Workshop 1: Workshop on Education in Bioinformatics (WEB 09)
Workshop 2: Bioinformatics Core Facilities

Workshop 1: Workshop on Education in Bioinformatics (WEB09)

Organizers: Fran Lewitter and Bruno Gaeta, ISCB Education Committee

Date: Tuesday, June 30
Start Time: 10:45 a.m. – 12:40 p.m.
Room: T5

The first Workshop on Education in Bioinformatics was launched at the ISMB meeting in Copenhagen in 2001. Meetings were held annually through ISMB 2005 to provide a forum for bioinformatics educators to discuss relevant issues. Early WEB meeting focused on bioinformatics degree and training programs. Later meetings addressed a wider range of issues including education in bioinformatics for biologists.
The need for this workshop is even greater than in the past because of the rapid pace of biological research and the multitude of new data resources and tools. How will experimentalists make use of the new tools? How will young scientists get exposed to computational methods in biology? These are only a few of the questions that will provide a basis for an interesting, informative and timely exchange of materials related to education in bioinformatics. This workshop will include two half-hour topics with talks and discussion, and a one-hour panel discussion session.

Michelle Brazas, Manager, Bioinformatics Education, Ontario Institute for Cancer Research
Expanding the Reach of Bioinformatics Training
Jennifer McDowall, Senior Scientist, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK
Evolution in Bioinformatics Training Programs

Kam D. Dahlquist, Assistant Professor, Department of Biology, Loyola Marymount University Integrating Bioinformatics into Undergraduate Courses: Meeting the Challenges
Murlidharan Nair, Assistant Professor of Bioinformatics, Department of Biological Sciences/Computer Science and Informatics, Indiana University South Bend
Restructuring undergraduate biology curriculum in the Post-genome era

Topic 3 - Panel on career paths in Bioinformatics from an education perspective: What’s the best kind of training? What types of jobs are out there?

Fran Lewitter, Director, Bioinformatics and Research Computing, Whitehead Institute
Runs a group of bioinformatics scientists who collaborate with lab scientists.

Mark Borodovsky, Director, Center for Bioinformatics and Computational Genomics, Regents' Professor, Department of Biomedical Engineering and School of Computational Science and Engineering,Georgia Tech
Perspective: The issue of merging bioinformatics and systems biology recently generated a lot of interest on the ISCB Education mailing list. His remarks will continue this discussion but from the perspective of training and future jobs.

Steven F. Jennings, Professor of Information Science, University of Arkansas at Little Rock, Executive Director, MidSouth Bioinformatics Center at UALR, Founder and Program Director, UALR/UAMS Bioinformatics Graduate Program
Perspective: Will describe the training provided and the different paths students take after finishing the program at UALR.

Scott Markel, Principal Bioinformatics Architect, Accelrys
Perspective: Hiring manager of people who need to know bioinformatics in order to develop software.

Lucia Peixoto, Ph.D. candidate, Department of Biology and PENN Genomic Frontiers Institute, U of Pennsylvania. Student Council Representative to ISCB Board of Directors.
Perspective: Experiences of job-hunting by student council members will be discussed.

Kimmen Sjolander, Faculty, Department of Bioengineering, U Cal Berkeley
Perspective: Has worked in industry (Celera Genomics, DoubleTwist, Molecular Applications Group) as well as academia. Former students/postdocs have ended up in industry (Genentech, Merck, Dupont).

Topic 1 Abstracts:
Jennifer S. McDowall
Expanding the Reach of Bioinformatics Training
Bioinformatics resources play an integral part in many research objectives, from clinical research to environmental and agricultural sciences. In addition, as bioinformatics, medical informatics and chemoinformatics become better integrated, our end-users will broaden. Therefore, training programs need to reach a wider spectrum of end-users, taking into account more diverse university programs, as well as those requiring professional development, such as clinical geneticists. There needs to be a better way of disseminating bioinformatics training material and to provide a variety of solutions to hands-on training. The European Bioinformatics Institute is part of the ELIXIR training program, which is developing an eLearning portal in order to provide freely accessible training materials for students, teachers and professionals. Any participating institute will be able to use the portal to provide training material. In addition, road shows that bring trained professionals to a variety of universities, institutes and industry, are a valuable way to reach a wider audience.

Michelle D. Brazas
Evolution in Bioinformatics Training Programs
Given the importance of bioinformatics in research today, most undergraduate and graduate level studies now include introductory bioinformatic skills. However, with the recent advances in technology and the concurrent explosion in biological data, there is a need for more advanced training programs in bioinformatics that better enable researchers in today’s research environment. We discuss how our open access training programs in bioinformatics have evolved from introductory overview style courses to more advanced topic specific courses, that focus on these new data types and aid the ever advancing user in data extraction, analysis and integration.

