HPC MSU

NIH Program of Excellence in Biomedical Computing

NIH planning grant for a National Program of Excellence in Biomedical Computing (NPEBC) targeting computational simulation in environmental health sciences


Biomedical Computing Cross-Training Seminar Schedule - Spring 2003
Biomedical Computing Cross-Training Seminar Schedule - Fall 2002

Biomedical Computing Seminar Series - Fall 2004
Biomedical Computing Seminar Series - Spring 2004
Biomedical Computing Seminar Series - Fall 2003
Biomedical Computing Seminar Series - Spring 2003
Biomedical Computing Seminar Series - Fall 2002
CO-PIs
Joe Thompson
ERC
662-325-7299
joe@erc.msstate.edu

Jan Chambers
Center for Environmental Health Sciences (CEHS)
662-325-1255
chambers@cvm.msstate.edu

http://www.cvm.msstate.edu/research/ContentsRERHandbook/LabProfiles/CEHS.html

Funding Source

National Institute of Environmental Health Sciences (NIEHS)

http://www.niehs.nih.gov/

- one of the National Institutes of Health (NIH)

http://www.nih.gov/

Program

NIH National Programs of Excellence in Biomedical Computing (NPEBC) in 2000

http://www.nih.gov/about/director/060399.htm

called for the creation of biomedical computing research centers by NIH.

Biocomputing at NIH:

http://grants.nih.gov/grants/bistic/

NIH

Purpose

This is a planning grant - not a research grant - and its entire purpose is to prepare MSU to submit a proposal to NIEHS in 2004 for a full biomedical computing research center targeting computational simulation in environmental health sciences.

Period

This planning grant is for three years, with a proposal for a full center to be submitted early in the third year (mid-2004).

Focus

Biomedical computing research encompasses an extremely broad area, and NIH welcomes biomedical computing research centers targeting research areas of any of its institutes. We have chosen to target computational simulation in environmental health science research for several strategic reasons. MSU has very significant and recognized strength in computational simulation in the physical sciences in the ERC. MSU also has such strength in environmental health sciences in the CEHS, and this is an NIH area expected to be less targeted by significant competitors for full centers. Bioinformatics (genomics, proteomics, etc), on the other hand, is now a crowded field. Thus computational simulation, as opposed to bioinformatics, is especially well suited to our opportunity. Therefore, computational simulation in environmental health sciences is felt to be a focus area in which we can build on appreciable MSU strength and in which we can establish ourselves as a unique capability of particular appeal to the NIEHS.

Funded Efforts

Funding through this planning grant will be used to cross-train MSU faculty in computational science and biomedical science, with emphasis continually on relevance to environmental health science research. This planning grant does not provide funds for faculty release time, summer funding, or research projects.

In addition, there is one project that will be conducted to demonstrate basic capability and build infrastructure. This project is to construct a computational portal for computational simulation in environmental health science research, and it will be done by Thomasz Haupt and co-workers in the ERC.

Participants

This effort is inherently cross-disciplinary among computational science, computer science, mathematics, and the biological and physical sciences. Therefore a very broad range of interested MSU faculty is needed who are willing to invest the time to develop a good multidisciplinary understanding across these relevant fields. It is not expected that faculty will become experts outside their home discipline, but it is necessary that good understanding and appreciation of the potential for computational simulation in biomedical research, and of the capabilities of computational simulation relevant to biomedical research, be developed - and that a working vocabulary be acquired for effective communication across the relevant disciplines.

All interested faculty from the relevant disciplines are welcome to participate. There is no limit on the number of participants; rather the natural limiting factor will be a sustaining commitment to stay the course through the two years as we develop the cross-disciplinary understanding and expertise necessary to submit a successful proposal for a full center.

We would like to compile a list of potentially interested faculty, so please let us know if you are interested in joining in this venture. Participation will not be restricted, however, to those expressing immediate interest.

Operation

We are in the process now of bringing this effort and opportunity to the attention of faculty in the relevant disciplines, with the objective of identifying interested faculty to participate in this extended cross-training activity, and a core of strongly committed faculty to join in planning this activity and develop related collaborations.

A series of seminars, workshops, and short courses for faculty will be planned and conducted over the next two years. Committed faculty will also be sent to certain appropriate meetings. These activities will be strategically planned and coordinated to achieve the goal of developing a group of committed faculty with cross-disciplinary understanding and expertise to form the nucleus for a full center and to join in the writing of the proposal for that full center.

We will also assemble relevant web-based information into the computational portal being developed in the course of this effort, and will investigate appropriate alliances with other institutions in mounting the ultimate full center.

Strategy

  1. Identify faculty committed to cross-training and developing collaborations in this emerging area who will become the core participating faculty.
  2. Set up seminars and workshops for cross-training of the core faculty, which will be available to other faculty, staff and students.
  3. Support short-term cross-training of the core faculty at meetings, courses, workshops or at other institutions.
  4. Facilitate the development of research collaborations among the core faculty, with this research supported through other mechanisms such as existing or new independent research grants.
  5. Development of collaborations or alliances with scientists at other institutions, as needed, to have the required expertise or depth for a competitive team.
  6. Submission of interdisciplinary grant applications for research in computational simulation in environmental health sciences, targeting primarily NIEHS.
  7. Submission in 2004 of a competitive, successful application to NIEHS for a National Center of Excellence in Biomedical Computing (NPEBC) targeting computational simulation in environmental health sciences.

