BioCoRE. A Biological Collaborative Research Environment. Investigators: Klaus Schulten*, PI
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1 BioCoRE A Biological Collaborative Research Environment Investigators: Klaus Schulten*, PI Gila Budescu, Laxmikant Kale Developers: Mike Bach, Robert Brunner, Kirby Vandivort, Hui Wang Graduate Assistants: Jay Desouza (CS), Sameer Kumar (CS), David Brandon (SPCOMM) October 27-29, 29, 2000 Pittsburgh, Pennsylvania NIH Resource for Biomolecular Modeling and Bioinformatics Beckman Institute, University of Illinois at Urbana-Champaign
2 BioCoRE Community b Structural Biology b Cellular Biology b Structural Genomics b Pharmacology HIV Protease image produced by VMD Ladinsky et. al. (1999). Golgi structure in three dimensions: Functional insights from the NRK cell. J. Cell Biol., 144: W. M. Keck Center for Comparative and Functional Genomics, University of Illinois Biotechnology Center
3 BioCoRE Community Needs Access to analysis tools Remote simulation control Shared visualization sessions Data sharing and storage Joint document preparation Distant mentoring and training Multi-channel communication (conferences, chat rooms, white boards, audio/video) Built-in in evaluation component yields continuous data on user expectations. Current needs, as identified by interviews, registration and feedback forms, user s comments, and bug reports.
4 BioCoRE Toolboxes Enhance Research
5 Logging into BioCoRE Web-based based collaborative environment Platform-independent technology Secure infrastructure Private and confidential interactions
6 BioCoRE Project Selection Functionality: Activities are project-based Privacy: : Users and projects identities are confidential Flexibility: Projects are created and managed by users
7 BioCoRE Control Panel Immediate feedback of user activity Java applet: dynamic and portable
8 Notebook Toolbox BioCoRE Notebook Lab book Notices Messages Repository for all project data Text Images Simulation results Graphs Data integrity and completeness Searchable Lab book Formatted, organized records Notice board Important messages Message board Archive of project activity Sortable
9 Notebook Message Board (available) Users leave messages for other project members Chat sessions auto- archived
10 BioCoRE Conference Toolbox Real-time teleconferences: text, audio, video Sessions fully archived in Notebook
11 Conference Chat Rooms (available) A project member starts a subject- specific chat session Project members join and leave chat session Transcript auto-saved in notebook
12 BioCoRE Document Toolbox Offers tools to aid collaborative document preparation: Web-based based access to revision control Interface to CVSLog,, or similar package A file repository, shared by project members
13 BioCoRE Workbench Toolbox Common interface to visualization, simulation, and analysis tools Collaborative visualization sessions Simplified job submission and monitoring Novel input devices
14 Workbench Job submission (soon) User specifies preferred computer account(s) User defines job parameters BioCoRE submits job following site-specific specific procedures Results of runs accessible to project members
15 Workbench Job Monitoring (available) Users can gauge the health of running simulations Resources are freed by stopping jobs which are not running properly Job status is viewable from any web browser
16 Training and Mentoring in Molecular Modeling EMBL course, July 2000 Participants in Heidelberg ran MD simulations in Urbana using workbench Progress review of research activities
17 BioCoRE Evaluation Upon joining the project BioCoRE users consent to be evaluated. Sources of user information include: Process Data: Registration form User-tool interactions User-user interactions Tool-tool interactions Tech support logs and bug reports Special-purpose purpose interviews Periodic surveys and a permanent feedback form Outcome Data: Users satisfaction Attrition Resulting publications Citations of resulting work Participants professional progress Funding resources
18 BioCoRE Distribution Development history February, 1999: BioCoRE development started March, 2000: Initial release October, 2000: First major update 171 registered users in 13 projects as of October 23; 46% projects NIH funded Current distribution policy: users register and use our server Soon: BioCoRE code will be available so others may set up their own servers
19 BioCoRE Case Study Human Frontier Science Program on Retinal Proteins Participating sites are in Japan, Italy, Israel, Germany, and USA
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