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2014 ISCB Fellows Keynote

Russ B. Altman, MD, PhD

Professor of Bioengineering, Genetics, and Medicine and Computer Science

Director, Biomedical Informatics Training Program
Stanford University, United States

website: http://helix-web.stanford.edu/people/altman/

Presentation Title: Informatics for understanding drug response at all scales

Presentation Time: Tuesday July 15, 4:40 pm - 5:40 pm

Introduction by: Reinhard Schneider, ISCB Treasurer

Abstract:

An understanding of drug action at multiple levels is required for optimal use of existing drugs, as well as for identifying new opportunities for therapeutics. Unlike many experimental programs, informatics programs for drug action can integrate data of length scales across length scales spanning more than 6 orders of magnitude: from molecular to global populations. In this talk, I will discuss how we have developed methods at the molecular, cellular, individual organism and population to understand drug response phenotypes, and the underlying molecular mechanism of these responses. This information can be used for understanding personalized medicine (pharmacogenomics), drug interactions, drug repurposing and druggability of orphan genes.

Biography
Russ Biagio Altman is a professor of bioengineering, genetics, & medicine (and of computer science, by courtesy) and past chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing and informatics technologies to basic biological problems relevant to medicine. He is particularly interested in methods for understanding drug action at molecular, cellular, organism and population levels. His lab studies how human genetic variation impacts drug response (e.g. http://www.pharmgkb.org/). Other work focuses on the analysis of biological molecules to understand the action, interaction and adverse events of drugs (http://features.stanford.edu/). He leads one of seven NIH-supported National Centers for Biomedical Computation, focusing on physics-based simulation of biological structures (http://simbios.stanford.edu/). Dr. Altman holds an A.B. from Harvard College, and M.D. from Stanford Medical School, and a Ph.D. in Medical Information Sciences from Stanford. He received the U.S. Presidential Early Career Award for Scientists and Engineers and a National Science Foundation CAREER Award. He is a fellow of the American College of Physicians, the American College of Medical Informatics, and the American Institute of Medical and Biological Engineering. He is a member of the Institute of Medicine of the National Academies. He is a past-president, founding board member, and a Fellow of the International Society for Computational Biology, and the President-Elect of the American Society for Clinical Pharmacology & Therapeutics. He currently chairs the Science Board advising the FDA Commissioner. He is an organizer of the annual Pacific Symposium on Biocomputing (http://psb.stanford.edu/), and a founder of Personalis, Inc. He won the Stanford Medical School graduate teaching award in 2000.

ISCB 2008 Accomplishments Report
January – June 2008
Download the PDF version here.

The International Society for Computational Biology is an individual membership organization that provides services and benefits to the bioinformatics and computational biology communities. In the first half of 2008 ISCB has counted 2,449 scientists and students among our membership – 55% are Professional Members, 11% are Post Docs and 34% are Students.The following summarizes the activities and accomplishments of the ISCB through its various committees, elected leadership and staff. All initiatives of the Society are undertaken by volunteer members, and therefore ISCB gratefully acknowledges these accomplishments and thanks those named and the many more not named in this report for their selfless contributions to helping ISCB advance the science of computational biology worldwide. The initiatives of the member volunteers are supported by the ISCB staff consisting of a full time Executive Officer, two part time staff providing administrative support and database programming, two contractors on retainer to direct the conference planning logistics and serve as webmaster, and three subcontractors dedicated to the ISMB conference website, graphic design/marketing and administrative support

.MAJOR ACCOMPLISHMENTS

ISCB-ECCB Agreement for Future Joint Meetings – The ISCB Board of Directors and Steering Committee of the European Conference on Computational Biology agreed to a long term plan to join ECCB and ISMB every other year when the Society’s ISMB meeting is held in Europe.

The agreement specifies shared responsibility for the scientific and logistical organization, and defines the financial responsibilities and profit sharing plan.
In the case of conference profits, the agreement ensures that each organization will receive an appropriate portion of the proceeds to sustain their own financial stability.
Thanks to ISCB President Burkhard Rost and ECCB Steering Committee Chair Michal Linial for their commitment to strengthening the relationship between the organizations in the spirit of amplifying the success of the joint meetings.

ISMB/ECCB 2007 Chairs Named – Motion presented by Executive Committee and approved by the Board of Directors to appoint the following as conference chairs for next year:

Gunnar von Heijne of the University of Stockholm, Sweden, to serve as Honorary Chair
Gene Myers of HHMI Janelia Farm Campus, USA, to serve as Conference Co-Chair
Marie-France Sagot of INRIA Grenoble-Rhône Alps Research Centre, France, to serve as Conference Co-Chair

ISMB Organizational Structure – Document created detailing the structure and organization of the annual ISMB conference and joint ISMB/ECCB when held together.

