PLoS E-Newsletter for Institutional Members

February 9, 2006

Table of Contents

A Society and an OA Journal ISCB and PLoS Computational Biology: A Perfect Match

The International Society for Computational Biology 10th Anniversary: Our First Ten Years

  • Lawrence Hunter, ISCB Founder and President 1997 – 2000
  • Russ B. Altman, ISCB President 2000-2001
  • Philip E. Bourne, ISCB President 2002-2003 and Editor in Chief of PLoS CB

PLoS Computational Biology is the official journal of the International Society for Computational Biology (ISCB), a partnership that was formed during the journal’s conception in 2005. As the only international body representing computational biologists, it made perfect sense for PLoS Computational Biology to be so closely affiliated with ISCB. The Society had to take more of a chance, stepping away from an existing financially beneficial subscription journal in order to align with an open access publication as a matter of principle. ISCB was the first major international scientific society to do so.

Now, as PLoS Computational Biology approaches its two year mark, ISCB is preparing to celebrate its tenth anniversary, having formed officially on June 18, 1997. We early presidents of ISCB reflect on the state of computational biology ten years ago, and how far we have come since.

The State of Computational Biology at the Founding of ISCB

It’s hard to imagine how much the computational bioscience world has changed in just 10 years. In 1996, there was no journal that had the word “bioinformatics" in its name, GenBank contained fewer than 200,000 DNA sequences (core genomic DNA/RNA, excluding mitochondria, ESTs, etc.), and NIH had yet to fund any institutional training programs in bioinformatics or computational biology. By 1996, however, high throughput molecular biology and the attendant need for informatics had clearly arrived. In addition to the founding of ISCB, 1996 saw the sequencing of the first genome of a free-living organism (yeast), and Affymetrix’s release its first commercial DNA chip.

The hot topics in bioinformatics circa 1996, at least as reflected by the conference on Intelligent Systems for Molecular Biology (ISMB) at Washington University St. Louis, included issues which have largely been solved (such as gene finding or sequence assembly), as well as ones which have proven richer than all expectations (such as ontological foundations for knowledge models). Although not yet as global as the current society, attendees in 1996 came from Canada, Denmark, Germany, Japan, the United Kingdom and the United States of America. ISMB ’96 attendees also included all of the presidents of the ISCB so far.

By the time the Society was founded, bioinformatics was gaining notice in the broader scientific community. In June of 1996 Science published a News and Comment piece entitled “Hot Property: Biologists Who Compute" suggesting that competition among drug companies and other industrial concerns for the relatively few people skilled in bioinformatics was so intense that universities would not be able to attract enough faculty to teach the field to new students. While perhaps not quite as dire as all that, in 1996 there were fewer than half a dozen training programs that offered Ph.D.’s in bioinformatics or computational biology.

ISCB Conferences: Join the Leaders in Your Field

More than most scientific societies, ISCB is closely tied to its conferences. A significant part of the original motivation for founding the Society was to provide a stable financial home for the ISMB conference. The first few conferences were sufficiently successful to create a financial nest egg that was used each year to start the process of planning and executing the next year's meeting. Initially, relatively modest checks were cut and sent from one organizer to another informally. As the size of these checks increased, the organizers (and their home institutions) became increasingly uncomfortable exchanging them informally, and decided that they needed an organization–thus the ISCB.

The basic rules and goals for ISCB were hashed out in an unforgettable late-night dinner on the beaches of Halkidiki, Greece, at ISMB 1997. Not surprisingly, the idea of an organization brought much more than the convenience of a bank account for the conferences. There were formative discussions about advocacy, education, travel support, and other activities. However, the role of conferences remained central. It was clear that the ISMB meeting was the primary "product" of the new society. That dinner also paved the way for the current relationship between ISCB and two of the other premier meetings in computational biology: RECOMB and PSB, many of whose organizers were present on that Greek beach.

In subsequent years, the society has formed alliances with other conferences as well, most notably the European Conference on Computational Biology (ECCB). When ISMB is held in Europe, as it will be this summer, ISMB and ECCB are held jointly. More recently, the ISCB has begun supporting smaller regional or specialty meetings such as the Rocky Mountain Regional Meeting on Informatics.

Merging the conference cultures of molecular biology (where conferences provide an unpublished way to share recent research results and speakers are largely invited) and computer science (where conferences are the primary publication venue for new results, and speaking slots are based on peer-reviewed submissions) has not always been easy. Today’s meetings are a remarkable blend that offer a snapshot of the latest, most important results, are published in Medline-indexed proceedings, and balance invited and reviewed talks.

