Jose Duarte | 28 Jun 18:46 2016

Re: Biojava 4.2, tarball link

Dear Prashanth Athri

I'm replying in the list so that this benefits all users. Please try to use the list for these questions as you are likely to get a faster response from the community.

Thanks so much for letting us know about the link. Unfortunately we are not offering anymore the one tarball with all files within. I've now removed the link. You need to get the individual jar files or if you want to browse the javadocs go to http://www.biojava.org/docs/api4.2.0/

In any case if you are developing your own java application based on biojava we recommend using maven, which makes things a lot easier (see some brief instructions in the readme: https://github.com/biojava/biojava).

Also instead of 4.2.0, try to use 4.2.2 which is the latest bugfix version.

All the best

Jose


On Tue, Jun 28, 2016 at 6:31 AM, Andreas Prlic <andreas.prlic <at> gmail.com> wrote:
Hi Jose,

Could you take a look what is missing there? Thanks!

A

---------- Forwarded message ----------
From: Prashanth Athri 
Date: Tuesday, June 28, 2016
Subject: Biojava 4.2, tarball link
To: "andreas.prlic <at> gmail.com" <andreas.prlic <at> gmail.com>


Hello Dr. Prlic:
This link to the Biojava (4.2) tarball does not seem to work. Thought I would let you know.
Thanks,

Prashanth Athri, Ph.D.
Associate Professor
Dept. of Computer Science & Engg.
Amrita University, Bangalore

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Andreas Prlic | 10 Jun 18:42 2016
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4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

Call for Submissions:

4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)
(http://wssspe.researchcomputing.org.uk/wssspe4/)

Location: School of Computer Science, Kilburn and IT Buildings, University of Manchester, Manchester, UK
Dates: 2 ½ days from Sept. 12th noon – Sept. 14th 5 pm, 2016
Immediately preceding and co-located in Manchester with First Conference of Research Software Engineers
(RSE Conference) (Sept 15-16 at Museum of Science and Industry, Manchester, UK)

Follow <at> wssspe, tweet with #wssspe

A nominal registration fee may be charged.

Abstract:

Progress in scientific research is dependent on the quality and accessibility of research software at all levels. It
is now critical to address many new challenges related to the development, deployment, maintenance, and
sustainability of open-use research software: the software upon which specific research results rely.  Open-use
software means that the software is widely accessible (whether open source, shareware, or commercial).
Research software means that the choice of software is essential to specific research results; using different
software could produce different results.

In addition, it is essential that scientists, researchers, and students are able to learn and adopt a new set of
software-related skills and methodologies. Established researchers are already acquiring some of these skills,
and in particular, a specialized class of software developers is emerging in academic environments who are an
integral and embedded part of successful research teams. WSSSPE provides a forum for discussion of these
challenges, including both positions and experiences, and a forum for the community to assemble and act.

WSSSPE4 will consist of two separate tracks with some joint sessions:

Track 1 – Building a sustainable future for open-use research software has the goals of defining a vision of the
future of open-use research software, and in the workshop, initiating the activities that are needed to get there.
The idea of this track is to first think about where we want to be 5 to 10 years from now, without being too
concerned with where we are today, and then to determine how we can move to this future.

Track 2 – Practices & experiences in sustainable scientific software has the goal of improving the quality of
today’s research software and the experiences of its developers by sharing practices and experiences.  This
track is focused on the current state of scientific software and what we can do to improve it in the short term,
starting with where we are today.

Topics of interest include but are not limited to:

• Development and Community
   • Best practices for developing sustainable software
   • Models for funding specialist expertise in software collaborations
   • Software tools that aid sustainability
   • Academia/industry interaction
   • Refactoring/improving legacy scientific software
   • Engineering design for sustainable software
   • Metrics for the success of scientific software
   • Adaptation of mainstream software practices for scientific software
• Professionalization
   • Career paths
   • RSE as a brand
   • RSE outside of the UK or Europe
   • Increase incentives in publishing, funding and promotion for better software
• Training
   • Training for developing sustainable software
   • Curriculum for software sustainability
• Credit
   • Making the existing credit and citation ecosystem work better for software
   • Future credit and citation ecosystem
   • Software contributions as a part of tenure review
   • Case studies of receiving credit for software contributions
   • Awards and recognition that encourage sustainable software
• Software publishing
   • Journals and alternative venues for publishing software
   • Review processes for published software
• Software discoverability/reuse
   • Proposals and case studies
• Reproducibility and testing
   • Reproducibility in conferences and journals
   • Best practices for code testing and code review

