Biology's new online archive

The physics community's arXiv site creates a space for quantitative biology papers | By Charles Q Choi

Coordinators of a new quantitative biology ("q-bio") archive on the arXiv.org open-access preprint server are urging scientists interested in biological physics, computational biology, neural science, systems biology, bioinformatics, mathematical biology, and theoretical biology to subscribe and to submit preprints and reprints to the physics and math site.

"It will help biology by indirectly guiding physicists to work on problems of direct biological relevance," said q-bio archive co-coordinator Terry Hwa of the University of California, San Diego (UCSD). "It will enrich physics by providing a fresh, steady supply of interesting but complex phenomena arising in biology." Both experimental and theoretical contributions are welcome, he said.

"Having a common ground is a great benefit," said physicist Nigel Goldenfeld of the University of Illinois at Urbana-Champaign. "It is a place that biologists can explore to see what physicists are thinking about their subject. Previously, there was no single place where one could easily see the strength of interest from the physics community and the breadth of topics that are engaging us."

Hwa and fellow q-bio co-coordinator Michael Lässig at the University of Cologne note that the number of biology-related submissions to arXiv.org has steadily risen over the past few years, averaging more than 40 per month in 2003.

Before the archive was formed, these interdisciplinary submissions were scattered across a number of arXiv.org's subarchives, such as physics, nonlinear science, and math, reflecting the home field of the contributors rather than the papers' topic. Lassig and Hwa said that many researchers expressed a desire to have a centralized archive to share their latest life science–linked results and to learn about related findings by others.

"At the moment, q-bio papers are published in at least a dozen different journals, many of which are not regularly read by a large fraction of q-bio archive subscribers. It is very difficult to get a picture or keep updated of progress of any given subject. I believe the archive will make q-bio into a coherent field with a cohesive community," Hwa added.

The q-bio archive was officially launched September 15. When the submissions "become more mature, I hope to see more wet-bench biologists get involved, with the archive mediating a virtual dialogue between biologists and theoreticians," Hwa said. "I envision that the biologists will pose problems that need quantitative help by submitting their experimental findings to the archive, and theoreticians will regularly browse the archive for interesting biological problems."

While Hwa noted that journals already perform that function, "By experience, the informal style of the archive encourages more discussion, and its timeliness—days rather than months between the time of submission and posting—can make a tremendous difference."

The physics community has proven very successful in creating open-access archives, said Chao Tang, a senior research scientist at NEC Laboratories America and an arXiv.org contributor. "Now, when people in physics write papers, they submit to arXiv.org before they send it to any journal, so others can read it quickly. It's become a very important depository for preprints to exchange ideas quickly," he noted. "People don't usually worry about others stealing their ideas. The biology community has been far behind. It's much more secret in this aspect."

So far, categories in the q-bio archive range from molecular structures and subcellular processes to tissues and organs, from cell behavior to population and evolutionary dynamics. A separate category is devoted to method-dominated (p)reprints, including computational algorithms, experimental methods, and novel approaches to analyzing experimental data. Many biology-related contributions submitted to arXiv.org over the past decade have already been categorized via automation.

The current category list is a compromise between the large number of subjects in biology and the areas in which arXiv.org has received the most contributions in the past. Hwa and Lassig expect the subject list to be updated as major active areas develop or shift over time. An advisory committee of biologists, including UCSD's William Loomis, Chuck Stevens of the Salk Institute, Gary Stormo of Washington University, and Diethard Tautz at the University of Cologne, will oversee the archive's continuous restructuring.