Francesco Strozzi | 30 Jul 10:46 2014
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EU OBF Codefest - September 18th and 19th 2014 <at> EBI - Hinxton UK

Dear all,
apologies if you receive this multiple times.

We are glad to announce that we are organising the European edition of
the OBF Codefest, which will take place on September 18th and 19th at
the EBI in Hinxton, UK. This is the second OBF Codefest this year, the
first was held this month in Boston just before the BOSC and ISMB
conferences and in September we will have the chance to expand and
carry on the work and discussions started in July in the USA.

The EU Codefest will precede the Genome
Informatics Conference in Cambridge, so we hope that developers
attending the main conference will be also interested in joining us
for a couple of days of coding and discussions on collaborative
projects and new ideas. The main topics that were proposed so far are:

* The OpenBio projects development (BioPerl, BioPython, BioRuby, BioJava)
* Semantic web technologies for biological data (e.g. RDF, OWL)
* Software deployment and bioinformatics pipelines, including
CloudBiolinux, Docker and GNU GUIX
* NoSQL databases and NGS data mining
* Biological data visualisation with e.g. D3/JS and BioJS.

We of course invite attendees to add other topics of interest.

For more information, you can visit the OBF Wiki page, which includes
also information on accommodation and registration:
http://www.open-bio.org/wiki/EU-Codefest_2014
If you plan to attend, please use the link in the registration section
and complete the simple steps on the EBI website, so that
(Continue reading)

Amandeep Sidhu | 17 Jul 02:51 2014

CFP: International Journal of Semantic and Infrastructure Services

Call for Regular Papers: International Journal of Semantic and Infrastructure Services
http://www.inderscience.com/jhome.php?jcode=ijsis
ISSN online: 2051-5081
ISSN print: 2051-5073

The goal of IJSIS is to propose novel semantic approaches and technologies and demonstrate how these help in improving big data management. It aims to establish an effective channel of communication between policy makers, government agencies, academic research institutions and persons concerned with the complex role of data infrastructure in society. It also intends to promote and coordinate developments in the field of semantic web and how these improve data and information infrastructure. The international dimension is emphasised in order to address the diversity of data and information that spreads across national barriers and to meet the needs of accelerating technological changes in a global economy.

IJSIS provides a vehicle to help professionals, academics, researchers and policy makers, working in the field of data management, semantic web and computing infrastructure, to disseminate information and to learn from each other's work. The intended audiences are data mining researchers/practitioners; specialists in academia and industry; experts who rely on computer tools for data integration, data management, data analysis; mathematicians/statisticians who are interested in model development and simulation for data; computer scientists; and post-graduate students with interests in developing and/or applying novel algorithms/methods in large-scale data management in any domain.

IJSIS publishes original papers, review papers, case studies, conference reports and book reviews. Special Issues devoted to important topics in semantics and infrastructure technology management will occasionally be published.

Topics covered include

• Big data and its management
• Data integration and interoperability
• Semantic web technologies and formalisms for data
• Language processing techniques/principles for building/maintaining ontologies
• Scientific workflows and data cloud
• Semantic image analysis
• Ontologies and semantic web tools
• Ontology representation and exchange languages
• Ontology-assisted extraction and information retrieval from text collections
• Web 2.0 and Web 3.0 applications
• Novel architectural models for high performance and cloud computing
• New parallel/concurrent programming models for high performance applications
• Data security, privacy and jurisdiction of applications in the cloud
• Interoperability between different utility computing platforms
• Semantics in platforms and software as a service

Paper Submission Guidelines

• All articles for this journal must be submitted using our online submissions system. Read our Submitting articles page (http://www.inderscience.com/info/inauthors/author_submit.php). You need to register to use our online submission system. This is a one-time process. Choose "Int. Journal of Semantic and Infrastructure Services" in the dropdown list.
• Submitted articles should not have been previously published or be currently under consideration for publication elsewhere.
• Conference papers may only be submitted if the paper has been completely re-written (taken to mean more than 50%) and the author has cleared any necessary permissions with the copyright owner if it has been previously copyrighted.
• All our articles are refereed through a double-blind process.
• All authors must declare they have read and agreed to the content of the submitted article. A full statement of our Ethical Guidelines for Authors is available (http://www.inderscience.com/www/authorethics.pdf).

