ISMB/ECCB 2009 Workshop Materials

Workshop on Bioinformatics Core Facilities
Organizers: Fran Lewitter, Michael Rebhan, Brent Richter and David Sexton.

Topic 1 - Setting priorities for a core

Topic 2 - Post-analysis of short-reads

Workshop on Education in Bioinformatics (WEB09)
Organizers: Fran Lewitter and Bruno Gaeta, ISCB Education Committee

Topic 1 - Bioinformatics training for biologists

Michelle Brazas, Manager, Bioinformatics Education, Ontario Institute for Cancer Research: Expanding the Reach of Bioinformatics Training
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.

Jennifer McDowall, Senior Scientist, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK: Evolution in Bioinformatics Training Programs

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.

Topic 2 - Integrating bioinformatics into existing undergraduate courses (biology, math, computer science)

Kam D. Dahlquist, Assistant Professor, Department of Biology, Loyola Marymount University: 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, 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
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.

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?

Mark Borodovsky, Director, Center for Bioinformatics and Computational Genomics, Regents' Professor, Department of Biomedical Engineering and School of Computational Science and Engineering,Georgia Tech

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

Scott Markel, Principal Bioinformatics Architect, Accelrys

Lucia Peixoto, Ph.D. candidate, Department of Biology and PENN Genomic Frontiers Institute, U of Pennsylvania. Student Council Representative to ISCB Board of Directors.

Kimmen Sjolander, Faculty, Department of Bioengineering, U Cal Berkeley