Full Center (to be proposed)

NIH NPEBCs are intended to:

  1. Promote bio-informatics and bio-computational research that enables the advancement of biomedical research;
  2. Develop useful and interoperable informatics and computational tools for biomedical research;
  3. Establish mutually beneficial collaborations between biomedical researchers and informatics and computation researchers; and
  4. Train a new generation of bio-informatics and bio-computation scientists.

The full NIH biomedical computing research centers are to be funded at a multi-million level for an extended period. These centers will involve faculty from multiple relevant disciplines, along with major computational facilities. Funding for research by faculty, graduate students, and post-docs will, of course, be included. And there will be an educational component. Computational simulation would be coupled in this full center with research in environmental health science as an enabling element. Ideally the center would have its own building, as does our present ERC, but NIH funding will not extend to providing that.

Since this full center will be inherently multidisciplinary, it will have to be administratively housed appropriately in the university across colleges. Our present ERC provides a good model for this full center in many ways. And the center would ultimately have the potential to attract funding from multiple agencies, as does the ERC. Clearly this full center would impact instruction at MSU on both the undergraduate and graduate levels, through the creation of multidisciplinary courses and possibly programs.

Prospects

Competition for a full center can be expected to be fierce. A committed and competent multidisciplinary faculty who have established communication with actual and potential collaboration will be essential. And a strong commitment of resources from the university is likely to be the point which differentiates among technically strong proposals. So our success in eventually winning a full center hinges directly on our efforts during the next two years to achieve the following:

  1. A committed multidisciplinary group of our own faculty.
  2. The addition of faculty with certain needed expertise through filling presently approved positions that come open.
  3. The commitment of the university to establish new faculty positions with certain needed expertise.
  4. The formation of alliances with other institutions in order to fill the need for certain faculty expertise.
  5. The commitment of the university to provide certain needed physical resources, including access to computer facilities and space for multidisciplinary research.

All of these can be done only by the voluntary interest of faculty in the relevant departments, with the support of the university administration.

Background

In the mid-90s, there was a strong push in the physical science community and in Congress for high performance computing (HPC) in major scientific challenges - "Grand Challenges" was the current term. The initial instantiation of this emphasis was the cross-agency High Performance Computing & Communications (HPCC) Program and the Next Generation Internet (NGI) Program. These were followed, at the recommendation of the President's Information Technology Advisory Committee (PITAC), by the Information Technology Research (ITR) Program which is still active now. The ITR Program is also cross-agency, and does include NIH. But the initial NIH participation was orders of magnitude smaller that that of NSF, NASA, DoD, and DOE. PITAC (of which Thompson is a member) called for significant increase of attention to the potential of HPC in biomedical research funded by NIH, and NIH commissioned its own study, culminating in the "BISTI Report" in 1999.

The BISTI Report:

http://www.nih.gov/about/director/060399.htm

called for the creation of biomedical computing research centers by NIH. NIH concurred with this recommendation and set about implementating it through the National Programs of Excellence in Biomedical Computing (NPEBC) in 2000:

http://grants.nih.gov/grants/bistic/bisti_recommendations.cfm

Additional relevant information is at:

http://grants.nih.gov/grants/bistic/

and the above two links are accessible in the "BISTI" section of this site. Our planning grant resulted from a successful proposal in the Pre-NPEBC Program, the announcement for which is available by clicking on the "Funding Opportunities" link in the "This Web Site" section, and then clicking the "Planning Grants: National Programs of Excellence in Biomedical Computing (Pre-NPEBC)" link.

In implementing these centers for biomedical computing research, NIH realized that few universities would already have the cross-disciplinary understanding and expertise in place, much less an established culture of multidisciplinary research in computational and biomedical science, necessary to mount such a center. Therefore, the NPEBC Program included planning grants to allow universities with demonstrated potential and separate expertise to develop the cross-disciplinary faculty necessary to hope for success in a later proposal for a full center. That is where MSU now stands - we have won one of the seven Pre-NPEBC planning grants awarded in the initial round of competition. We join six other institutions previously announced: Stanford, Washington, Columbia, Utah, Rutgers, and Yale. These other six efforts are briefly described at the "Latest Information of PreNPEBC Awards Added to Website" link on the site noted above.

Computational Simulation

Computational simulation is the use of computers to simulate physical/biological phenomena and processes through the computer solution of complex mathematical models, and computational assistance of researchers in the assimilation, analysis, and presentation of results of scientific experiments and concomitant simulations. While the concentration is on the formulation and solution of the mathematical models, this also includes scientific visualization, data structures, database analysis, remote collaboration and access to data, and, of course, disciplinary science.

Environmental Health Science

The field of environmental health science, as supported by the NIEHS, encompasses research studying the health of humans as adversely impacted by environmental factors, primarily environmental toxicants. Environmental toxicants include pesticides and other agricultural chemicals, and industrial effluents including organic pollutants and metals; these toxicants would be available to humans from contaminated air, water, food and surfaces. Not included would be natural toxins or pharmaceuticals. Types of toxicities which could be caused by environmental toxicants would include short term adverse effects as well as long term effects such as chronic diseases or developmental toxicities. Research encompasses molecular mechanisms within cells to effects on whole organisms (including impacts on populations).