Editor in Chief
Sidhu, Amandeep S., Curtin University, Sarawak, Malaysia
(ijsis <at> biomap.org)

Associate Editors
Dhillon, Sarinder K., University of Malaya, Malaysia
McGregor, Carolyn, University of Ontario Institute of Technology, Canada
Wang, Jason T.L., New Jersey Institute of Technology, USA

Editorial Board Members
Bansal, Srividya Kona, Arizona State University at the Polytechnic Campus, USA
Batini, Carlo, University of Milano–Bicocca, Italy
Bhowmik, Rajdeep, Cisco Systems, Inc., USA
Byna, Suren, Lawrence Berkeley National Laboratory, USA
Ceravolo, Paolo, Università degli Studi di Milano, Italy
Ciuciu, Ioana, Vrije Universiteit Brussel, Belgium
Ferber, Marvin, University of Bayreuth, Germany
Hong, Wei-Chiang Samuelson, Oriental Institute of Technology, Taiwan
Jarrar, Mustafa, Birzeit University, Palestinian Territory, Occupied
Ko, Ryan, University of Waikato, New Zealand
Li, Wei, University of Sydney, Australia
Lukose, Dickson, MIMOS Berhad, Malaysia
Panahizar, Maryam, Wright State University, USA
Qian, Weining, East China Normal University, China
Rajaraman, Kanagasabai, Institute for Infocomm Research (I2R), Singapore
Roche, Christophe, Université de Savoie, France
Sahoo, Satya, Case Western Reserve University, USA
Sakharkar, Meena Kishore, University of Tsukuba, Japan
Serafini, Luciano, Fondazione Bruno Kessler, Italy
Town, Christopher, University of Cambridge, UK

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Michael Heuer | 1 Jul 18:43 2014
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BioJava Legacy 1.9.0 released

== BioJava Legacy 1.9.0 released ==

BioJava Legacy 1.9.0 was released on June 25th 2014 and is available
from http://biojava.org/wiki/BioJava:Download_1.9.0 as well as from
the Maven Central repository.

The biggest change since version 1.8.5 is the release to Maven
Central.  Just include module dependencies such as

  <dependencies>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>core</artifactId>
      <version>1.9.0</version>
    </dependency>
  </dependencies>

and you are ready to go.  For a list of modules, see
http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.biojava%22

For a detailed comparison see here:
https://github.com/biojava/biojava-legacy/compare/biojava-legacy-1.8.5...biojava-legacy-1.9.0

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.

On behalf of all the BioJava developers,

   michael
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Michael Heuer | 17 Jun 20:56 2014
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biojava-legacy version 1.9.0-rc1 release candidate on Maven Central

All,

As described in issues here

https://github.com/biojava/biojava/issues/130
https://github.com/biojava/biojava-legacy/issues/14

we are trying to move from our maven repo at biojava.org to the Maven
Central repository for the next releases of biojava and
biojava-legacy.

I've cut a biojava-legacy version 1.9.0-rc1 release candidate and
promoted it to the releases repository, so it should be synced to
Maven Central in a few hours.  If you have a minute, please review the
1.9.0-rc1 artifacts.  Note that the biojava-legacy das module will not
be available in this version, and as mentioned in issue #130 above
we're not quite sure the best way to use the <developers> pom.xml
element for attribution yet.

If no issues are found with the 1.9.0-rc1 release candidate, I'll
release and promote version 1.9.0 proper next Tuesday, June 24th.

   michael
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Detlef Boehm | 10 Jun 00:20 2014
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ABI trace into a Biojava Sequence?