This really makes perfect sense–bioinformatics and computational biology are fundamentally collaborative, interdisciplinary fields where high-bandwidth two-way communication is critical. Of course such a group of scientists would base their professional society on opportunities to meet in person, interact, tutor and present work! Our financial dependence on meetings is also rational in the face of our relationship to PLoS. To rest primarily on income from journals, as most scientific societies do these days, appears to trade short-term windfalls for long-term uncertainty, not to mention failing to address the important issues of open access and dissemination. To rest our Society’s finances more on the health of its meetings may turn out to be a more robust strategy. When funding is good, the meetings flourish and attract many newcomers and the curious, allowing us to build a nest-egg. Even when times are hard, meetings provide a critical lifeline for essential scientific communication, and are hard for practicing scientists to skip. A high quality meeting is much more likely to yield value to the individual scientist in terms of ideas, scouting the competition and offering collaborative opportunities, than a personal journal subscription.

ISCB’s conference strategy also aims at creating a truly global community for bioinformatics and computational biology. ISCB conference venues have included not only North American and European sites, but also Hawaii, Australia, Japan, and most recently Brazil. The policies of moving the conference around the world in a regular, judicious manner have allowed the field to promote its importance and vitality in multiple venues. There is sometimes a cost in terms of total attendance figures. These must certainly be strategically considered in light of our financial dependence on meetings, but the benefits of engaging new regions and new groups of scientists are quite significant.

Finally, the ISCB conferences play an important role with respect to publication. More than any other biological meeting, ISCB conference proceedings are an important part of the archival literature in bioinformatics and computational biology. These proceedings are peer- reviewed at a level rivaling some journals, and some are indexed in Medline and PubMED. References to these often seminal papers often appear in more traditional archival journals, and this should be a point of pride. Our conferences are previewing work that is of high and lasting impact. PLoS Computational Biology contains several examples of work that was first presented at an ISCB conference, and then published in expanded form in the journal. PLoS is also experimenting with the publication (in revised form) of tutorials presented at the meetings as well. This is a two-way relationship: the PLoS track at ISMB facilitates presentation of some of the most important work published in the journal in the previous year. We believe that the unique relationships among the Society, its conference and PLoS Computational Biology are an important strength for all of us, and invite you to ISMB ’07 in Vienna to see this synergy first hand.

ISCB and PLoS Computational Biology: Leaders in Open Access Publishing

ISCB has changed a great deal in the ten years since it began – but so has scientific publishing. Societies and journals are often intimately linked, such as the Journal of the American Chemical Society, although of course there are both societies and journals without such links. The current relationship between ISCB and the Public Library of Science through PLoS Computational Biology journal falls somewhere in the middle. Both ISCB and PLoS exist as separate organizations and formed a partnership through a letter of agreement. In reality this means each disseminating the work done by the other. It would be easy to stop there, but the relationship is much more than that. With such a partnership the journal becomes a collective voice for the scientific community it represents. PLoS Computational Biology should represent the best work and interests of ISCB members.

The need for a relationship between ISCB and journals was recognized early. In 1998 Russ Altman forged a relationship between the Oxford University Press (OUP) establishing the journal Bioinformatics as the official journal of ISCB. This was very valuable for increasing the visibility of both a fledgling society and a fledgling journal as well as having financial incentives. The majority cost of being a member of ISCB went to OUP in return for a subscription to Bioinformatics; royalties went back to ISCB based on overall journal subscription sales. A publications committee was established in 2000 to oversee these activities.

In 2004, when this contract was up for renewal, a very bold initiative was undertaken. With much heated debate, and with a narrow margin, the ISCB Board of Directors chose PLoS Computational Biology as the official journal of ISCB. Why the controversy? PLoS is an open access publisher and is not likely to provide such large profit margins as a subscription-based publisher and so the society is likely to benefit less financially from the arrangement. There is no income to ISCB other than one PLoS sponsored membership for each published research article, and authors must pay to publish their work, although they can request a fee waiver if they don’t have access to sufficient funds. The good news is that funding agencies are helping to provide funds to cover open access publishing fees and most important of all anyone can read a paper for free and reuse it without restriction. One could think of this as ISCB underwriting part of the cost of disseminating our science to the broadest audience.

We former presidents (including PEB, now the Editor in Chief of PLoS Computational Biology) believe that it is incumbent on the Society to be an “early adopter", particularly of computational technologies that have the potential to transform the conduct of our science. The Society has long supported Open Source approaches to distribution of scientifically significant computer code (leaving room for other means as well), and the Board of Directors felt that Open Access was similarly important to our field, despite the financial cost to this far-from-wealthy scientific society.

Being the first among the very first scientific societies to officially adopt an open access journal was a bold move. Ten years hence, it will be fascinating to look back and see what came of this experiment, how the Society weathers the financial storms of middle age, and whether other societies have followed our lead.