Important Dates:
• Submission of lightning talks: July 10
• Submission of Track 1 idea papers: July 10
• Submission of Track 2 position papers, experience papers, presentations of previously
  published works, and demos: July 10
• Submission of travel support requests: July 10
• Lightning talk decisions announced: Aug 1
• Track 1 idea papers decisions announced: Aug 1
• Track 2 position papers, experience papers, presentations of previously published works,
  and demo decisions announced: Aug 1
• Travel support decisions announced: Aug 2

Submission types and formats:
• Lightning talks: a short paper, up to 2 pages, that if accepted can be conveyed in a 5 to 7 minute talk,
  either on Track 1: Building a sustainable future for open-use research software or Track 2: Practices & experiences
  in sustainable scientific software.  Lightning talks may be based on either novel or previously published work, but
  must contain a core idea that will contribute to the discussion in the workshop.
• Idea papers: a longer paper, up to 8 pages, that presents implementable proposals related to Track 1: Building a
  sustainable future for open-use research software. Track 1 participants will build on the proposals and ideas in
  these papers, with the goal of initiating the planning, development, and execution of some of the ideas during the
  workshop itself. Given the magnitude and importance of the task at hand, the WSSSPE4 organizing committee
  encourages these proposals to be developed on an open, public, and inclusive basis. Submitters are invited to
  present a vision of some aspect of the future of open-use research software, and a plan of activities to gather and
  organize the resources needed to get there.
    Example idea paper topics:
        • Adaptation of industrial software engineering principles into the research software community with a plan to
          fund the work
        • Funding and scaling software carpentry style training in advanced topics
        • Infrastructure and funding for community maintenance of open use research software
        • Scaling the SSI beyond the UK
        • Specific proposals of how to bridging/network the various research software engineering communities in scalable
          manner without destroying independence and unique foci of each community
• Position papers: a longer paper, not previously published, up to 8 pages, that if accepted can be conveyed in
  a 15 to 20 minute talk, on Track 2: Practices & experiences in sustainable scientific software, specifically discussing
  what we can do to improve sustainable scientific software in the short term, starting with where we are today.
• Experience papers: a longer paper, not previously published, up to 8 pages, that if accepted can be conveyed
  in a 15 to 20 minute talk, on Track 2: Practices & experiences in sustainable scientific software, specifically discussing
  current practices and experiences and how they have been used to improve the quality of today’s research software
  and/or the experiences of its developers.
• Presentation of previously published work: a short paper, up to 2 pages, that if accepted can be conveyed in
  a 15 to 20 minute talk, describing a previous published work by the authors and its relevance to Track 2: Practices &
  experiences in sustainable scientific software on the topic of improving the quality of today’s research software and
  the experiences of its developers by sharing practices and experiences.
• Demos: a short paper, up to 2 pages plus 2 pages of screenshots, that if accepted can be conveyed in a 10 to
  15 minute demonstration, showing a tool or process relevant to Track 2: Practices & experiences in sustainable
  scientific software, that improves the quality of today’s research software and/or the experiences of its developers.
  Demo submissions may be based on previously published work.

Submission process:
All submissions should be created in PDF format.  They should begin with a title, author names and affiliations, a short
abstract, then the body of the submission.  The title should begin with “Lightning talk:” or “Position paper:” or
“Experience paper:” or “Idea paper:” or “Previously published:” or “Demo:”.  Submissions should also include a statement
of their license, preferably CC BY 4.0.  Submissions should be made via https://easychair.org/conferences/?conf=wssspe4.
WSSSPE4
 accepted submissions (except presentations of previously published work) will be published by WSSSPE as a
special collection in http://ceur-ws.org/.  Authors retain copyright to their work and are free to self-publish their submissions
or accepted papers elsewhere in addition.


