INTRODUCTION 17
for academic work at the interface. The Keck Foundation and the Sloan Foundation supported training,
and numerous database activities have been supported by federal agencies. As the impact of the Human
Genome Project and comparative genomics began to reach the community as a whole, the situation
changed. An important step came from the Howard Hughes Medical Institute, which in 1999 held a
special competition to select professors in bioinformatics and thus provided a strong endorsement of
the role of computing in biology.
In 1999, the National Institutes of Health (NIH) also took a first step toward integrating ad hoc
support by requesting an analysis of the opportunities, requirements, and challenges from computing
for biomedicine. In June 1999, the Botstein-Smarr Working Group on Biomedical Computing presented
a report to the NIH entitled The Biomedical Information Science and Technology Initiative.^16 Specifically
tasked with investigating the needs of NIH-supported investigators for computing resources, including
hardware, software, networking, algorithms, and training, the working group made recommendations
for NIH actions to support the needs of NIH-funded investigators for biomedical computing.
That report embraces a vision of computing as the hallmark of tomorrow’s biomedicine. To acceler-
ate the transition to this new world of biomedicine, the working group sought to find ways “to discover,
encourage, train, and support the new kinds of scientists needed for tomorrow’s science.” Much of the
report focuses on national programs to create “the best opportunities that can be created for doing and
learning at the interfaces among biology, mathematics, and computation,” and argues that “with such
new and innovative programs in place, scientists [would] absorb biomedical computing in due course,
while supporting the mission of the NIH.” The report also identifies a variety of barriers to the full
exploitation of computation for biological needs.
In the intervening 4 years, the validity of the Botstein-Smarr Working Group report vision has not
been in question; if anything, the expectations, opportunities, and requirements have grown. Computa-
tion in various forms is rapidly penetrating all aspects of life sciences research and practice.
- State-of-the-art radiology (and along with it other fields dependent on imaging—neurology, for
example) is highly dependent on information technology: the images are filtered, processed reconstruc-
tions that are acquired, stored, and analyzed computationally. - Genomics and proteomics are completely dependent on computation.
- Integrative biology aimed at predictive modeling is not just computationally enabled—it literally
cannot occur in a noncomputational environment.
Biomedical scientists of all stripes are increasingly using public resources and computational tools
at high levels of intensity such that very significant fractions of the overall effort are in this domain, and
it is highly likely that these trends will continue. Yet many of the barriers to full exploitation of compu-
tation in the biological sciences that were identified in the Botstein-Smarr report still remain. One
primary focus of the present report is accordingly to consider the intellectual, organizational, and
cultural barriers that impede or even prevent the full benefits of computation from being realized for
biomedical research.
1.4.3 The Biology-to-Computing Interface
The application of biological ideas to the design of computing systems appears through much of the
history of electronic computers, in most cases as an outgrowth of attempts to model or simulate a
biological system. In the early 1970s, John H. Holland (the first person in the United States to be
awarded a Ph.D. in computer science) pioneered the idea of genetic algorithms, which use simulated
genetic processes (crossover, mutation, and inversion) to search a large solution space of algorithms.^17
(^16) Available at http://www.nih.gov/about/director/060399.htm.
(^17) J.H. Holland, Adaptation in Natural and Artificial Systems, University of Michigan Press, Ann Arbor, 1975.