Hi all,

I prefer to do Java Programming in bioinformatics, but I cannot build 
the examples from
the BioJava:Cookbook:SeqIO:ABItoSequence - Examples from
http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ABItoSequence.

I used maven in Eclipse IDE for Java Developers  Version: Kepler Service 
Release 2 Build id: 20140224-0627
with
M2E - Maven Integration for Eclipse

I tried both examples with Biojava 1.8.5 using the pom.xml as follows, 
but both examples gave failure with
import org.biojava.bio.chromatogram.*;
using the Chromatogram and  ChromatogramFactory classes

and
import org.biojava.bio.program.abi.*;
using the ABITrace class.

both packages and classes are described in the API.

What is going wrong ? Any idea and help.

Many thanks
Detlef

<project xmlns="http://maven.apache.org/POM/4.0.0" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 
http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>IGVScreenShots</groupId>
     <artifactId>IGVScreenShots</artifactId>
     <version>0.0.1-SNAPSHOT</version>
     <build>
         <sourceDirectory>src</sourceDirectory>
         <plugins>
             <plugin>
<artifactId>maven-compiler-plugin</artifactId>
                 <version>3.1</version>
                 <configuration>
                     <source />
                     <target />
                 </configuration>
             </plugin>
         </plugins>
     </build>
     <repositories>
         <repository>
             <id>biojava-maven-repo</id>
             <name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
         </repository>
     </repositories>
     <dependencies>

         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>core</artifactId>
             <version>1.8.5</version>
         </dependency>
     </dependencies>
</project>
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Andreas Prlic | 13 May 21:36 2014
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CFP: 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2)

2nd Workshop on Sustainable Software for Science: Practice and Experiences
(WSSSPE2)
http://wssspe.researchcomputing.org.uk/wssspe2/
(to be held in conjunction with SC14, Sunday, 16 November 2014, New
Orleans, LA, USA)

Progress in scientific research is dependent on the quality and
accessibility of software at all levels and it is critical to address
challenges related to the development, deployment, and maintenance of
reusable software as well as education around software practices. These
challenges can be technological, policy based, organizational, and
educational, and are of interest to developers (the software community),
users (science disciplines), and researchers studying the conduct of
science (science of team science, science of organizations, science of
science and innovation policy, and social science communities).

The WSSSPE1 workshop (http://wssspe.researchcomputing.org.uk/WSSSPE1)
engaged the broad scientific community to identify challenges and best
practices in areas of interest for sustainable scientific software. At
WSSSPE2, we invite the community to propose and discuss specific mechanisms
to move towards an imagined future practice of software development and
usage in science and engineering. The workshop will include multiple
mechanisms for participation, encourage team building around solutions, and
identify risky solutions with potentially transformative outcomes.
Participation by early career students and postdoctoral researchers is
strongly encouraged.

We invite short (4-page) actionable papers that will lead to improvements
for sustainable software science. These papers could be a call to action,
or could provide position or experience reports on sustainable software
activities. The papers will be used by the organizing committee to design
sessions that will be highly interactive and targeted towards facilitating
action. Submitted papers should be archived by a third-party service that
provides DOIs. We encourage submitters to license their papers under a
Creative Commons license that encourages sharing and remixing, as we will
combine ideas (with attribution) into the outcomes of the workshop.

The organizers will invite one or more submitters of provocative papers to
start the workshop by presenting highlights of their papers in a keynote
presentation to initiate active discussion that will continue throughout
the day.