Preliminary Agenda:

Sept 12 pm – Joint session of both tracks

  Introduction
  Keynote
  Lightning talks
  Updates on actions and activities from WSSSPE3 working groups
  Discussion and planning for the remainder of WSSSPE4

Sept 13 (all day) and 14 (until 3 pm) – Parallel tracks

  Track 1: This will be a set of working sessions with a facilitated discussion, breakout sessions, report backs, and active
  writing towards the track goal of defining a vision of the future of open-use research software, and a plan of activities that
  are needed to get there.
  Track 2: presentations of position papers, experience papers, previously published works, and demos; and breakout
  sessions or unconference sessions.

Sept 14 (1:30 pm – 5 pm) – Joint session of both tracks

  Panel on best practices
  Summary and discussion of each tracks’ progress
  Planning for future events

Organizing Committee:
• Gabrielle Allen, University of Illinois Urbana-Champaign, USA
• Jeffrey Carver, University of Alabama, USA
• Sou-Cheng T. Choi, Illinois Institute of Technology, USA
• Tom Crick, Cardiff Metropolitan University, UK
• Michael R. Crusoe, Common Workflow Language project
• Sandra Gesing, University of Notre Dame, USA
• Robert Haines, University of Manchester, UK
• Michael Heroux, Sandia National Laboratory, USA
• Lorraine J. Hwang, University of California, Davis, USA
• Daniel S. Katz, University of Illinois Urbana-Champaign, USA
• Kyle E. Niemeyer, Oregon State University, USA
• Manish Parashar, Rutgers University, USA
• Colin C. Venters, University of Huddersfield, UK

Program Committee:
• (in progress, see web site for additions)
• David Abramson, University of Queensland, Australia
• Lorena A. Barba, George Washington University, USA
• Ross Bartlett, Sandia National Laboratories, USA
• Christoph Becker, University of Toronto, Canada
• David Bernholdt, Oak Ridge National Laboratory, USA
• Stefanie Betz, Karlsruhe Institute of Technology, Germany
• Coral Calero, Universidad Castilla La Mancha, Spain
• Ishwar Chandramouli, National Cancer Institute, National Institutes of Health, USA
• Ruzanna Chitchyan, University of Leicester, UK
• Neil Chue Hong, Software Sustainability Institute, University of Edinburgh, UK
• Karen Cranston, Duke University, USA
• Ewa Deelman, Information Sciences Institute, University of Southern California, USA
• Dave De Roure, Oxford e-Research Centre, University of Oxford, UK
• Charlie E. Dibsdale, O-Sys, Rolls Royce PLC, UK
• Alberto Di Meglio, CERN, Switzerland
• Anshu Dubey, Argonne National Laboratory, USA
• Nadia Eghbal, Independent Researcher (via Ford Foundation), USA
• Martin Fenner, DataCite, Germany
• David Gavaghan, University of Oxford, UK
• Mike Glass, Sandia National Laboratories, USA
• Carole Goble, University of Manchester, UK
• Joshua Greenberg, Alfred P. Sloan Foundation, USA
• Michael K Griffiths, University of Sheffield, UK
• James Hetherington, University College London, UK
• Fred J. Hickernell, Illinois Institute of Technology, USA
• Caroline Jay, University of Manchester, UK
• Matthew B. Jones, University of California Santa Barbara, USA
• Nick Jones, New Zealand eScience Infrastructure (NeSI), NZ
• Jong-Suk Ruth Lee, National Institute of Supercomputing and Networking, KISTI (Korea Institute
  of Science and Technology Information), Korea
• Sedef Akinli Kocak, Ryerson University, Canada
• James Lin, Shanghai Jiao Tong University, China
• Frank Löffler, Louisiana State University, USA
• Gregory Madey, University of Notre Dame, USA
• Ketan Maheshwari, University of Pittsburgh, USA
• Steven Manos, University of Melbourne, Australia
• Chris A. Mattmann, NASA JPL & University of Southern California, USA
• Abigail Cabunoc Mayes, Mozilla Science Lab, USA
• Robert H. McDonald, Indiana University, USA
• Lois Curfman McInnes, Argonne National Laboratory, USA
• Chris Mentzel, Gordon and Betty Moore Foundation, USA
• Peter Murray-Rust, University of Cambridge, UK
• Christopher R. Myers, Cornell University, USA
• Jarek Nabrzyski, University of Notre Dame, USA
• Cameron Neylon, Curtin University, Australia
• Aleksandra Pawlik, New Zealand eScience Infrastructure (NeSI), NZ
• Fernando Perez, Lawrence Berkeley National Laboratory & University of California, Berkeley, USA
• Marian Petre, The Open University, UK
• Marlon Pierce, Indiana University, USA
• Andreas Prlic, University of California, San Diego, USA
• Karthik Ram, University of California, Berkeley, USA
• Morris Riedel, Juelich Supercomputing Centre, Germany
• Norbert Seyff, University of Zurich, Switzerland
• Arfon Smith, GitHub Inc, USA
• Borja Sotomayor, University of Chicago, USA
• Edgar Spalding, University of Wisconsin, USA
• Maria Spichkova, RMIT University, Australia
• Victoria Stodden, University of Illinois Urbana-Champaign, USA
• Matthew Turk, University of Illinois Urbana-Champaign, USA
• Ewout van den Berg, IBM Watson, USA
• Nancy Wilkins-Diehr, San Diego Supercomputer Center, University of California, San Diego, USA
• James Willenbring, Sandia National Laboratories, USA
• Scott Wilson, Cetis LLP, UK
• Theresa Windus, Iowa State University and Ames Laboratory, USA
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Andreas Prlic | 9 Jun 23:14 2016
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New BioJava Logo Design Competition

