{ C O N T E N T S }
Volume 11, Issue 1

President’s Letter

SCS4 Highlights

ISCB Honors
David Haussler
& Aviv Regev

The ISMB Organization
& Future Vision

PLoS Computational Biology Overview

11th Israeli Bioinformatics
Symposium Report

Taking a Stand on Software Sharing

ISCB Members Speak Out on US Entry Visa Issues

ISCB’s New Software
Sharing Statement


ISCB Student Council

Post Your Events with ISCB

MentorNet Report Card: Year Two

Calling all Leaders!

Become an ISMB Reporter

In Memory of
Kamalakar-Rao Mettani

FASEB Update

Rocky ‘08

Key Dates for Key Conferences

Conferences & Events

Cover Image




Copyright © 2008
International Society for
Computational Biology.
All rights reserved.


Taking a Stand on Software Sharing

The ISCB board of directors recently released a new statement about software sharing as the Society’s formal position on this topic of tremendous importance to our scientific community. The ISCB Software Sharing Statement (see below) replaces the previously released ISCB Statement on Bioinformatics Software Availability from 2002 (www.iscb.org/policy _statements2002May21.htm).

Evaluation of the previous statement got underway over 18 months ago among subsets of the ISCB public affairs & policies committee, ISCB executive committee, Public Library of Science board of directors and thought leaders from the open source community. A meeting at ISMB/ECCB 2007 in Vienna presented several viewpoints through a panel discussion that included audience comments and questions answered by the panelists. That meeting was preceded and followed up by ISCB blogs that encouraged a worldwide audience to express their opinions. All of these activities were organized by then ISCB board member and public affairs & policies committee chair, Barbara Bryant, who also collected the input and feedback and wrote the first draft of a revised statement, which went through committee review and redraft before presentation to the ISCB board. A statement agreed upon by the board was then offered for a public comment period through the ISCB blog, (see http://iscbdiscussion.blogspot.com/2008/03/iscb-member-feedback-sought-on-revised.html) and those comments were considered in a final revision that became the board approved statement for public release.

ISCB’s reevaluation of this topic prompted the Society’s official journal, PLoS Computational Biology, to do the same. The initial result is an editorial published in this month’s issue (www.ploscompbiol.org/doi/pcbi.1000136) on the post-publication difficulties and frustrations experienced due to non availability of software and web servers essential to reproducing results of research articles. Plans for a full length follow up article are also in the works.

At ISMB 2008 in Toronto David States, ISCB Public Affairs & Policies Committee Chair, will moderate a session entitled “Effective Implementation of Software Sharing” to include talks and a panel of experts to take audience questions and engage in discussion on implementing ISCB’s new statement. All conference attendees are invited to attend, and more news will follow on the ISCB website for those wishing to get involved in the months ahead.

ISCB Software Sharing Statement
Approved by the ISCB board of Directors on June 12, 2008

I. Introduction

Bioinformatics software availability is extremely important to the field of bioinformatics. The International Society for Computational Biology (ISCB) is committed to the advancement of the understanding of living systems through computation. In support of that mission, we believe that research results should be shared with the scientific community so that they can be reproduced and built upon. Scientific research may include the development of software and algorithms. Therefore, ISCB is disseminating this statement to make recommendations on software availability policies for funders of bioinformatics research, for scientific journals that publish bioinformatics research, for bioinformatics researchers, and for their employers.

This statement has been revised from the original 2002 statement, incorporating feedback from the ISCB membership.

II. Recommendations

1. Publishers, granting organizations, employers and researchers have a responsibility to uphold the core principle of sharing methods and results. If a researcher's software is necessary to understand, reproduce and build on scientific results, then the software should be made available. This principle is imperative for peer-reviewed scientific publications, recommended policy for granting agencies, and encouraged practice wherever individuals and organizations are committed to advancing science. ISCB supports the recommendations of the National Academies of Sciences report, "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences."

2. Grantors and publishers should require statements of software availability in grant proposals and research reports. These statements should clearly describe how to obtain the software, and terms of use. The statements should be specific about cost, source code availability, redistribution rights (including for derived works), user support, and any discrimination among user types.  The nature of software distribution is an appropriate criterion for consideration in the review of manuscripts and grant proposals, to assess the significance and impact the work is likely to have.  Authors of statements of availability should be held accountable by journals, granting agencies and employers for delivering on their software's promised availability.  The rights granted to the software user should be irrevocable.

3. No single licensing or distribution model is appropriate for all research projects, and therefore no single model should be mandated by either publishers or grantors.

4. Individuals, institutions, and businesses engaged in research in computational biology should recognize the primacy of dissemination and further research and choose licenses accordingly.

III. Implementation when software sharing is warranted

1. In most cases, it is preferable to make source code available. We recommend that executable versions of the software should be made available for research use.

2. Open source licenses are one effective way to share software. For more information, see the definition of open source, and example licenses, at www.opensource.org.