Areas of interest for WSSSPE2, include, but are not limited to:

• defining software sustainability in the context of science and
engineering software
• how to evaluate software sustainability
• improving the development process that leads to new software
• methods to develop sustainable software from the outset
• effective approaches to reusable software created as a by-product of
research
• impact of computer science research on the development of scientific
software
• recommendations for the support and maintenance of existing software
• software engineering best practices
• governance, business, and sustainability models
• the role of community software repositories, their operation and
sustainability
• reproducibility, transparency needs that may be unique to science
• successful open source software implementations
• incentives for using and contributing to open source software
• transitioning users into contributing developers
• building large and engaged user communities
• developing strong advocates
• measurement of usage and impact
• encouraging industry’s role in sustainability
• engagement of industry with volunteer communities
• incentives for industry
• incentives for community to contribute to industry-driven projects
• recommending policy changes
• software credit, attribution, incentive, and reward
• issues related to multiple organizations and multiple countries, such as
intellectual property, licensing, etc.
• mechanisms and venues for publishing software, and the role of publishers
• improving education and training
• best practices for providing graduate students and postdoctoral
researchers in domain communities with sufficient training in software
development
• novel uses of sustainable software in education (K-20)
• case studies from students on issues around software development in the
undergraduate or graduate curricula
• careers and profession
• successful examples of career paths for developers
• institutional changes to support sustainable software such as promotion
and tenure metrics, job categories, etc.

Submissions:

Submissions of up to four pages should be formatted to be easily readable
and submitted to an open access repository that provides unique identifiers
(e.g., DOIs) that can be cited, for example http://arXiv.org<http://arxiv.org/>
 or http://figshare.com.

Once you have received an identifier for your self-published paper from a
repository, submit it to WSSSPE2 by creating a new submission at
https://www.easychair.org/conferences/?conf=wssspe2, and entering:

• author information for all authors
• title
• abstract (with the identifier as the first line of the abstract, for
example, http://dx.doi.org/10.6084/m9.figshare.791606 or
http://arxiv.org/abs/1404.7414 or alternative)
• at least three keywords
• tick the abstract only box
Do not submit the paper itself through EasyChair; the identifier in the
abstract that points to the paper is sufficient.

Deadline for Submission:

14 July 2014 (any time of day, no extensions)

Travel Support

Funds are available to support participation in WSSSPE2 by 1) US-based
students, early-career researchers, and members of underrepresented groups;
and 2) participants who would not otherwise attend the SC14 conference.
Priority will be given to those who have submitted papers and can make a
compelling case for how their participation will strengthen the overall
workshop and/or positively impact their future research or educational
activities.

Submissions for travel support will be accepted from September 1st to
September 15th 2014 following instructions posted on the workshop web site.

Financial support to enable this has been generously provided by 1) the
National Science Foundation and 2) the Gordon and Betty Moore Foundation.

Important Dates:

July 14, 2014 Paper submission deadline
September 1, 2014 Author notification
September 15, 2014 Funding request submission deadline
September 22, 2014 Funding decision notification
November 16, 2014 WSSSPE2 Workshop

Organizers:

• Daniel S. Katz, d.katz <at> ieee.org, National Science Foundation, USA
• Gabrielle Allen, gdallen <at> illinois.edu, University of Illinois
Urbana-Champaign, USA
• Neil Chue Hong, N.ChueHong <at> software.ac.uk, Software Sustainability
Institute, University of Edinburgh, UK
• Karen Cranston, karen.cranston <at> nescent.org, National Evolutionary
Synthesis Center (NESCent), USA
• Manish Parashar, parashar <at> rutgers.edu, Rutgers University, USA
• David Proctor, djproctor <at> gmail.com, National Science Foundation, USA
• Matthew Turk, matthewturk <at> gmail.com, Columbia University, USA
• Colin C. Venters, colin.venters <at> googlemail.com, University of
Huddersfield, UK
• Nancy Wilkins-Diehr, wilkinsn <at> sdsc.edu, San Diego Supercomputer Center,
University of California, San Diego, USA

Program Committee:

