Project: Indiana METACyt Initiative
Primary UITS contacts: Malinda Lingwall, Dick Repasky
Last update: October 16, 2009
Description: The Indiana Metabolomics and Cytomics Initiative (METACyt), funded by a $53 million grant from the Lilly Endowment, seeks to advance life sciences research at IU Bloomington and in the state of Indiana. METACyt funding directly affects four broad areas of campus science:
- Research initiatives
- Service/research facilities
- Infrastructure
- Economic development
METACyt comprises five research nodes and four Integrating Science and Technology Centers (ISTCs). Through the end of the grant term, the METACyt Initiative will invest approximately $25 million in its research nodes and $10 million in its ISTCs. The METACyt Initiative provides extensive funding for investment in infrastructure: new greenhouse facilities, transgenic animal facilities, supercomputing, and nuclear magnetic resonance instrumentation.
A booklet describing METACyt in detail and giving a brief overview of many of the projects it has funded is available at METACyt News and Publications (PDF format; Adobe Reader or equivalent required).
METACyt has moved to a rolling preproposal process, meaning that any IU Bloomington researcher may present a short preproposal to a node director at any time. For details, see Information for IUB researchers.
The Research Technologies division of UITS, along with the Center for Genomics and Bioinformatics (CGB), manages the Center for Computational Cytomics (CCC), one of four ISTCs. The Center facilitates the use of quantitative and computationally intensive approaches in the study of biomolecules and cell functions. It provides a link between life scientists and statisticians/informaticists working on related problems, and it is intended to become the first stop for scientists on either side of that divide who are seeking assistance or collaboration. Its interests and expertise include:
- Cellular DNA analysis and genome annotation
- Genome alignment and analysis
- Phylogenetic analysis
- Motif identification and phylogenetic footprinting
- Microarray design and data analysis
- Proteomics data analysis
- Integrated tools for the analysis of the entire genome's or proteome's design, statistics, syntax, and structure for large repositories of data and metadata
- Cell modeling software, including the best open source and commercial cell models
Outcome and benefits: METACyt funding has significantly increased the profile of Indiana University in the national computing community. IU is one of the best places on the NSF TeraGrid to run molecular dynamics codes because the architecture of the Big Red supercomputer (purchased in part with METACyt funding) natively supports vector operations and so is ideally suited to run these codes. The largest academic labs in the US that seek national computing resources for molecular dynamics now seek to use the Big Red supercomputer.
During 2007, the CCC formed a faculty advisory committee to provide strategic advice to the center.
Six infrastructure projects are under way:
- A software pipeline to perform phylogenetic footprinting analyses
- A data management system for a new imaging facility being built in the IU biology department
- A Lab Information Management System (LIMS) for genome sequencing
- A facility that will sequence, assemble, and annotate bacterial genomes in collaboration with the systems microbiology group
- A web-based classified ad system to link informatics students with biology faculty
- Assessment of faculty data management requirements, using interns from the IU Kelley School of Business
Existing infrastructure continues to be heavily used. Existing infrastructure projects that are underway or supported include:
- A system microbiology pipeline, from DNA sequencing to functional genomics
- A community database for Daphnia genomics
- A web-based database system for 454 sequencing and data management
- A web interface to an oligonucleotide probe design pipeline
- A web interface to GBrowse
- Bioportal web interface to bioinformatics applications
- Data Capacitor storage system
- Big Red supercomputer
- A web server that automatically assembles and annotates large-scale EST data sets
Client impact: CCC/CGB services funded by METACyt are instrumental to research in the biology department. The area of greatest effect is gene expression microarrays: Virtually all work in the area makes use of CCC/CGB for the statistical design of experiments, processing of data, and the statistical analysis and interpretation of data. Short courses and workshops teach people how to do things for themselves. Consultants work with difficult problems. And, of course, there are the software and computing systems. Without the support and facilities of the CCC/CGB as a center, labs would have to build expertise on their own in a piecemeal fashion by sending students out for training or by hiring post-docs and faculty to fill the void. The same is true for the bioinformatics methods in biology: The CCC/CGB provides a locus where graduate students and faculty can come for short courses, consulting, and computing power. On the whole, the CCC/CGB has influenced the work of 22 IU faculty, 12 external faculty (visitors, faculty on sabbatical leave, and external collaborators), 3 post-doctoral fellows, and 9 IU graduate students.
Additional information
- PI: M. A. McRobbie
- Co-PIs: K. Subbaswamy, T. Widlanski, P. Cherbas, C.A. Stewart
- Funding agency and grant number: Lilly Endowment, Inc. 2004 2058-000
- Grant dates: January 1, 2005-December 31, 2009
- Funding to UITS/CGB: $6,250,000
- Total funding to IU related to this project: $53,000,000
- Project web site: http://metacyt.indiana.edu/
