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Show Me the Money


By William Langbein

Though it’s drought season for venture wells as investors lose patience with bioinformatics, there’s still money out there for tool developers. The key is to check out public sources of funding, such as NIH or MRC grants.

The 2003 budget isn’t finalized, but sizable increases are expected for funding and grants to support bioinformatics programs at the NIH. Applications for bioinformatics research still must compete against other science programs for NIH funds, but bioinformatics tools are proving essential for several new initiatives — and that means better chances for bioinformaticists to win those dollars.

For example, the Pharmacogenetic Research Network at the National Institute of General Medical Sciences seeks to enhance its PharmGKB database dramatically. Growth of the database, which details drug interactions in humans, will require new computational tools and systems to analyze a potentially exponential number of drug interactions.

At NHGRI, the haplotype project, designed to study genetic variation in humans, is collecting hundreds of thousands of variations across three populations. To understand the disease implications of such variations, the project needs new tools for data reduction and new methods of data analysis.

“We’re interested in new proposals for basic [analytical] methods,” says Lisa Brooks, director of the project at the NHGRI. “We’re [aggregating] data from SNPs, haplotype patterns, linkage disequilibrium, and association studies. To use the map efficiently, we need statistical methods to allow researchers to retrieve the information they need.” Brooks expects to receive bioinformatics proposals from theoretical and quantitative population geneticists.

To improve the odds of getting grants, NHGRI is working with bioinformaticists to help prepare more hypothesis-driven applications. Past informatics grant applications frequently have been weighted toward systems development; applications that can theoretically address statistical and genetic hypotheses, Brooks says, should be more competitive.

Overall, NHGRI proposed a 2003 budget of $374 million for extramural research and $92 million for intramural programs, up from $346 million and $83 million in 2002. The intramural budget includes support for bioinformatic tools and methods to improve existing model organism databases.

NHGRI isn’t the only institute with coffers. The National Cancer Institute is funding epidemiological cohort studies that will require bioinformatics tools, for example, and the National Institute of Mental Health is working with NHGRI to develop new algorithms for disease analysis.

Outside the US, the Wellcome Trust likewise has a targeted bioinformatics program in cancer and brain sciences. And both the UK Medical Research Council and the Sixth European Framework Programme have identified genomics and bioinformatics as high-priority research for long-term programs to be initiated between 2002 and 2007. Actual funding decisions are planned for later this year.

The next four pages provide a map to the current, competitive funds and programs for your latest bioinformatics brainchild.


Planning Grant for National Programs of Excellence in Biomedical Computing, PAR-00-102

Amounts Available: Up to $10 million

Deadline(s): November 27, 2002

Description: An ongoing, cross-institute program to use informatics in management and analysis of data and modeling biological processes. Biomedical computing includes database design, graphical interfaces, querying approaches, data visualization and manipulation, data integration through the development of integrated analytical tools, synthesis, data archiving, data exchange, tools for electronic collaboration, and computational research including the development of structural, functional, integrative, and analytical models and simulations.


Planning Grants for Integrated Advanced Information Systems, PAR-02-079

Amounts Available: Two to four years, $150,000 to $400,000 per year

Deadline(s): March 15, annually, through 2005

Description: The National Library of Medicine provides IAIMS grants to health-related institutions and organizations to produce a written plan for action in one or more of the fundamental IAIMS activity areas such as integrating data, information, and knowledge resources into a comprehensive networked information management system. The networked systems can link and relate the published biomedical knowledge base with individual and institutional databases and information files, within and external to an institution.


Pilot Study Grant for IAIMS, PAR-02-080

Amounts Available: Up to $75,000 per year for two years

Deadline(s): March 15, annually, through 2005

Description: Provide seed money for early, innovative studies to address a fundamental integrated advanced information systems activity area. Can include projects to link biomedical information within institutional databases and with external databases.


Testing and Evaluation Grant for IAIMS, PAR-02-082

Amounts Available: Up to $100,000 per year for two years

Deadline(s): March 15, annually, through 2005

Description: A development grant to assist organizations that want to deploy an information resource, system, or service on a limited scale in a live setting and evaluate its efficiency, effectiveness, and usability. New informatic systems need to be designed to serve the clinical, research, educational, and administrative needs of the healthcare or research institution.


IAIMS Fellowship Grant, PAR-02-096

Amounts Available: Salary stipend of up to $50,000 plus an administrative supplement

Deadline(s): March 15, annually, through 2005

Description: The IAIMS program seeks to provide a comprehensive and convenient information management system that delivers usable knowledge to practitioners in health care, education, and research. These fellowships are available to for-profit and non-profit organizations that seek to prepare researchers for in-depth involvement in IAIMS work. The fellowship should include formal instruction, mentoring by an appropriate IAIMS mentor, and the completion of a hands-on project.