Hi,

It is time to upgrade the BioJava logo and make it look like it is 2016.

We are organizing a design competition to come up with a new logo. Anybody can participate:

- The logo should look modern and be better than the current one (yellow circle)

- The logo should be able to be rendered as a favicon, as well as large (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.

- Logos shall not look similar in any way to the trademarked Java programming language logo. This means no coffee cups in any way.

Deadline:
Deadline for submissions is July 4th. 

Announcement of Winner:
The winner of the new logo competition will be announced during BOSC 2016.

Prize:
We will print t-shirts with the new logo and the designer will get a free t-shirt.

If the designer of the winning new logo will be attending ISMB 2016, the attending BioJava developers will take the winner out for dinner.

BioJava will carry the new logo on its homepage and GitHub Profile

Details:
For full details of the competition and how to make a submission please view here:



Andreas






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Andreas Prlic | 4 Jun 01:04 2016
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Re: Get Consensus after MSA

Hi Mao,

Please don't mail me directly, but keep questions on the mailing lists, or on github. This is so other people who have the same question can benefit from this as well. 

Unfortunately there is currently no method implemented to get the consensus of an alignment. That's something you would need to build yourself.

You need to iterate over all columns of an alignment and get the consensus for each column.

Any pull requests that add this feature in a convenient way are welcome,

Thanks,

Andreas



On Wed, Jun 1, 2016 at 2:51 AM, mao qin <mqin <at> outlook.com> wrote:

Hi Andreas,

Greetings!

I am using BioJava jar packages of alignment, core and genome under version 4.1.0 and forester-1.038.jar.

And after multiple sequences alignment, I want to get the consensus of MSA output. I have check the example of BioJava Cookbook for two seqs but it was not suitable for MSA. And I looked up the codes of related class, but did not afford the method for directly getting the consensus seq.

Do you have any suggestions about doing that? Do I need to implement this object by myself?

Thanks!

The example output is as follow:

Clustalw:
CLUSTAL W MSA from BioJava

null   GGTTAA-TTAATT 12
null   ----AACTAAATT  9
null   AGTTAA-TTAACC 12

Code:
public class TestMSA {
public static void main(String[] args) throws CompoundNotFoundException {
        // TODO Auto-generated method stub
        DNASequence s1 = new DNASequence("GGTTAATTAATT", AmbiguityDNACompoundSet.getDNACompoundSet());
        DNASequence s2 = new DNASequence("AACTAAATT", AmbiguityDNACompoundSet.getDNACompoundSet());
        DNASequence s3 = new DNASequence("AGTTAATTAACC", AmbiguityDNACompoundSet.getDNACompoundSet());
        List<DNASequence> seqs = new ArrayList<DNASequence>();
        seqs.add(s1);
        seqs.add(s2);
        seqs.add(s3);
        Profile<DNASequence, NucleotideCompound> profile = Alignments.getMultipleSequenceAlignment(seqs);       
        System.out.printf("Clustalw:%n%s%n", profile.toString(StringFormat.CLUSTALW));
        ConcurrencyTools.shutdown();
    }
}

