I533 OBJECTIVES
Updated: 19 January 2006
I533 Molecular Informatics, the Data Grid, and an
Introduction to e-Science will present essential topics
for effectively integrating cheminformatics and bioinformatics techniques
and databases into the research practices of academic and other research
groups. Modules on interfacing with the Grid, database modeling and design,
and targeted programming are
among the key topics to be included. Material in the seminar will be related
to the
projects underway in the NIH-funded Chemical Informatics and
Cyberinfrastructure Collaboratory (ChemBioGrid), and students will have an
opportunity to participate in those projects (see below).
Topics to be presented in the seminar include:
- Introduction to Chemistry and Life Sciences Databases (Gary Wiggins)
- The NIH Roadmap Program and PubChem (Gary Wiggins)
- Cheminformatics Programming Tools and Challenges (David Wild)
- Open Source Software in Cheminformatics (David Wild)
- Database Modeling and Design (Melanie Wu)
- General Data Mining Techniques (Melanie Wu)
- Data Warehousing (Melanie Wu)
- XML Documents, Schema, and CML (Chemical Markup Language) (Malika Mahoui)
- Querying XML Data (Melanie Wu)
- Text Mining Techniques for PubMed (Luis Rocha)
- Chemical Ontologies (Kent Holaday)
- Life Sciences Ontologies (Gary Grumbling)
- Introduction to Grids (Marlon Pierce)
- Building Clients to Grids (Portals) (Marlon Pierce)
- Basic Web Services (Marlon Pierce)
- eScience and Data Grids (Beth Plale)
- Computational Chemistry Approaches (Kevin Gilbert)
- Data Needs in Proteomics (Randy Arnold)
- Chemogenomics (Horst Hemmerle)
- Systems Biology (Santiago Schnell)
- Integration of Chemical Text Tools with Connotea and CiteULike (Geoffrey Fox)
CICC Projects
I533 students will be required either to participate in the following projects or
to write a substantial research paper that explores in depth one of the
lecture topics and shows how it could apply to one of the projects.
- Innovative cross-screen analysis of NIH
Developmental Therapeutics Project Human Tumor Cell Line data
- Development of cheminformatics web services and use cases in Taverna
- Development of a novel interface for the analysis of PubChem HTS data
- A structure storage and searching system for Distributed Drug Discovery
- Quantum chemical computer simulations database
- Training modules for cheminformatics instruction on the Web
- Web guide for essential cheminformatics resources
- Design of a grid-based distributed data architecture for chemistry
- Wrapping NIH and Other Applications as Grid Services
- Developing Web Service Interfaces and Clients to NIH Online Data
- Developing Generic VOTables Services and Tools
- Developing CICC VOTable Applications
- Developing Taverna Client Plugins
- Developing Workflow Scenarios for Taverna
- Developing Portal Interfaces to CICC Tools
- Developing Portal Tools to Support Collaboration
- Evaluating Cambridge/Blue Obelisk Tools for CICC integration
- Supporting CICC Portals
- Research Data Archive and Provenance Activities
- Data Model Evaluation
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