I647 CLASS PROJECTS
Updated: 9 August 2006
I647 Bridging Bioinformatics and Chemical Informatics will
explore areas where chemistry and biology touch with respect to the databases and
computational tools used in chemoinformatics and bioinformatics. Material in the seminar will be related
to the
projects underway in the NIH-funded Chemical Informatics and
Cyberinfrastructure Collaboratory (ChemBioGrid).
Potential class projects include:
Create a list that indicates why we have included some things in our CICC work, e.g., why is Toxtree there?
-
Produce a chart with chemical tool space and what we are covering in the CICC projects.
How does this compare to other things that are available--both commercial and public data?
Primary HTS data:
- What assays are used in analyzing HTS data?
- What problems arise in interpreting the data?
- What data are available in PubChem and how can they be used
Data format standardization
- What standards exist in biology and chemistry?
- Are there incompatabilities?
Chemoinformatics and bioinformatics analysis tools
- What tools do we have available on campus for analyzing bioinformatics and
cheminformatics data
Linking biological and chemical information in computational approaches to predict biological activity,
ADME profiles, and adverse drug reactions (ADR)
- What differences are there between selection criteria for small molecules that are to be used as drugs vs. those that
may be useful for perturbation of biological processes?
Discovery informatics platforms that facilitate archival, sharing, integration, and exploration of synthetic methods and
biological activity data
- Are there freely available synthesis databases?
- What are the biological activity data repositories
Data pipelining approaches that make it possible to apply bioinformatics and chemoinformatics data and analyses together
- A comparison of Pipeline Pilot and Taverna
Visualization of data in biology and chemistry
- What tools are available to us on this campus, e.g., Spotfire?
Tools that combine multiple approaches and consolidate data, such as Metaphorics Cabinet and iSpecies.org
- How do these tools work?
- Are they capable of pulling together the most relevant data?
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