• Aron Ahmadia, U.S. Army Engineer Research and Development Center, USA
• Liz Allen, Wellcome Trust, UK
• Lorena A. Barba, The George Washington University, USA
• C. Titus Brown, Michigan State University, USA
• Coral Calero, Universidad Castilla La Mancha, Spain
• Jeffrey Carver, University of Alabama, USA
• Ewa Deelman, University of Southern California, USA
• Gabriel A. Devenyi, McMaster University, Canada
• Charlie E. Dibsdale, O-Sys, Rolls Royce PLC, UK
• Alberto Di Meglio, CERN, Switzerland
• Anshu Dubey, Lawrence Berkeley National Laboratory, USA
• David Gavaghan, University of Oxford, UK
• Paul Ginsparg, Cornell University, USA
• Josh Greenberg, Alfred P. Sloan Foundation, USA
• Sarah Harris, University of Leeds, UK
• James Herbsleb, Carnegie Mellon University, USA
• James Howison, University of Texas at Austin, USA
• Caroline Jay, University of Manchester, UK
• Matthew B. Jones, National Center for Ecological Analysis and Synthesis
(NCEAS), University of California, Santa Barbara, USA
• Jong-Suk Ruth Lee, National Institute of Supercomputing and Networking,
KISTI (Korea Institute of Science and Technology Information), Korea
• James Lin, Shanghai Jiao Tong University, China
• Frank Löffler, Louisiana State University, USA
• Chris A. Mattmann, NASA JPL & University of Southern California, USA
• Robert H. McDonald, Indiana University, USA
• Lois Curfman McInnes, Argonne National Laboratory, USA
• Chris Mentzel, Gordon and Betty Moore Foundation, USA
• Kenneth M. Merz, Jr., Michigan State University, USA
• Marek T. Michalewicz, A*STAR Computational Resource Centre, Singapore
• Peter E. Murray, LYRASIS, USA
• Kenjo Nakajima, University of Tokyo, Japan
• Cameron Neylon, PLOS, UK
• Aleksandra Pawlik, Software Sustainability Institute, Manchester
University, UK
• Birgit Penzenstadler, University of California, Irvine, USA
• Marian Petre, The Open University, UK
• Mark D. Plumbley, Queen Mary University of London, UK
• Andreas Prlic, University of California, San Diego, USA
• Victoria Stodden, Columbia University, USA
• Kaitlin Thaney, Mozilla Science Lab, USA
• Greg Watson, IBM, USA
• Theresa Windus, Iowa State University and Ames Laboratory, USA

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Spencer Bliven | 12 May 10:56 2014

Brainstorming feature requests

Hi everyone,

The recent thread on the dev list about participating in BioJava made me
realize that our list of feature requests is pretty sparse and
disorganized. In the current state of things, I think we are missing out on
getting contributions from new developers who want to help but don't know
where to start. The github
issues<https://github.com/biojava/biojava/issues>consist mostly of
very technical bugs best fixed by the developer who wrote
the code, and the wiki
page<http://biojava.org/wiki/BioJava3_Feature_Requests>is short,
general, and hasn't been updated in a while.

Let's brainstorm some more feature requests. Where are the holes in our
API? Are there any algorithms that would be useful to have in Java? I know
that I have a list of features which I plan to implement "some day" but
never bothered to write down anywhere. Let's add all those ideas to github,
so that potential contributors or potential summer of code students can get
some ideas. I'll start by creating issues for the current feature requests.

-Spencer

P.S. Should we use the 'enhancement' or 'new feature' label on github for
feature requests? They are used inconsistently right now.
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Shakuntala Baichoo | 18 Apr 12:08 2014
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Re: Biojava-l Digest, Vol 134, Issue 2

Hi!
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?

Thanks.

