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Bioinformatics Workshopfor HHMI bioinformatics workshop for Student/Scientist Partnerships Program & Abstracts June 14 - 16, 2012 ii Contents Agenda 1 Abstracts 5 Mark Adams 6 The Genomics Scholars Program: Encouraging a research path for under- represented minorities in community colleges Charles F. Aquadro 7 The Cornell Genetic Ancestry Project: Engaging Undergrads Through Participation Lois Banta 8 Metagenomic Analysis of Microbial Diversity in Winogradsky Columns Vincent Buonaccorsi 9 The Genome Consortium on Active Teaching using Next Generation Sequencing Steven G. Cresawn 10 Mycobacteriophages Genomics and Bioinformatics As a Positive Feedback Loop E.A. Dinsdale 11 Microbes, Metagenomes and Marine Mammals: Enabling the Next Generation of Students to Enter the Genomic Era Sam Donovan 12 Teaching and Learning Scientific Data Literacy Skills David J. Dooling 13 Making Sequence Analysis Accessible, or Even Invisible Todd T. Eckdahl 14 GCAT SynBio: Building a Community of Faculty Conducting Synthetic Biology Research with Undergraduate Student Sean Eddy 15 Thoughts on bioinformatics education Sarah C. R. Elgin 16 GEP: The Genomics Education Partnership Alex Hartemink 17 Course: Introduction to computational genomics Ian Korf 18 Teaching new bioinformatics programmers Robert M. Kuhn 19 Using the UCSC Genome Browser to Teach Fundamental Genetic Concepts -- Student-Produced Video Library Carolyn Lawrence 20 Structural Annotation of the Maize Genome: Tools for Community Contributions iii Contents Wilson Leung 21 GEP: The Web Framework Suzanna E. Lewis 22 WebApollo: A Web-Based Sequence Annotation Editor For Distributed Community Annotation Jennifer Mansfield 23 Research in an undergraduate biology curriculum: investigating the functional genomics of chemosensation in the tobacco hornworm Manduca sexta Juan C. Martínez-Cruzado 24 Caribbean-Focused Genomics Research Projects with Tailored Courses for Developing Human and Computational Infrastructure in Puerto Rico David Micklos 25 DNA Subway: An Intuitive Interface to Introduce Genome Informatics William R. Pearson 26 Bioinformatics Theory and Practice - Striking a Balance Mihaela Pertea 27 Using Next-gen Sequencing Data to Explore the Human Genome Antonis Rokas 28 A Genomics Approach to Identifying the Factors Influencing Phylogenetic Accuracy Anne Rosenwald 29 Mining the Human Microbiome - An Opportunity for Student Research Daniel A. Russell 30 PhagesDB.org: A port in a storm of mycobacteriophage genomic information Susan R. Singer 31 Scaffolding Whole Transcriptome Analysis for Genetics Students James Taylor 32 Galaxy: an accessible, collaborative environment for reproducible research Matthew Vaughn 33 The iPlant Collaborative: Bringing Together High Performance Computing and Biology Spencer Wells 34 The Genographic Project as a model for student scientific engagement Susan R. Wessler 35 Transposing from the Research Laboratory to the Undergraduate Classroom Participants 37 Logistics 41 iv Agenda HHMI Bioinformatics Workshop for Student/Scientist Partnerships June 14-16, 2012 Howard Hughes Medical Institute Chevy Chase, MD There is compelling evidence that the best approach to science education is to engage students in scientific research. One strategy for providing research experiences for significant numbers of students is to create student-scientist partnerships, and the general area of genomics/bioinformatics offers an important opportunity to promote such partnerships at the undergraduate level. There are already a number of research problems that have been addressed in this way, and we think the area has great potential. The goals of the workshop are to identify research problems that are well suited for student-scientist partner- ships, and to identify the tools that exist and the tools that are needed for the computing infrastructure, includ- ing the integration of research and education. The workshop will bring together a distinguished group of life scientists who are using genomics to address interesting questions, computational scientists devising informatics tools for data mining and analysis, and scientist-educators who are experienced in teaching undergraduates using a research format. We anticipate that the group will enunciate a number of interesting problems that can be adapted for partnership, identifying any computer infrastructure needs and possible strategies for meeting those needs. Thursday, June 14 3:00 – 5:00 pm Check in at HHMI Headquarters, Chevy Chase Conference Center 5:00 pm Reception Great Hall 6:00 pm Dinner Dining Room 7:15 pm Session I: Overview – Where are we? Where do we want to go? Small Auditorium Chair: David Asai Welcome: Sean Carroll, HHMI Sarah Elgin, Washington University in St. Louis David Micklos, Dolan DNA Learning Center, Cold