ISMB 2008 Conference Chair and ISCB President Burkhard Rost wrote first draft based on the major expansion of the conference first introduced at the 2007 joint ISMB/ECCB.
Members of ISMB 2008 steering committee, including ECCB steering committee chair Michal Linial, provided input and feedback toward final document.
Document now serves to provide current and future organizers of ISMB and ISMB/ECCB with a roadmap, and will be updated annually with the previous version retained for institutional memory.

ISCB Software Sharing Statement – The Board of Directors approved a new Software Sharing Statement for public release to replace the statement previously released in May 2002.

The Public Affairs & Policies Committee gathered input during a year long process of discussion within the committee, with external proponents of open source, and through a community blog to determine recommended access guidelines and draft the new statement for board approval.

Thanks to past committee chair Barbara Bryant along with the members of the committee and all other contributors for the tireless and sometimes trying efforts to draft a statement that encompasses the ISCB spirit of sharing software for the benefit of computation biology.

Commitment to Start an ISCB Reserves Fund – Motion presented by Treasurer David Rocke and approved by the Board of Directors to set aside 20,000 USD annually in a reserves fund.

Best practices in association management suggest a minimum of six months to a year of basic operating costs be held in reserve to provide a cushion in the event of lower than necessary income
ISCB has never had a specific reserves fund and therefore the board felt it prudent to establish such a fund and gradually grow it to the recommended level.

C-SHALS Meeting – The Conference on Semantics in Healthcare and Life Sciences in Cambridge, MA, USA, was held in March 2008 as the first new meeting of the Society in over five years.

Two-day conference was attended by 67 scientists
Four keynotes and 14 invited speakers made up the oral presentations which were augmented by planned discussion sessions.
Half-day tutorial organized by the World Wide Web Consortium (W3C) preceded the conference with 25 attendees.
The conference was financially successful thanks to sponsorships by Pfizer, Merck & Co. and IO Informatics, and discussions are beginning on the possibility of C-SHALS 2009.
Thank you to Eric Neumann, Sanjoy Ray and Ted Slater who developed the concept for the conference and served as Conference Co-chairs.

Annual ISCB Awards – Selected by the Awards Committee and approved by the Executive Committee; both award winners will deliver keynote talks at ISMB 2008 in Toronto in July.

David Haussler of University of California Santa Cruz has been named as the ISCB 2008 Accomplishment by a Senior Scientist Award winner.
Aviv Regev of the Broad Institute of MIT and Harvard was named as the ISCB 2008 Overton Prize winner.
Thank you to Søren Brunak, Awards Committee Chair, and the members of the committee for the diligence in reviewing the nominations received and selecting the ultimate winners of the ISCB’s most prestigious awards of recognition.

COMMITTEE ACCOMPLISHMENTS

The committees of ISCB are made up of members volunteering their time and expertise to a particular area of interest or an important function of the Society and the membership-at-large. The following summarizes the accomplishments of ISCB committees during the first half of 2008.Affiliates & SIGs Committee - Tan Tin Wee, Chair

The Finnish Society for Bioinformatics was approved by the committee as a new ISCB Affiliated Regional Group.

Awards Committee - Søren Brunak, Chair

Aviv Regev (Broad Institute) was selected for the ISCB 2008 Overton Prize.
David Haussler (University of California, Santa Cruz) was selected for the ISCB 2008 Accomplishment by a Sr. Scientist Award.

Conferences Committee - Janet Kelso, Chair

Proceeds from ISMB/ECCB 2007 contributed 20,000 USD in seed funds to ECCB 2008 and 166,000 USD in seed funds to ISMB 2008.
Proceeds from Rocky ’07 and C-SHALS 2008 contributed a combined 30,650 USD to ISCB to help fund the operation of the Society and provide seed funds for future conferences.
Stockholm was approved as the site of ISMB/ECCB 2009.
Boston was approved as the site of ISMB 2010.

Three officially affiliated conferences to ISCB were held as follows:
- PSB, January 2008, Hawaii, USA
- AMIA Conference on Translational Medicine, March 2008, San Francisco, USA
- RECOMB, March 2008, Singapore

Education Committee – Bruno Gaeta, Chair; Fran Lewitter, Co-chair

After two years in the position, Kevin Karplus stepped down as Chair of this committee in June 2008, enabling his vice chair to rise to the position of committee chair.
Renewed the MentorNet E-Mentoring Network Membership for a 3^rd Year

Finance Committee – Jean-Francois Tomb, Chair

A six month plan was drafted by Dr. Tomb outlining the steps toward establishment of an endowment fund campaign.
All ISCB committees were polled for funding needs as the first step in the endowment fund campaign.

