How Perl Saved the Human Genome Project

by Lincoln Stein

http://www.bioperl.org/wiki/How_Perl_saved_human_genome

THE PROBLEM: Although the two centers use almost identical laboratory techniques, almost identical databases, and almost identical data analysis tools, they still can't interchange data or meaningfully compare results.

THE SOLUTION: Perl.

The human genome project was inaugurated at the beginning of the decade as an ambitious international effort to determine the complete DNA sequence of human beings and several experimental animals. The justification for this undertaking is both scientific and medical. By understanding the genetic makeup of an organism in excruciating detail, it is hoped that we will be better able to understand how organisms develop from single eggs into complex multicellular beings, how food is metabolized and transformed into the constituents of the body, how the nervous system assembles itself into a smoothly functioning ensemble. ..... Altogether, people estimate that some 1 to 10 terabytes of information will need to be stored in order to see the human genome project to its conclusion.

So what's Perl got to do with it? From the beginning researchers realized that informatics would have to play a large role in the genome project. An informatics core formed an integral part of every genome center that was created. The mission of these cores was two-fold: to provide computer support and databasing services for their affiliated laboratories, and to develop data analysis and management software for use by the genome community as a whole. .....

Perl has been the solution of choice for genome centers whenever they need to exchange data, or to retrofit one center's software module to work with another center's system.

So Perl has become the software mainstay for computation within genome centers as well as the glue that binds them together. Although genome informatics groups are constantly tinkering with other "high level" languages such as Python, Tcl and recently Java, nothing comes close to Perl's popularity.