-- All the best! Mao Qin Agricultural Genomes Insititute at Shenzhen mqin <at> outlook.com


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Andreas Prlic | 24 May 20:30 2016
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Re: Documentation, tutorials and cookbook about pairwise sequence alignment

Hi Andreas,

please don't mail me directly with questions, but keep them on the list, for the benefit of other users who might be in the same situation.

You are right, the signature of SubstitutionMatrix has changed at some point in the past. Try this:

SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
There is also another example in the "demo" package of the alignment module, that you could take a look at.

About the tutorial: When you have the basics figured out, any contributions/pull requests to improve the tutorial will be welcome! ;-)

A


On Tue, May 24, 2016 at 5:51 AM, Andrea Battistelli <andreyas.1688 <at> gmail.com> wrote:
Hi Andreas.

I have seen the codes in the page you suggested me.
I have encountered some errors about:

import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;

Regarding all the other imports, there are not problems.
Indeed in the code I have errors in this part:

SubstitutionMatrix<AminoAcidCompound> matrix = new SimpleSubstitutionMatrix<AminoAcidCompound>();
List<SequencePair<ProteinSequence, AminoAcidCompound>> alig = Alignments.getAllPairsAlignments(lst,
                PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);
for (SequencePair<ProteinSequence, AminoAcidCompound> pair : alig) {
            System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);
}
It is told me to create these two classes.

I am using the last version of the BioJava project (4.2.1) by means of Maven (as described in the site).
Probably in that version there are not anymore those classes. Could be this the problem?
How could I solve this?

Thanks a lot.

P.S.
Regarding the "BioJavaTutorial page - book 2: The Alignment module" (https://github.com/biojava/biojava-tutorial/blob/master/alignment/README.md), could be possible kindly to have the explanation of the pages?
Unfortunaltely it is the onyl part of the tutorial without explanation.


2016-05-24 14:12 GMT+02:00 Andrea Battistelli <andreyas.1688 <at> gmail.com>:
Hi Andreas.

Thank you very much for the fixes. Surely it will help me.
I have understood the problem you encountered with the old site.
Now I will try to apply those things.

Thanks again,
Andrea

2016-05-23 19:27 GMT+02:00 Andreas Prlic <andreas <at> sdsc.edu>:
Hi Andrea,

Sorry for the inconvenience. We had to turn the old site off, since there were too many security breaches which resulted in content spamming. This is across all bio* projects...

I fixed the links on the CookBook4 page. Checking some of the related pages, there are still a lot of formatting issues. That will take a bit to fix them all up. However, each page at the bottom has an "edit this page" link, which makes it easy to access the raw markdown content.  It is possible to see the code in a more readable way. I also fixed up this page for now: http://biojava.org/wikis/BioJava:CookBook3:PSA/

Hope that helps,

Andreas



On Sat, May 21, 2016 at 4:09 AM, Andrea Battistelli <andreyas.1688 <at> gmail.com> wrote:
Hello everyone.

I have been studying the pairwise sequence alignment concept for a project that I need to do for an exam.
In particular I am interested in the global and local alignments and all the things related to them (how they are implemented, how I can generate a paiwise alignment, ect.).
I would implement my project in Java employing indeed BioJava as starting point.
I set up correctly the Maven project on Eclipse so no problem under that point of view.

Few months ago I have seen there was all the documentation, tutorials and specifications about the BioJava project based on the Wiki pages.
I have seen it has been all migrated into a new web site but now I am not finding any documentation, tutorial or cookbook about the topic of personal interest.

- In the BioJavaTutorial page - book 2, the alignment module has no pages of explanation.
- In the CookBook4.0, all the links relative to the paiwise sequence alignment give me back an "address uninterpretable" message.
- Finally in the Wiki Pages section there are many links. In some of these there are links interesting for me but they contain not well formatted codes.

