Andreas Prlic | 7 Oct 20:52 2014

The NIH Software Discovery Index | We invite your comments -- a system for linking software, publications and users in the research community.

Greetings Everyone,


On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which will be fully integrated with the software system.

The product of this workshop and the subsequent discussion is a document which details the opportunities and challenges of developing a Software Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challenges, and recommendations detailed in the document reflect the breadth of experience from the community, we are seeking your input.  In conjunction with related efforts already under way at NIH, including the development of a Data Discovery Index, the final document will be used by the NIH Office of the Associate Director (ADDS) to inform a strategy for the development of a Software Discovery Index and a commons ecosystem for data, software, and resources.


We need your help to ensure that this critical task is achieved: to guide the development of a community based system that gives credit and acknowledgment to the builder and maintainers of the software we all depend on! We invite all users, software developers, publishers, and software repository administrators to review our report prior to its submission to the NIH. Please complete your review and post comments by November 1, 2014.


The link to the report is here:


On behalf of the organizing committee, thank you for your assistance!


Organizing Committee


Owen White

Director of Bioinformatics, University of Maryland, Baltimore, School of Medicine

Co-Chair of NIH BD2K  Software Index Workshop


Asif Dhar

Principal & Chief Medical Informatics Officer

Co-Chair of NIH BD2K  Software Index Workshop


Vivien Bonazzi

Senior Advisor for Data Science Technologies (ADDS)

Co-Chair of BD2K Software and Methods Group


Jennifer Couch

Chief, Structural Biology and Molecular Applications Branch

NCI Co-Chair of BD2K Software and Methods Group


Chris Wellington

Program Director (NHGRI)


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Mike Noseworthy | 19 Sep 21:33 2014


Hi there,

I recently started working on a project the uses BioJava 3.0.4 and am encountering a   NoClassDefFound exception when I try to run it. This leads me to believe something is wrong with the classpath. However all the biojava jars are included. Has anyone had a similar problem or have any insight into where I should look next? Are there any other jars that biojava depends on other than the biojava jars from the downloads page. Any help would be greatly appreciated!

Here are the errors:
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
at org.biojava3.alignment.SimpleAlignedSequence.setLocation(
at org.biojava3.alignment.SimpleAlignedSequence.<init>(
at org.biojava3.alignment.SimpleProfile.<init>(
at org.biojava3.alignment.SimpleSequencePair.<init>(
at org.biojava3.alignment.SimpleSequencePair.<init>(
at org.biojava3.alignment.NeedlemanWunsch.setProfile(
at org.biojava3.alignment.template.AbstractMatrixAligner.align(
at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(
at org.biojava3.alignment.FractionalIdentityScorer.align(
at org.biojava3.alignment.FractionalIdentityScorer.getScore(
at Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$ Source)
at Source)
java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
at Source)
at java.util.concurrent.FutureTask.get(Unknown Source)
at org.biojava3.alignment.Alignments.getListFromFutures(
at org.biojava3.alignment.Alignments.runPairwiseScorers(
at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(
at externalcalcs.BLASTRunner.writeBlast(
at externalcalcs.Conservation.runConservation(
at externalcalcs.ExternalCalculations.runExternalCalcs(
at runtime.PACE.externalCalcs(
at runtime.PACE.main(


Michael Noseworthy
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Michael Heuer | 3 Sep 04:11 2014

BioJava Legacy 1.9.1 released

== BioJava Legacy 1.9.1 released ==

BioJava Legacy 1.9.1 was released on September 2nd 2014 and is
available from as well
as from the Maven Central repository.

To use BioJava Legacy in your Maven-based JVM project, just include
module dependencies such as


and you are ready to go.  For a list of modules, see

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>

Spencer Bliven | 26 Aug 11:45 2014

New Release of BioJava 3.1.0

== BioJava 3.1.0 released ==

BioJava 3.1.0 was released on August 25th 2014 and is available from as well as from the
BioJava maven repository at

While most development is going towards the upcoming 4.0.0 release, this release provides bug fixes and a few new features:

* CE-CP version 1.4, with additional parameters
* Update to SCOPe 2.04
* Improvements in FASTQ parsing
* Fix bugs in PDB parsing
* Minor fixes in structure alignments

For a detailed comparison see here:

This version is compatible with Java 6 and 7. If you're using Java 8, please use the latest snapshot build. Snapshots are now available from Maven central just by setting your pom.xml file to version '4.0.0-SNAPSHOT'!

Thanks to the contributors who submitted code to this release–heuermh, Elinow, Siarhei, sbliven and andreasprlic–and to those who contributed to the 4.0.0 branch!

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


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Francesco Strozzi | 30 Jul 10:46 2014

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:
If you plan to attend, please use the link in the registration section
and complete the simple steps on the EBI website, so that
we can be aware of the total number of attendees and arrange the
organisation accordingly. Registration is also completely free.

We will be grateful if you could also share this announce over your
network and social media, this will help spreading the word.

Thanks and we hope to see many of you in September!

Francesco Strozzi
James Malone
Raoul Bonnal
Pjotr Prins
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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
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 ( 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 (

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

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

Biojava-l mailing list  -  Biojava-l <at>
Michael Heuer | 1 Jul 18:43 2014

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 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


and you are ready to go.  For a list of modules, see

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>

Michael Heuer | 17 Jun 20:56 2014

biojava-legacy version 1.9.0-rc1 release candidate on Maven Central


As described in issues here

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

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.

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Detlef Boehm | 10 Jun 00:20 2014

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

I used maven in Eclipse IDE for Java Developers  Version: Kepler Service 
Release 2 Build id: 20140224-0627
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
using the Chromatogram and  ChromatogramFactory classes

using the ABITrace class.

both packages and classes are described in the API.

What is going wrong ? Any idea and help.

Many thanks

<project xmlns="" 
                     <source />
                     <target />
             <name>BioJava repository</name>

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Andreas Prlic | 13 May 21:36 2014

CFP: 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2)

2nd Workshop on Sustainable Software for Science: Practice and Experiences
(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 (
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
• impact of computer science research on the development of scientific
• 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
• 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
• 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 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<>

Once you have received an identifier for your self-published paper from a
repository, submit it to WSSSPE2 by creating a new submission at, and entering:

• author information for all authors
• title
• abstract (with the identifier as the first line of the abstract, for
example, or 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

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


• Daniel S. Katz, d.katz <at>, National Science Foundation, USA
• Gabrielle Allen, gdallen <at>, University of Illinois
Urbana-Champaign, USA
• Neil Chue Hong, N.ChueHong <at>, Software Sustainability
Institute, University of Edinburgh, UK
• Karen Cranston, karen.cranston <at>, National Evolutionary
Synthesis Center (NESCent), USA
• Manish Parashar, parashar <at>, Rutgers University, USA
• David Proctor, djproctor <at>, National Science Foundation, USA
• Matthew Turk, matthewturk <at>, Columbia University, USA
• Colin C. Venters, colin.venters <at>, University of
Huddersfield, UK
• Nancy Wilkins-Diehr, wilkinsn <at>, 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

Biojava-l mailing list  -  Biojava-l <at>
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<>consist mostly of
very technical bugs best fixed by the developer who wrote
the code, and the wiki
page<>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.


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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