Spring Harbor Laboratory Matt Vaughn, Texas Advanced Computing Center Charge to the workshop – Sarah Elgin 8:30 pm Social (Posters set up in the Atrium) The Pilot & Atrium Poster presenters include: Lois Banta, Williams College Wilson Leung, Washington University in St Louis Dan Russell, University of Pittsburgh Friday, June 15 7:30 am Breakfast Dining Room 1 HHMI bioinformatics workshop for student/scientist partnerships 8:30 – 10:10 am Session II: Visualizing Genomes Small Auditorium Chair: David Micklos Juan Carlos Martinez-Cruzado, University of Puerto Rico-Mayaguez Jennifer Mansfield, Barnard College Suzi Lewis, University of California at Berkeley Robert Kuhn, University of California at Santa Cruz James Taylor, Emory University 10:10 – 10:30 am Coffee break Outside Small Auditorium 10:30 – 11:50 am Session III: Extracting Meaning from Sequence Data Small Auditorium Chair: Suzi Lewis Steve Cresawn, James Madison University David Dooling, Washington University in St Louis William Pearson, University of Virginia Susan Singer, Carleton College 12:00 pm Lunch Dining Room 1:00 – 2:40 pm Session IV: Transcriptomes; Metagenomics Small Auditorium Chair: Susan Singer Vince Buonaccorsi, Juniata College Mihaela Pertea, The Johns Hopkins University Sean Eddy, Janelia Farm Research Campus, HHMI Anne Rosenwald, Georgetown University Liz Dinsdale, San Diego State University 2:40 – 3:00 pm Coffee break Outside Small Auditorium 3:00 – 4:30 pm Session V : Genomic Explorations Small Auditorium Chair: Sean Eddy Antonis Rokas, Vanderbilt University Sue Wessler, University of California – Riverside Todd Eckdahl, Missouri Western State University Lightning Talks Carolyn Lawrence, USDA-ARS, Iowa State University Sam Donovan, University of Pittsburgh Alex Hartemink, Duke University Ian Korf, University of California at Davis Mark Adams, J. Craig Venter Institute 4:30 – 6:00 pm Poster session (with open bar); suggest working groups, sign-up for working groups Atrium 6:00 pm Dinner Dining Room 7:15 pm Session VI: Bringing Genomics to the Public Small Auditorium Chair: Sean Carroll Spencer Wells, National Geographic Society Chip Aquadro, Cornell University 8:15 pm Social (posters available in the Atrium) The Pilot & Atrium (Posters removed at the end of the evening) 2 Agenda Saturday, June 16 7:30 – 8:30 am Breakfast (and room checkout) Dining Room 8:30 – 9:30 am Working Group Session I* Conference rooms** 9:30 – 9:45 am Coffee Great Hall 9:45 – 10:45 am Working Group Session II* Conference rooms 11:00 am – 12:15 pm Reporting out from Working Groups Small Auditorium 12:15 pm Boxed Lunch and departure for airport Conference Center *Most working group topics will be discussed in both Session I and Session II, so that everyone will have a chance to contribute to the small-group discussion on two topics. **Conference rooms will be C122, C123, D115, D116, D124, and D125. 3 4 Abstracts HHMI bioinformatics workshop for student/scientist partnerships Mark Adams, Ramana Madupu, and Lisa McDonald J. Craig Venter Institute The Genomics Scholars Program: Encouraging a research path for under- represented minorities in community colleges The J. Craig Venter Institute (JCVI) conducts a broad range of educational activities Adams, M. targeting middle school through PhD students. The DiscoverGenomics! mobile lab program provides hands-on experience to middle-schoolers and is supported by a teacher professional development program. Over 20,000 students have participated in this program in the last six years. Summer and academic year internship programs provide research experience for motivated high-school and undergraduate students. In an effort to promote development of a career path in research for under-represented minorities, we have proposed to develop a transition program to facilitate the transition from community college to four-year college using a combination of activities including undergraduate research experience with mentoring and professional development. The program will incorporate multiple avenues of support for students through a multi-year research experience with mentors at JCVI and supplemental professional development. The research experience will be designed to encompass access to experimental designs that emphasize genomics, proteomics, and or metabolomics datasets, thereby introducing students to both “wet lab” and “dry lab” activities. Professional development will include introduction to the responsible conduct of research, record-keeping and lab notebooks, scientific reading and writing, and presentation skills. Additionally, selected students will have the opportunity to participate in undergraduate minority research conferences, which will expose them to various aspects of research and programs. Collaborative contacts are in place and
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