Joint Initiative to Support Research in the Area of Mathematical Biology, from the Division of Mathematical Sciences of NSF & NIGMS, NSF 02-125

Amounts Available: From $100,000 to $400,000 per award per year (total costs), for up to five years

Deadline(s): First deadline, August 11, 2002, then June 30, 2003, and June 30, 2004

Description: The DMS and NIGMS anticipate making 20 to 25 awards totaling about $6 million, in each of fiscal years 2003 through 2005. Both agencies recognize the need for additional research at the boundary between the mathematical sciences and the life sciences. This competitive grant program was designed to encourage new collaborations at the boundary, as well to support and expand existing research. Appropriate topics include: evolutionary theory and practice arising from genomics advances; statistical and other approaches to the discovery of genes contributing to complex behavior, and their environmental interactions; explanatory and predictive models of the cellular state; informational molecule dynamics; and new approaches to the prediction of molecular structure.


Biological Information Technology & Systems, NSF 01-102

Amounts Available: $100,000 to $500,000 per year, three to five years in duration, ongoing program

Deadline(s): second Friday in February

Description: The ongoing BITS program seeks to maximize the potential of biological information technology and systems by developing new computational models and theories, potentially leading to new information technology systems and hardware platforms. In the past two years, $13 million has been committed to emphasize development of hybrid (bio-silical) systems as a means to experiment with and validate new theories of biological information technologies. Award amounts tend to range between $100,000 to $200,000 per year for theoretical proposals and $100,000 to $500,000 per year for hybrid systems and other experimental projects.


Quantum and Biologically Inspired Computing, NSF 02-017

Amounts Available: Between $100,000 and $500,000 over three years

Deadline(s): First Monday in February

Description: The ongoing program centers on biologically inspired research and strongly considers cross-disciplinary approaches to topics in bioinformatics or molecularly inspired computing. Topical areas of research include but are not limited to: understanding of the optical, electrical, mechanical, and other properties of biomolecules at various scales; development of computational models, techniques, and tools capable of predicting sub-cellular and intra-cellular processes and systems; modeling of the mechanisms whereby cells undergo phase changes; and modeling of intra-cellular processes governed by the network of molecular interactions including gene-gene, gene-protein, and protein-protein interactions. About 15 awards have been issued annually.


Biological Databases and Informatics, NSF 02-058

Amounts Available: $50,000 to $500,000 for up to five years

Deadline(s): Second Monday in July and second Monday in January, annually

Description: An ongoing grant program to fund new approaches to the management of biological knowledge that render greater utility to the scientific community by enhanced collection, maintenance, and query of biological and genomic data. About $8 million set aside each year. Particular emphasis on proposals that seek to develop new types of informatics tools and database structures for community databases. The program does not support disease-oriented research, including the etiology, diagnosis, or treatment of physical or mental disease. The NSF typically issues 25 new awards per year.


Advanced Technology Program, NIST

Amounts Available: Approximately $1 million to $6 million per project, annual competition

Deadline(s): Delivered or stamped by July 31, 2002 or September 30, 2002

Description: The ATP awards fund high-risk, high-payoff projects in all areas of technology. In bioinformatics, the program issues awards through two offices: Information Technology and Applications, and Chemistry and Life Sciences. While $61 million was set aside for the total ATP budget in 2002, the sum may triple in 2003. In previous years, the program has funded about three to five bioinformatic programs in both the non-profit and for-profit sector. The ATP views bioinformatics infrastructure as essential in facilitating data harvesting, data exchange, data mining, and analysis for target selection applications in areas such as cancer and AIDS. The ATP also supports bioinformatic research in gene prediction methods, genome annotations, and gene function correlation.


Society for Biomolecular Screening Small Grants Program

Amounts Available: $15,000 per year, renewable for an additional year

Deadline(s): March 2003

Description: Supports research in drug discovery to include programs in molecular biology, high-throughput screening, chemoinformatics, and bioinformatics for full-time researchers at universities or other non-profit institutions. Applicants must hold PhD or MD.


Innovations in Biomedical Information Science and Technology: Phased Innovation Award (R21/R33), PA-00-117

Amounts Available: $100,000 to $200,000 per year, up to two years

Deadline(s): November 27, 2002

Description: Broad, core research program designed to promote research in biomedical information science and biomedical computing to include database design, graphical interfaces, querying approaches, data retrieval, data visualization and manipulation. Computational research agenda includes the development of structural, functional, integrative, and analytical models.