Nominations Committee - Dietlind Gerloff, Chair

Gained board approval to adopt as the standard timeline and procedure for nominations and elections of board member, officers and student council representatives.

Public Affairs & Policies Committee – David States, Chair; John Wooley, Co-chair

After four years in the position Barbara Bryant stepped down as Chair of this committee and nominated committee member David States to replace her.
Gained approval from the Board of Directors of a new ISCB Statement on Software Sharing to replace the 2002 statement of the board.
ISCB renewed its membership in the Federation of American Societies for Experimental Biology (FASEB).
- Jean-Francois Tomb attended the annual Finance Committee meeting as ISCB’s representative to this committee.
- Scott Markel attended the annual Publications & Communications Committee meeting as ISCB’s representative to this committee.
- BJ Morrison McKay attended the annual June FASEB Board Meetings in Bethesda, Maryland, as a member of the Executive Officers Advisory Committee (EOAC), and the monthly EOAC teleconferences.
- John Wooley attended the monthly FASEB Board teleconferences as ISCB’s voting representative to the FASEB Board of Directors.
Surveyed ISCB members on the challenges and issues of securing a visa for entry into the U.S.
- Provided our member’s feedback stories to FASEB inclusion in testimony at the U.S. House of Representatives Science Committee about scientists' problems with visas in February 2008.
- The survey and its results were mentioned in an editorial about the negative impact of visa issues published in PLoS Computational Biology in June 2008.

Publications Committee – Scott Markel, Jill Mesirov and David Rocke, Co-Chairs

Negotiations with Oxford University Press to reinstate “official journal” status to Bioinformatics journal have led to the ISCB Board of Directors approval of the financial arrangements and an expectation that a full contract will be ready for signature by July.
A survey has been designed for release in the 3^rd Quarter to help ISCB understand the uses and preferences among our members of open access and traditional subscription model journals.
A task force was formed to investigate ISCB publishing its own journal(s).
An article detailing the new and exciting features of ISMB 2008 in Toronto was published in the ISCB pages of PLoS Computational Biology.

NEW TASK FORCES TARGETED TOWARD KEY NEED AREASThe executive committee identified eight areas of need for ISCB and several members of the board of directors have agreed to lead task forces to establish strategies and action plans for addressing them. Terry Gaasterland and BJ Morrison McKay will be working with the leaders to help refine and implement those strategies and action plans.Task Force Areas and Leaders:

Increasing ISCB membership - Nir Ben-Tal and Hannah Xue
Defining an ISCB Fellows program fellowship - Patricia Babbitt and Mona Singh
Fundraising with emphasis on corporate support - Scott Markel and Harel Weinstein
Financial strategies and building a reserve fund - Harel Weinstein and Patricia Babbitt
Filling the web portal with useful information - Olga Troyanskaya and Nir Ben-Tal
Recruiting affiliates - Fran Lewitter and Bruno Gaeta
Solidifying a role for ISMB Special Interest Groups in ISCB - Mona Singh and Fran Lewitter
Developing stronger Asian ties and an ISCB-North Asia meeting - Hannah Xue and Bruno Gaeta

MEMBER BENEFITS OFFERED IN THE FIRST HALF OF 2008Each year ISCB leaders and staff work on behalf of all members to ensure an array of relevant and tangible benefits are offered. In addition to the discounted journal subscription benefits that have been in place for several years, the following additional benefits were also offered during the first half of 2008:Conference Registration Discounts Secured Exclusively for ISCB Members

75 USD discount to attend PSB-Pacific Symposium on Biocomputing, The Big Island of Hawaii, USA, January 2008
100 SGD discount to attend RECOMB-Conference on Research in Computational Molecular Biology, Singapore, March 2008
10% discount to attend Cambridge Healthtech Institute conferences:
- BioIT World Conference & Exhibition, Boston, MA, USA, April 2008
- Beyond Genome Conference, San Francisco, CA, USA, June 2008

Travel Fellowships from ISCB Funds Awarded to ISCB Student and Post Doc Members

PSB-Pacific Symposium on Biocomputing, The Big Island of Hawaii, USA, January 2008
- 5,000 USD distributed among five paper and/or poster presenters
RECOMB-Conference on Research in Computational Molecular Biology, Singapore, March 2008
5,000 USD distributed among ten paper and/or poster presenters

SOCIETY MARKETING & PROMOTIONAL ACTIVITIES

ISCB leaders and staff members participate at varying levels in several affiliated and co-sponsored bioinformatics-related conferences throughout the year in order to show support of these conferences and promote ISCB membership to prospective attendees. Additionally, e-mailings throughout the year provide news and information to ISCB members and prospects about these conferences and other matters of interest to our community. Below is a list of conferences where ISCB had a specific presence, as well as our direct mail/email marketing activities during the first half of 2008.

