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WS1 Synthetic Biology This workshop will cover the design and construction of biological
systems that exhibit complex dynamical or logical behavior. As such it will appeal to a diverse audience
including those working in biological engineering, biochemistry, quantitative biology, biophysics, molecular
and cellular biology, bioethics, policy and governance, and biotechnology. The workshop's organization
will introduce researchers to the emerging and rapidly developing field of synthetic biology.
Organizer and Speaker
Return to index • Return to Program WS2 Plant Genomics
This workshop will showcase an array of cutting-edge computational
strategies and applications that assist in the integration and
aggregation of life sciences data for plant genomics and genomics
research.
Each session will have three facets: brief lectures, brief software or problem demonstrations, and independent case study work by participants. Upon conclusion of this workshop, participants will have (1) experienced the vital role of software tools in modern plant biological research, (2) increased their understanding of the bioinformatics challenges that these tools address, and (3) identified those challenges that remain unmet. Organizer and Speaker
Return to index • Return to Program WS3 Exploring 3D Molecular Structures Using NCBI Tools The National Center for Biotechnology Information
(NCBI) presents a
workshop that includes lectures and training that teach the effective
use of NCBI databases, search services, and analysis tools that focus
on 3D macromolecular structure data.
The workshop is intended for principal investigators, postdoctoral
fellows, graduate students, advanced undergraduates, and other
scientific staff who either work with 3D structural data or are
interested in understanding how to incorporate such data into their
research. No prior experience with structural data is
required. Familiarity with basic computer operation and common Web
browsers is assumed. Organizer and Speaker
Return to index • Return to Program WS4 Comparative Genome Analyses of Bacterial Genomes and Applications
The world-wide genome sequencing efforts have produced roughly 400
complete bacterial genomes, and this number is expected to extend
beyond 10,000 within the next few years. As the pool of complete
bacterial genomes rapidly grows, comparative genomic analysis surfaces
as one of the most important classes of tools both for mining the
genomes and for studying bacterial biology and evolution at a systems
level. The community urgently needs more powerful methodologies,
tools, and application protocols to help address fundamental
biological problems related to the mechanisms of bacterial genome
evolution and associated areas of research.
The workshop is aimed at eliminating barriers and providing a platform for researchers from different disciplines to exchange visions, insights, ideas, and discoveries about the challenges and opportunities in the field, to share and appreciate research efforts that have been devoted to the field, to provide and seek advice/suggestion/solutions to some problems in the field, and to establish face-to-face collaboration. Speakers
Organizers
Return to index • Return to Program WS5 Symbolic Systems Biology Symbolic systems biology is the qualitative and quantitative study of biological processes and integrated systems rather than isolated parts. In addition to traditional models based on differential equations or statistical/probabilistic methods, formal logics and formal methods techniques are applied to modeling and analysis of biological systems. Abstraction techniques and formal logic are well suited to relate and integrate quantitative mathematical and qualitative algebraic/logical models. This workshop will bring together biologists, computer scientists, and mathematicians to exchange ideas and discuss new logical and mathematical techniques for biological modeling and analysis. In particular, the workshop emphasizes techniques that increase our understanding of biological processes such as metabolism, signal transduction, gene regulation, inter-cellular communication (immune system, neurons, ...). Expected benefits for participants:
The workshop program will include presentations from two keynote speakers, short presentations of selected position papers, and group discussions focused on possible new directions and challenge problems. Keynote speakers
Professor Vito Quaranta---Multiscale Modeling Vito Quaranta is professor of cancer biology at Vanderbilt University, director of the Vanderbilt Integratice Cancer Biology Center and co Director of the Vanderbilt Center for Matrix Biology. (http://www.mc.vanderbilt.edu/cmb/indiv_member.php?id=2) Ananth Annapragada (http://www.sahs.uth.tmc.edu/AANNAPRAGADA/) is a member of the faculty of the School of Health Information Sciences at U. Texas-Houston. His research interests includer targeted drug delivery; respiratory drug delivery; computational methods in biomedicine; and targeted delivery of contrast agents for various imaging modalities. Prospective participants are encouraged to send a 1-4 page position paper (ascii text or pdf preferred) discussing ideas and issues related to the workshop topic to Andy Poggio (poggio@csl.sri.com) by July 21, 2006. The workshop is sponsered by the SRI Center for Computational Biology (http://ccb.csl.sri.com/).
Organizer: Carolyn Talcott Return to index • Return to Program WS6 An Interdisciplinary Approach towards Fluorescence Microscopy
This workshop will cover the latest advances and future
directions in the field of fluorescence microscopy. We will
discuss strategies to answer biological questions through an
integrated approach that takes into account innovative designs
and solutions at all levels of the imaging and image data
analysis process. The main workshop topics include:
Workshop participants will better understand the frontiers of fluorescence microscopy and will be able to discuss their interests and needs with a group of outstanding experts. The workshop addresses both the users of advanced microscopy tools as well as developers interested in creating solutions at the different levels of the imaging process. Students, postdocs, principal investigators as well as researchers and users within the corporate world will equally benefit from participation. Organizers and Speakers
Return to index • Return to Program WS7 Bioinformatics Curriculum Development Workshop The rapid increase in interest in bioinformatics has created great pressure on faculty to offer courses at both the introductory and advanced levels. These teaching opportunities are difficult to meet because there are still only a few faculty members in bioinformatics. The mission of the effort (originated at this workshop) is to bring together faculty with active teaching missions to share curricular philosophy as well as detailed course materials, syllabi and lectures. By bringing together those who teach bioinformatics at the introductory graduate (or advanced undergraduate) level, the goal of the initial workshop is to assess the teaching resources that are available, outline and assess extant curriculum, and make teaching materials available to others The format of the meeting will include 1-2 plenary presentations and if the group is large, breakout groups on individual topics in the curriculum (e.g. sequence analysis, structure analysis, functional analysis, simulation). The groups will return with a plan for sharing of course materials, and recommendations on the focus on followup workshops. Special Notes: Attendance: By invitation, preference given to those who have taught courses in bio/biomedical informatics, and are in a position to share materials. If you wish to attend please contact bioinfws@olympus.compbio.iupui.edu. You should provide a CV, a synopsis of your teaching experience and a course description plus outline. Fees: There are no fees to attend this workshop. Lunch will not be provided; we will adjourn to nearby eateries on campus. Speakers Russ Altman, Stanford University Organizers
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