
> I have a huge number of small sequences in an Array (ListArray<Sequence<?>>) which for server start and
stop I would like to store on disk. Unfortunately Sequence is not serilizable, so I searched and found that
GenbankWriterHelper.writeSequences(OutputStream os, Collection<Sequence<?>> seqs) should be
able to do the job. 
> However when looking at GenbankReaderHelper, there are no methods which correspond to the above writer
method. Am I on the wrong track completely? 
> 
> When looking at the writer/reader helpers, I think I remember reading that they are rudimentary and save
only the sequence (fasta)? I would expect in such an advanced verision of biojava (4.0 is being prepared?)
that there must be a standard way to serialize rich sequences/arrays of them in order to send them around on
streams/Json etc?
> 
> Any help would be appreciated
> CheersStefan
> 
> 
> 
> 
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.open-bio.org/pipermail/biojava-l/attachments/20150130/7b1260cf/attachment-0001.html>
> 
> ------------------------------
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
> 
> End of Biojava-l Digest, Vol 143, Issue 2
> *****************************************


-----
Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and
are solely for the use of the addressee. It may contain material which is legally privileged. If you are not
the addressee or the person responsible for delivering to the addressee, please notify that you have
received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could
notify the author by replying to it.

_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Andreas Prlic | 30 Jan 21:59 2015
Picon

BioJava 4.0.0 released

BioJava 4.0.0 has been released and is available from Maven Central as well as from http://biojava.org/wiki/BioJava:Download.

BioJava 4.0.0 is a major release, with many new features as well as core API changes. In accordance with semantic versioning nomenclature, the jump to 4.x.x indicates that existing applications may need to be modified (e.g. due to the removal of deprecated methods). In most cases there should be a clearly documented replacement method. See below for details on how to upgrade.

This release contains over 500 commits from 17 authors:

<at> andreasprlic <at> benjamintboyle <at> christiam <at> dmyersturnbull <at> Elinow <at> emckee2006 <at> jgrzebyta <at> josemduarte <at> kevinwu1 <at> pibizza <at> heuermh <at> paolopavan <at> parit <at> pwrose <at> sbliven <at> sroughley <at> willishf

New Features:

  • General
    • Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations. (many contributors, including <at> benjamintboyle and <at> josemduarte)
    • Improved handling of exceptions ( <at> dmyersturnbull)
    • Removed deprecated methods
    • Expanded the BioJava tutorial ( <at> andreasprlic, <at> josemduarte, and <at> sbliven)
    • Updated dependencies where applicable
    • Available on Maven Central ( <at> andreasprlic and <at> heuermh)
  • biojava3-core
    • Improved Genbank parser, including support for feature records, qualifiers, and nested locations. ( <at> paolopavan and <at> jgrzebyta)
  • biojava3-structure
    • Better support for crystallographic information, including crystallographic operators, unit cells, and protein-protein interfaces. ( <at> josemduarte)
    • Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR environmental variables) ( <at> sbliven)
    • Better command-line tools for structure alignment ( <at> sbliven)
    • New algorithm for symmetry detection in biological assemblies ( <at> pwrose)
    • New algorithm for fast contact calculation, both intra-chain and inter-chain ( <at> josemduarte)
    • Support for Accessible Surface Area (ASA) calculation through and implementation of the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) ( <at> josemduarte)
    • Support for large structures (memory permitting) and multi-character chain IDs.
    • Default to mmCIF file format, as recommended by the wwPDB

This version is compatible with Java 6, 7, and 8.

Upgrading 

Since we renamed all package names to be consistent across the whole project, there will be import errors when upgrading to this version. These can automatically get resolved using IDEs such as Eclipse or IntelliJ by selecting the Optimize Import menu item.

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 language.

Happy BioJava-ing,

Andreas

_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l
stefan harjes | 30 Jan 12:01 2015
Picon

file i/o with ArrayList

Hi biojava-l



I have a huge number of small sequences in an Array (ListArray<Sequence<?>>) which for server start and stop I would like to store on disk. Unfortunately Sequence is not serilizable, so I searched and found that GenbankWriterHelper.writeSequences(OutputStream os, Collection<Sequence<?>> seqs) should be able to do the job.
However when looking at GenbankReaderHelper, there are no methods which correspond to the above writer method. Am I on the wrong track completely?

When looking at the writer/reader helpers, I think I remember reading that they are rudimentary and save only the sequence (fasta)? I would expect in such an advanced verision of biojava (4.0 is being prepared?) that there must be a standard way to serialize rich sequences/arrays of them in order to send them around on streams/Json etc?

Any help would be appreciated

Cheers
Stefan





_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l
Jose Manuel Duarte | 20 Jan 10:23 2015
Picon

Biojava 4 release

For anyone not following the github issues, we've had an agreement that 
the Biojava 4 release will happen in about 2 weeks with a code-freeze 
declared for the 29th of January. So please submit any uncommitted 
patches before that time. If the modules and/or packages are renamed, 
merging will become much more complicated after that.

Follow the release process here: 
https://github.com/biojava/biojava/issues/238

Jose

_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Dave Roe | 20 Dec 22:41 2014
Picon

create Profile from a file in biojava3

I can't figure out how to create a Profile object from a MSA file (e.g., .msf) in biojava3. Any suggestions?
--
Dave
_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l
Rose, Peter | 5 Dec 19:28 2014

[Job] Senior Scientist and Senior Java Web Developer positions at RCSB PDB/UCSD

The RCSB PDB at UC San Diego seeks candidates with a track record of
achievement in Structural and Computational Biology combined with strong
Scientific Software Development expertise.

 
For details and direction
to apply please follow this link:
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/j
ob_listings.html

 
For more information about UCSD, please visit http://www.ucsd.edu/. As
part of the University of California, we offer a generous benefits package
plus many educational opportunities.

 
Please contact Dr. Peter Rose at pwrose <at> ucsd.edu for more information
about the positions.

 

Peter Rose, Ph.D.
Scientific Lead, RCSB Protein Data Bank (http://www.rcsb.org)
San Diego Supercomputer Center
University of California, San Diego

_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Dropbox | 26 Nov 23:53 2014

Shashank Gupta invited you to check out Dropbox

Hi there,

Shashank Gupta wants you to try Dropbox! Dropbox lets you bring all your photos, docs, and videos with you anywhere and share them easily.

Accept invite
Thanks!
- The Dropbox Team
If you prefer not to receive invites from Dropbox, please go here.
Dropbox, Inc., PO Box 77767, San Francisco, CA 94107
© 2014 Dropbox
_______________________________________________
Biojava-l mailing list  -  Biojava-l <at> mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biojava-l

Gmane