Shakuntala

On Tue, Apr 15, 2014 at 8:00 PM, <biojava-l-request <at> lists.open-bio.org>wrote:

> Send Biojava-l mailing list submissions to
>         biojava-l <at> lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://lists.open-bio.org/mailman/listinfo/biojava-l
> or, via email, send a message with subject or body 'help' to
>         biojava-l-request <at> lists.open-bio.org
>
> You can reach the person managing the list at
>         biojava-l-owner <at> lists.open-bio.org
>
> 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 14 Apr 2014 16:11:49 -0300
> From: Kelvin Vieira Kredens <kredens <at> gmail.com>
> Subject: [Biojava-l] doubt about version...
> To: biojava-l <at> lists.open-bio.org
> Message-ID:
>         <CACU5nmcdA+cRqXMDoSmgzu+eBkJSxuk=
> ZqtHzahPHerRNB-W3A <at> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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?
>
> --
> Atenciosamente,
>
> Kelvin Vieira Kredens
> ?N?o seria ci?ncia se tivesse garantias, e, francamente, seria um pouco
> chato. Mas n?o buscar?amos algo se fosse uma causa perdida? - Rick
> Gaitskell (f?sico procurando evid?ncias de mat?ria escura)
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 14 Apr 2014 13:59:41 -0700
> From: Andreas Prlic <andreas <at> sdsc.edu>
> Subject: Re: [Biojava-l] doubt about version...
> To: Kelvin Vieira Kredens <kredens <at> gmail.com>
> Cc: Biojava <biojava-l <at> lists.open-bio.org>
> Message-ID:
>         <
> CALthepx81HNvpiWpn3Pbs7oDsBxaqdRyv0ogXKaJ2XYQj69-0A <at> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Kelvin,
>
> It depends what specific features you want.
>
> Take a look at the cookbook
>
> http://biojava.org/wiki/BioJava:CookBook
>
> and also the javadoc...
>
> http://www.biojava.org/docs/api/index.html
>
> Andreas
>
>
> On Mon, Apr 14, 2014 at 12:11 PM, Kelvin Vieira Kredens
> <kredens <at> gmail.com>wrote:
>
> > 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?
> >
> > --
> > Atenciosamente,
> >
> > Kelvin Vieira Kredens
> > ?N?o seria ci?ncia se tivesse garantias, e, francamente, seria um pouco
> > chato. Mas n?o buscar?amos algo se fosse uma causa perdida? - Rick
> > Gaitskell (f?sico procurando evid?ncias de mat?ria escura)
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l <at> lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> ------------------------------
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> End of Biojava-l Digest, Vol 134, Issue 2
> *****************************************
>

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Kelvin Vieira Kredens | 14 Apr 21:11 2014
Picon

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?

--

-- 
Atenciosamente,

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)

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Michael Heuer | 3 Apr 07:56 2014
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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
http://biojava.org/wiki/BioJava:Download_1.8.5 as well as from the
BioJava maven repository at http://www.biojava.org/download/maven/.

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

For a detailed comparison see here:
https://github.com/biojava/biojava-legacy/compare/biojava-legacy-1.8.4...biojava-legacy-1.8.5

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.

On behalf of all the BioJava developers,

   michael
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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 (http://www.rcsb.org)
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.

Qualifications:

* MS degree in Computer Science or comparable combination of education and
experience with considerable focus in web development and software
architecture.
* 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.
* Advanced experience developing the presentation layer of a dynamic,
database-driven web application using HTML, CSS, JavaScript, JSP, XML,
Java. Experience resolving browser and cross-platform compatibility issues.
* Advanced experience in an agile software development environment and
test-driven design. Experience with build tools such as Maven and Ant,
continuous integration systems such as Cruise Control, web applications
testing with tools such as Selenium, and project tracking tools such as
Jira or Mylyn.
* Advanced degree in bioinformatics, computational biology or chemistry,
or related scientific field or comparable combination of education and
experience with extensive knowledge and research experience with
biological and chemical application software and data analyses preferred.

The successful candidate will be located at the University of California
San Diego. 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 send your resume to Dr. Peter Rose at pwrose <at> ucsd.edu

For more details and other job openings see:
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/j
ob_listings.html

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Gmane