ISCB presentations and conference exhibition presence

PSB-Pacific Symposium on Biocomputing, The Big Island of Hawaii, USA, January 2008
- Larry Hunter, ISCB Founder, held an open members meeting where he reported on the leadership structure, 2007 activities and preliminary year-end financial status of ISCB and made a promotional presentation on ISMB 2008.
- BJ Morrison McKay, ISCB Executive Officer, represented the Society with an ISCB display in the poster hall, and presence during the conference at the PSB registration and information desk.
- Society brochures and information were inserted in the delegate bags.

RECOMB-Conference on Research in Computational Molecular Biology, Singapore, March 2008

Terry Gaasterland, ISCB Vice President, made an presentation during the open business meeting where she reported on the leadership structure, 2007/2008 activities including upcoming conferences, and financial status of ISCB
BJ Morrison McKay represented the Society with a booth in the exhibition area.
ISCB brochure and ISMB 2008 poster were inserted in the delegate bags.

CHI’s BioIT World Conference & Exhibition, Boston, MA, USA, April 2008

BJ Morrison McKay represented the Society with a booth in the exhibition area.
ISCB brochure and ISMB 2008 poster were included on the literature table.

CHI’s Beyond Genome Conference, San Francisco, CA, USA, June 2008

BJ Morrison McKay represented the Society with a booth in the exhibition area.
ISCB brochure and ISMB 2008 poster were included on the literature table.

Mailings to Members and Colleagues

ISMB 2008 poster mailed to over 5,000 members of the bioinformatics and computational biology community
14 separate ISCB announcements and conference updates distributed to over 12,000 scientists on ISCB mailing lists via email campaign.

ELECTED LEADERSHIP

ISCB is governed by the leadership of 27 Board Members, including five Officers elected by the membership and who serve on the Executive Committee. The Board and Executive Committee activities during the first half the 2008 were as follows.

Board of Directors

Several Board Members terms expired on January 21, 2008:
- Barbara Bryant, Millennium Pharmaceuticals, USA
- Michael Gribskov, Purdue University, USA
- Vijaya Parthiban, Student Council Representative to the Board, Germany
- Terry Speed, University of California-Berkeley, USA and Walter & Eliza Hall Institute of Medical Research, Australia
- Lisa Vawter, Aventis, USA
Newly elected members of the Board took office on January 21, 2008
- Nir Ben-Tal, Tel Aviv University, Israel
- Fran Lewitter, Whitehead Institute, USA
- Mona Singh, Princeton University, USA
- John Wooley, University of California-San Diego, USA
- Hannah Xue, Hong Kong University of Science & Technology, Hong Kong
Additional Board Members serving continuing terms throughout 2007 were:
- Patricia Babbit, University of California, San Francisco, USA
- Rita Casadio, University of Bologna, Italy
- Manuel Corpas, Student Council Representative to the Board, EBI, UK
- Sandro de Souza, Ludwig Center for Cancer Research, Brazil
- Terry Gaasterland, University of California-San Diego, USA
- Bruno Gaeta, University of New South Wales, New Zealand
- Dietlind Gerloff, University of California-Santa Cruz, USA
- Kevin Karplus, University of California-Santa Cruz, USA
- Janet Kelso, Max Planck Institute for Evolutionary Anthropology, Germany
- Thomas Lengauer, Max Planck Institute for Informatics, Germany
- Michal Linial, The Hebrew University of Jerusalem, Israel
- Scott Markel, Accelrys, USA
- Jill Mesirov, The Broad Institute of Harvard and MIT, USA
- David Rocke, University of California-Davis, USA
- Burkhard Rost, Columbia University, USA
- Reinhard Schneider, European Molecular Biology Laboratory, Germany
- Tan Tin Wee, National University of Singapore, Singapore
- Jean-Francois Tomb, DuPont, USA
- Anna Tramontano, University of Rome, Italy
- Olga Troyanskaya, Princeton University, USA
- Alfonso Valencia, Spanish National Cancer Research Center, Spain
- Harel Weinstein, Cornell University, USA

The Board met three times between January and June 2008 by teleconference.

Executive Committee

The Executive Committee members for 2008 are:
- Burkhard Rost, President
- Terry Gaasterland, Vice President
- Reinhard Schneider, Vice President
- David Rocke, Treasurer
- Janet Kelso, Secretary
- BJ Morrison McKay, Executive Officer (non-voting staff appointment)
The Executive Committee met 22 times between January and June 2008 by teleconference
- 11 formal meetings that included key ISCB staff were conducted by teleconference.
- 11 informal meetings of the elected officers only were conducted by teleconference.