I know that it may taketime to migrate all the things but in the meantime:
Is there any possibility to have the reference to the old web site?
Anyone can help me to indicate me where I can find some good pages of documentation, tutorial, etc. about pairwise sequence alignment for BioJava?

Thanks a lot.

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--
-----------------------------------------------------------------------
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section 
PLOS Computational Biology

BioJava Project Lead
-----------------------------------------------------------------------






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Andrea Battistelli | 21 May 13:09 2016
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Documentation, tutorials and cookbook about pairwise sequence alignment

Hello everyone.

I have been studying the pairwise sequence alignment concept for a project that I need to do for an exam.
In particular I am interested in the global and local alignments and all the things related to them (how they are implemented, how I can generate a paiwise alignment, ect.).
I would implement my project in Java employing indeed BioJava as starting point.
I set up correctly the Maven project on Eclipse so no problem under that point of view.

Few months ago I have seen there was all the documentation, tutorials and specifications about the BioJava project based on the Wiki pages.
I have seen it has been all migrated into a new web site but now I am not finding any documentation, tutorial or cookbook about the topic of personal interest.

- In the BioJavaTutorial page - book 2, the alignment module has no pages of explanation.
- In the CookBook4.0, all the links relative to the paiwise sequence alignment give me back an "address uninterpretable" message.
- Finally in the Wiki Pages section there are many links. In some of these there are links interesting for me but they contain not well formatted codes.

I know that it may taketime to migrate all the things but in the meantime:
Is there any possibility to have the reference to the old web site?
Anyone can help me to indicate me where I can find some good pages of documentation, tutorial, etc. about pairwise sequence alignment for BioJava?

Thanks a lot.
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Rose, Peter | 17 May 22:49 2016

Postdoctoral Fellow Position in Structural Bioinformatics at RCSB PDB/UC San Diego

Summary: We are looking for a talented and highly motivated postdoc to join our multidisciplinary team at UC San Diego.

 

The Challenge: Develop innovate analysis, data integration, query, and visualization tools for 3D biomolecular structures to help accelerate research and training in biology, medicine, and related disciplines. In this project, we will employ the latest advances in computer science to develop highly interactive features and scalable services and workflows for the RCSB PDB website (http://www.rcsb.org).

 

This position is a unique opportunity to engage in leading edge research, development, and outreach activities of the RCSB PDB with worldwide impact.

 

Qualifications: Ph.D. in one or more of the following research areas

·       Structural Bioinformatics, or related field with a focus on software development

·       Structural Biology with a focus on software development

·       Computer Science with a focus on bioinformatics algorithm development or visualization

 

Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Experience with front-end programming languages (JavaScript) and libraries. Strong skills in problem solving and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development of modern web applications, user interface design, or scientific visualization is a plus. Excellent written and oral communication skills.

 

Note, this position is reviewed annually on the basis of performance and can be renewed.

 

Our Environment:

 

The Structural Bioinformatics Group (http://bioinformatics.sdsc.edu) at the San Diego Supercomputer Center (SDSC) (http://www.sdsc.edu) is involved in research and development activities centered around 3D structures of proteins and nucleic acids, the integration of structural data with other domains such as Medicine, Genomics, Biology, Drug Discovery, and the development of scalable solution to Big Data problems in Structural Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) west-coast operations. The RCSB PDB (http://www.rcsb.org) represents the preeminent source of experimentally determined macromolecular structure information for research and teaching in biology, biological chemistry, and medicine. With over 300,000 unique users from over 160 countries around the world, the RCSB PDB is one of the leading worldwide Biological Databases. Our group is also involved in the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

 

As an Organized Research Unit of UC San Diego, SDSC is a world leader in data-intensive computing and cyber infrastructure, providing resources, services, and expertise to the national research community, including industry and academia.

 

To apply, please send cover letter and resume to Dr. Peter Rose (peter.rose <at> rcsb.org).

 

--

Peter Rose, Ph.D.