Supplement for the Study of Complex Biological Systems, NOT-GM-02-004

Amounts Available: Up to $75,000 per year in direct costs

Deadline(s): Variable

Description: Can be used to recruit mathematicians, physicists, engineers, and computer scientists to support cross-disciplinary collaborations between NIGMS PLS and other established investigators to support the study of complex biological systems. These collaborations should be used to enhance the outcome of original projects and establish new conceptual directions from previous, parent projects.


Bioengineering Research Partnerships, PAR-02-010

Amounts Available: Up to $2 million

Deadline(s): August 12, 2002

Description: Bioengineering Research Partnerships offered through the National Institutes of Health aim to integrate physical, engineering, and computational science principles for the study of biology, medicine, behavior, or health. The cross-disciplinary partnerships should advance fundamental concepts and knowledge from the molecular to the organ systems level, and develops innovative approaches in materials, processes, devices, and informatics through collaborations in quantitative and biomedical sciences.


Cohort Studies in Cancer Epidemiology, PAS-02-009

Amounts Available: Up to $500,000 in a study year

Deadline(s): January 17, 2003

Description: With the rise in recent research in gene-gene and gene-environment interactions, the National Cancer Institute seeks to advance the study of the role of cohorts within various cancers by integrating, prioritizing, and funding epidemiologic cohort studies. Issues of key interest to the NCI include the balance of cohort characteristics, rigor of exposure assessment, biospecimen collection and storage, bioinformatics, and availability of biospecimen resources to outside qualified investigators.


Technology Development for Biomedical Applications: Phased Innovation Award (R21/R33), PAR-02-091

Amounts Available: N/A

Deadline(s): June 1 and October 1, annually

Description: Sponsored by the National Center for Research Resources (, NHGRI (, and National Institute for Biomedical Imaging and Bioengineering (, the award supports new instruments, methodologies, and software to be used in biomedical research. The research may involve conceptualization, design, fabrication, and/or testing of new instruments, devices, or software. NHGRI maintains its support of bioinformatics and computational biology systems that would enhance research in genomic sequencing, human sequence variation (e.g., genotyping), functional genomics, and comparative genomics. High priority previously has been awarded to technologies to support comprehensive analyses of entire genomes or their products in cells and tissues.


AHRQ Small Research Grant Program, PAR-01-040

Amounts Available: Up to $100,000 for 12 to 24 months

Deadline(s): July 24, November 24

Description: The Agency for Healthcare Research and Quality sets aside a modest amount of funding to advance clinical informatics as a means of improving primary care practice, including evaluation of its impact on quality, outcomes, cost, and patient satisfaction. Projects can involve feasibility studies or pilots aimed at research to test the design of a large-scale study, and collection and analysis of quantitative or qualitative information for the purpose of hypothesis generation.


Large-Scale Collaborative Project Awards, GM-02-007

Amounts Available: $300,000 to $5 million

Deadline(s): January 15, 2003

Description: NIGMS sponsors these awards (known as large-glue grants) to help researchers form teams to solve a complex biological problem that would be beyond the means of any one research group. In addressing complex biomedical problems, research groups may need to develop core resources for information collection, coordination, and dissemination. Researchers can form a separate bioinformatics core to include assemblage and organization of data, developing tools for its querying, computation, and modeling. This bioinformatics core group may be combined with resources for instrumentation, genomics, proteomics, or high-throughput assay cores. Investigators should already hold funded research grants in the area of the proposal.

The deadline for smaller, phase I awards was in June 2002. Between $10 million and $15 million has been set aside in FY 2003 for the phase II deadline above, which generally reviews previous, amended submissions to the project awards.


University of California Discovery Grant

Amounts Available: Between $500,000 and $4 million per project, annually

Deadline(s): Three times per year: October, January, and May

Description: The UC Discovery Grant program is a three-way partnership between university researchers and students, private companies, and the state of California. Of the $60 million annually, about one-third has been directed toward biotechnology, one of six areas funded by the grants. Another area is life sciences information technology. Bioinformatics projects have been funded in both areas. The research has to be conducted through a University of California principal investigator. Private companies match contributions from the state on a dollar-for-dollar basis, and can contribute more than 50 percent of the funds in a project. Past participating companies include Maxygen and Neurogenetics.


Genomes to Life, US DOE Office of Science, Notice 02-13

Amounts Available: $50,000 to $2 million

Deadline(s): April 2003, estimated

Description: The DOE’s Genomes to Life program aims to develop the experimental and computational capabilities to predict the behavior of important microbes and microbial communities. Most recently, the program has begun to back projects on bioterrorist disease threats such as smallpox, but the agency remains open to the study of other microbes, metabolic pathways, regulatory networks, and whole-cell functions. Computational research on models and simulations relating to microbes, metabolic pathways, and high-throughput experimental data amounts to 25 percent of the program budget. In FY 2002, the budget totaled $15 million. The figure could double in FY 2003, according to DOE officials.