The world of scientific publishing will continue on its path of radical change, driven in part by developments in information technology. The members of ISCB are makers and users of those developments and PLoS is a dynamic organization willing to work with those making change. What can we do together?

Here is a challenge to future ISCB presidents: Journals are becoming more like databases and databases are becoming more like journals; can we not capitalize on that to further scientific comprehension? How a paper’s impact is measured (in the future perhaps as a knowledge blob in cyberspace) is changing. Beyond traditional citations, downloads are becoming important, as is how collaborative the work is. How can we capitalize on this to further highlight the work of Society members? Then there is the content as a subject of scientific study. ISCB includes members who are experts in ontologies, semantic content, data and literature mining; how can these technologies be applied to our own journal to make it more valuable to scientists? Can we bring further recognition to the journal and ISCB as leaders of innovation in scientific publishing? ISCB has the expertise and the motivation to make this happen, so stay tuned.

PLoS Update and Information

PLoS Neglected Tropical Diseases Call for Papers. Submit your work today.

Read our guidelines for authors, send us your questions, and submit your papers.

The 2007 launch of PLoS Neglected Tropical Diseases is supported by a grant from the Bill and Melinda Gates Foundation.

PLoS ONE Launch Stats!

  • PLoS ONE launched with over 100 research articles
  • Over 100 submissions per month
  • Over 3000 unique visitors per day in January

Couldn’t Make it to a PLoS Editors Presentation? Look and Listen Online!

PLoS/BMC/SPARC/Science Commons presentation on-line and podcast

NetSquared: Podcast of Open Access and PLoS ONE

Listen to the NetSquared Podcast Interviews with Barbara Cohen, Executive Editor, and Richard Cave, IT Director for PLoS. Barbara and Richard describe the "open access" movement to publish scientific papers using the low cost platform of the web so that scientific information can be made accessible worldwide at a fraction of the price of current journal publishing. They discuss how PLoS continues to make headway and recently launched PLoS ONE, a transformative platform for science publishing with the breakthrough idea of "community involvement."

Open Access News and Resources

Another landmark open access development was announced yesterday in the UK–UK PubMed Central (UKPMC) has been launched.

One of the very encouraging aspects is that the funding agencies have either mandated, or are considering mandating, deposition of the articles that arise from the research that they fund into UKPMC within six months of publication. This means that the vast majority of medical research literature funded by UK agencies will be open access

Students Rally for Access to Publicly Funded Research

Campuses declare "National Day of Action" in support of federal legislation

Freeculture.org, the international student movement for free culture, in collaboration with the Alliance for Taxpayer Access (ATA), today announced that February 15, 2007 will be a "National Day of Action" for students that support open sharing of scientific and scholarly research findings on the Internet. Events nationwide will highlight the importance of taxpayer access to publicly funded research and rally support for Congressional passage of the Federal Research Public Access Act. The day also marks the fifth anniversary of the landmark Budapest Open Access Initiative, when the worldwide open access movement first took form, and will be supported by the launch of a new Web resource and petition for public access, produced jointly by freeculture.org and the ATA.

Campuses nationwide will be announcing individual events and support for the National Day of Action in the coming weeks. For more information, please visit the freeculture.org–Alliance for Taxpayer Access student resource

Open Access to Research is in the Public Interest: Read the Editorial in the February 13 Issue of PLoS Biology

Bevin P. Engelward, Associate Professor of Molecular Toxicology, Massachusetts Institute of Technology and Richard J. Roberts, Chief Scientific Officer for New England Biolabs , a 1993 Nobel Prizewinner for Physiology or Medicine.

Keep Informed on OA Issues: PLoS Journal Sites Makes it Easy

Look for the OA icons on the PLoS Journal sites to provide you with updated information on Action Alerts, Links to OA News, and OA Blogs, etc.

PLoS Out and About

May 18-23, 2007, Philadelphia, Pennsylvania
Medical Library Association Annual Meeting

May 21-25, 2007, Toronto, Canada
American Society for Microbiology General Meeting

July 21-25, 2007, Vienna, Austria
15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB)

ISMB/ECCB will feature the PLoS Track of oral presentations of work of exceptional scientific merit focusing on the application of computational methods to solve problems of biological significance. Call for abstracts opened December 1, 2006; deadline for submission is April 6, 2007.

October 23-27 2007, San Diego, California
American Society for Human Genetics Annual Meeting

November 4-8 2007, Philadelphia, Pennsylvania
American society for Tropical Medicine and Hygiene Annual Meeting

Feedback or comments?

We would love to hear from our Members! Contact Donna Okubo, Institutional Relations Manager at dokubo@plos.org

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