Topic 2 Abstracts:
Kam Dahlquist
Integrating Bioinformatics into Undergraduate Courses: Meeting the Challenges
Current undergraduate curricular reform movements in biology (outlined in the BIO2010 and Math & Bio 2010 reports) emphasize teaching the practice of scientific research through coursework that emphasizes hands-on activities with open-ended questions and through providing opportunities for students to conduct faculty-mentored original research. These movements also emphasize the need to increase the quantitative and computational skills of undergraduate biology majors, along with the ability to perform interdisciplinary teamwork. By its very nature, bioinformatics can lead to innovative teaching in biology, and two examples of how to integrate bioinformatics into undergraduate courses will be given. However, teaching bioinformatics at this level also presents several challenges such as recruitment of students to courses and dealing with the different backgrounds and preparation levels of students. We will discuss how to overcome these challenges.

Murlidharan Nair Restructuring undergraduate biology curriculum in the Post-genome era
Technological advances have enabled scientists to produce biological data at an unprecedented rate. This has given rise to the field of bioinformatics that uses computational, statistical and mathematical methods to handle and interpret the huge volume of data and generate computationally derived hypothesis. It is literally transforming the very field of biology itself. We are racing toward the $1000 genome project and towards capturing human diversity in 1000 Genomes. These large projects are making biology a more data driven science. The next generation sequencing technology is bound to make its way to the practice of medicine in the future enabling doctors to make effective choice in prescribing medication. While all these developments have been happening at a rather rapid pace, is there a corresponding redefinition of the undergraduate biology curriculum? Are students made aware of these advances? It is time that we address the changing scenario in biology by reflecting it in the undergraduate biology curriculum to ensure that the next generation biology/premed students are well prepared to face the challenges.

Workshop 2: Bioinformatics Core Facilities

Organizers: Fran Lewitter, Michael Rebhan, Brent Richter and David Sexton.

Date: Thursday, July 2
Start Time: 10:45 a.m. – 12:40 p.m.
Room: C8

Many institutions have invested in building a centralized team of computational biologists and informatics specialists to support and collaborate with the experimental biologists. Some of the issues these bioinformatics core facilities address include, but are not limited to, managing and analyzing large amounts of data, supporting new technologies as they arise, collaborating on computational projects yielding biological discovery and building tools for experimental biologists. With this in mind, the Bioinformatics Core Facility group ( formed at ISMB 2002 in Edmonton. The purpose of this international group is to exchange ideas about how best to build and develop Bioinformatics Core Facilities. Since 2002, the group has grown in size and experience. In addition to meeting in-person at ISMB (previously as BOFs), we have a mailing list (, a Wiki (, and quarterly conference calls.

During this session, we have chosen two topics for discussion. The format will include 3 ten-minute talks and 20 minutes of discussion. Speaker information to follow.

In addition to this session, there will be other opportunities to meet informally with other members of during ISMB 2009. Please join the mailing list mentioned above to get notifications of events.

Topic 1. Setting priorities for a core
What is the best use of a core’s capabilities? Successful bioinformatics core facilities have more requests than can be handled by the available staff. What are the strategies core facilities use to prioritize requests? What is a reasonable time for someone to wait for completion of a project? Does it work to outsource some projects to consultants? What types of projects are appropriate to outsource? What projects should the scientists do for themselves? What projects should be handled by the core? These and additional questions will be discussed during this session.

Simon Andrews, Head, Bioinformatics Department, Babraham Institute, Cambridge UK

David Sexton, Director, Research Informatics Core, Vanderbilt University, Nashville TN
Matthew Eldridge - Head, Computational Biology Core at Cancer Research UK (Cambridge Research Institute), Cambridge UK
Fran Lewitter, Director, Bioinformatics and Research Computing, Whitehead Institute for Biomedical Research, Cambridge MA

Topic 2. Post-analysis of short-reads
Bioinformatics core facilities have developed infrastructure to manage the flow of next-gen sequencing experiments. Standard analysis of short read sequence includes image analysis, basecalling, and alignment to a reference genome. What value-added service could be offered post-alignment to put the sequence into biological context? For those with experience what questions are your end users asking about the data they are receiving from next-gen sequencing? What software or hardware is necessary to properly analyze this data? Are these analyses similar or are they custom for each project? These topics will be addressed during this session.

David Sexton, Director, Research Informatics Core, Vanderbilt University, Nashville TN

Simon Andrews, Head, Bioinformatics Department, Babraham Institute, Cambridge UK
Dawei Lin, Director, Bioinformatics Core, UC Davis, Davis CA
Brent Richter, Director, Enterprise Research IS, Partners Healthcare Systems, Boston MA