Site Head, RCSB Protein Data Bank West (http://www.rcsb.org)

Principal Investigator, Structural Bioinformatics Laboratory (http://bioinformatics.sdsc.edu)

San Diego Supercomputer Center (http://www.sdsc.edu)

University of California, San Diego

+1-858-822-5497

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Jose Duarte | 4 May 02:08 2016

BioJava 4.2.1 released

BioJava 4.2.1 has been released and is available using Maven from Maven Central as well as manual download. This is purely a bug fix release correcting issues found since the 4.2.0 release.

Please see the full release notes at:




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!

Jose
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Rose, Peter | 2 May 23:46 2016

Postdoc position: Structural Bioinformatics/Big Data at UC San Diego

Summary: We are looking for a highly motivated postdoc as part of our new project “Compressive Structural Bioinformatics” funded by the US National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

 

The Challenge: To enable efficient research on the rapidly growing number of 3D molecular structures of ever increasing size and complexity. Current algorithms used in Structural Bioinformatics do not scale well with the rapid growth in structural data. In this project, we will employ the latest advances in computer science to develop highly scalable, distributed parallel algorithms to overcome these limitations.

 

Qualifications: Ph.D. in one or more of the following research areas

·      Computer Science with a focus on large scale scientific computing

·      Structural Bioinformatics with a focus on new methods development

·      Computational Structural Biology with a focus on improved structure solution methods

 

Experience with the development and performance optimization of scientific software. Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Strong skills in applied mathematics and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development and application of modern distributed parallel computing environments, such as Apache Big Data projects including Apache Spark is a plus. Excellent interpersonal, written, and oral presentation skills are essential.

 

Note, this position is reviewed annually on the basis of performance and can be renewed for a maximum of two years.

 

Our Environment:

 

The Structural Bioinformatics Group (http://bioinformatics.sdsc.edu) at the San Diego Supercomputer Center (SDSC) (http://www.sdsc.edu) is involved in research and development activities centered around 3D structures of proteins and nucleic acids, the integration of structural data with other domains such as Medicine, Genomics, Biology, Drug Discovery, and the development of scalable solution to Big Data problems in Structural Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) west-coast operations. The RCSB PDB (http://www.rcsb.org) represents the preeminent source of experimentally determined macromolecular structure information for research and teaching in biology, biological chemistry, and medicine. With over 300,000 unique users from over 160 countries around the world, the RCSB PDB is one of the leading worldwide Biological Databases. Our group is involved in the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

 

As an Organized Research Unit of UC San Diego, SDSC is a world leader in data-intensive computing and cyber infrastructure, providing resources, services, and expertise to the national research community, including industry and academia.

 

To apply, please send cover letter and resume to Dr. Peter Rose (pwrose <at> ucsd.edu).

 

--

Peter Rose, Ph.D.

Site Head, RCSB Protein Data Bank West (http://www.rcsb.org)

Principal Investigator, Structural Bioinformatics Laboratory (http://bioinformatics.sdsc.edu)

San Diego Supercomputer Center (http://www.sdsc.edu)

University of California, San Diego

+1-858-822-5497

 

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Andreas Prlic | 9 Apr 21:08 2016
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biojava wiki update

Hi,

The BioJava wiki page at biojava.org went down a few days ago due to a server hack that is still being investigated. In the meanwhile we have switched the homepage 


to the developmental new homepage that is built on top of jekyll and github pages at


I just did another conversion of the mediawiki database to markdown and pushed it there. There is still a lot of cleanup required but I feel that we should move forward and work on making this the new and permanent biojava.org site.

There are still some unsolved problems: e.g. how do we host javadocs and the downloads that we used to provide. Much of the download nowadays happens via maven central, but we still have a few custom files.

Andreas

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Spencer Bliven | 15 Mar 15:58 2016
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BioJava Wiki

I have finished upgrading the BioJava wiki. In an effort to curb spam, users are now required to log in using a Google account. This is more secure for you, since your password is seen only by Google and not by this wiki, and also greatly reduces spam accounts.

If you previously used the email address associated with your google account on this wiki, your account should be automatically connected. If not, a new user will automatically be created based on your email address. If you previously used non-google email with your account and would like to keep the same username, DO NOT log in. Instead, email spencer.bliven <at> gmail.com with your username and google-associated email for manual conversion.

Sorry for the hassle, and please let me know if anything appears broken.


-Spencer

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Gmane