Large-scale genotyping for the haplotype map of the human genome, RFA HG-02-005

Amounts Available: Up to $16 million in FY 2003, generally awarded to two to four institutions

Deadline(s): May 2003, estimated

Description: A program directed toward large-scale genotyping across the genome based on samples from three populations. Researchers will develop a map of the haplotype patterns and of the genetic variants that can help detect these patterns. The haplotype map should aid in finding genes affecting health, disease, and human response to drugs and environmental factors.


Centers of Excellence in Genomic Science program, PAR-02-021

Amounts Available: $2 million to $5 million per year, for up to five years

Deadline(s): October 1, February 1, and June 1

Description: Institution-oriented grant designed to foster the integration of genomics with biomedical research. About five institutions should be funded between 2002 and 2003. Innovative ideas in bioinformatics and computational biology to increase public access and the number of user-friendly databases are encouraged as part of institutional applications that also may address comparative genomics, technology for functional genomics and human genome sequence variation.


Biotechnology Training and Technology Initiative, German Federal Ministry of Education and Research

Amounts Available: Variable

Deadline(s): Ongoing

Description: The ministry committed DM 100 million ($45.5 million) to fund six bioinformatics centers of excellence earlier this year as part of its Biotechnology 2000 program. The centers will include both academic and industry partners to promote public/private collaborations. The overarching goals of the program are to create unified standards for data integration, new bioinformatics tools, and to train new bioinformaticists.


Biomedical Research Collaboration Grants, The Wellcome Trust

Amounts Available: £6,000

Deadline(s): August 20, 2002

Description: An organizational grant designed to promote collaborations between research groups in the UK or Republic of Ireland and researchers in other countries. Generally, the trust favors collaboration between a UK or Ireland group and group based in another country to establish closer ties among scientists engaged in related fields of research. The grants are not designed to cover individual research programs at respective institutions.


Developing technologies, bioinformatics, and training solutions relevant to functional genomics, The Wellcome Trust

Amounts Available: £150,000 to £300,000 per year, typically over three years

Deadline(s): Ongoing

Description: Goals of the program include developing new tools relevant to single-cell imaging, proteomics, array technologies, and bioinformatics. Pilot, high-risk approaches are encouraged by the trust. Applicants also should consider novel approaches to training to include support for developing training courses and/or collaborative visits among researchers and students.


Bioinformatics Cross Committee, the UK Biotechnology and Biological Sciences Research Council

Amounts Available: To be determined

Deadline(s): N/A

Description: A priority area of the Biotechnology and Biological Sciences Research Council (BBSRC), the program aims to support the development and use of algorithms, software, and analytical methods to solve defined biological problems. In past years, the group received £8 million to support an e-science initiative. Recently, the BBSRC established the committee to encourage interaction between the biological sciences, bioinformatics, IT, computer science, mathematics, statistics, physics, and other related disciplines. Grant details will be decided in the second half of 2002.


Strategic grant focused on application of biomedical and health informatics to cancer or brain sciences, Medical Research Council, UK

Amounts Available: Typically £10,000 to £100,000 per year

Deadline(s): Ongoing

Description: As the focus of biomedical research shifts to protein structure, function, and interactions, as well as physiological pathways and systems biology, the council is inviting proposals in computational biology, health informatics, and/or e-science related to the priority areas of cancer and brain sciences. The expectation is that by studying large numbers of genes and proteins simultaneously, and by relating results to phenotype, scientists can begin to understand how component parts interact and how the interactions vary in normal and disease states. The UK government provides the majority of funding for the Medical Research Council through the Office of Science and Technology.


Genetic Information & Biological Function, Medical Research Council, UK

Amounts Available: To be determined

Deadline(s): N/A

Description: A continuation of the council’s work in genomics and biomedical science, decisions on the program should become available later this year when the governmental spending review (SR2002) is established for the years 2003 through 2006. In the SR2000 review, priorities were established for the years 2001 through 2004, which included £65 million in genomics research. About £8 million was awarded for health informatics, bioinformatics, and e-science. A sizable amount of funding also is available for open competition to universities in the UK. The UK government provides the majority of funding for the MRC through the Office of Science and Technology.


Sixth European Framework Programme 2002-2006

Amounts Available: To be determined

Deadline(s): N/A

Description: A major research initiative by the European Commission, the program has earmarked Euro 2.2 billion for genomics research in human health to be launched in the second half of 2002. Biotechnology and genomics for health are the top priority for the sixth program. In March, the commission awarded Euro 39.4 million to three research projects involving the genetics of twins, mouse genomics, and structural proteomics. The project involving the genetics of twins included bioinformatic scientists as well as geneticists, epidemiologists, and mathematicians.

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