Skip to main content

Pathways and Language Processing are Hot Topics at PSB


Despite the difficulty many people say they have convincing the home office of the necessity to be at an academic conference in Hawaii in January, attendance at the Pacific Symposium for Biocomputing this year was up 60 percent from last year. About 400 scientists from academia and industry made it to Mauna Lani for the four-day meeting, January 4-7.

And according to attendees’ responses to a survey conducted by the organizers, the meeting was no boondoggle. Co-chair Larry Hunter, director of the Center for Computational Pharmacology at the University of Colorado, said attendees’ assessments were “uniformly positive.” Posters and presentations got raves for high scientific quality, timeliness, and variety. And when asked if future conference agendas should allow for free time, respondents made remarks such as “10 pm to 8 am is already free time,” and “lunch and dinner is free time.” What beach?

Indeed, most scientific presentations were well attended. The meeting opened with a discussion of high-performance computing for computational biology, followed by David Haussler’s keynote address on the challenges of assembling and finding genes in the human genome.

But attendees rated discussions of pathways, natural language processing, and clinical informatics as favorites. Several papers on the subject of pathway informatics were followed by an afternoon meeting of the Biopathways Consortium, which now claims nearly 200 members. According to Eric Neumann and Vincent Schachter, who, with Peter Karp, have fostered the consortium, the group’s goal is to develop a high-level lingua franca that will allow integration of pathways informatics tools.

Seven separate presentations addressed methods for text extraction from biological literature. Discussion after one presentation led the audience to spontaneously agree to establish a website for collaborative work in the area of structure prediction by natural language processing (write to [email protected]).

And despite Isaac Kohane’s gloomy assessment of the state of clinical data — where antiquated systems have been designed with multiple, conflicting purposes — many attendees were heartened by a discussion of integrating genomics data with clinical informatics. “That’s the reason we’re here,” remarked an industry bioinformatician. “How do you integrate all this information so it becomes useful for medical applications?”

An evening lecture on ethics also got people talking. Hunter, who spoke about scientists’ ethical responsibilities, later remarked, “We’re privileged by virtue of our education and experience and understanding, and there’s a payback principle. We’re responsible for understanding and anticipating the consequences and making clear what we need to worry about.”

All but a few attendees suggested that registration should be capped at 400 to keep the meeting at its current size. Organizers say that’s just fine with them. If the Intelligent Systems for Molecular Biology meeting becomes the larger annual venue for discussion of some of these topics, PSB’s organizers are pleased to be the more intimate gathering.

Said cochair Teri Klein, a senior scientist at Stanford and director of the PharmGKB database, “The meeting is designed to foster networking and interactions and impromptu conversations.” That just might require cutting off registration early next year.

— Adrienne Burke

Filed under

The Scan

US Supports Patent Waivers

NPR reports that the Biden Administration has announced its support for waiving intellectual property protections for SARS-CoV-2 vaccines.

Vaccines Versus Variants

Two studies find the Pfizer-BioNTech SARS-CoV-2 vaccine to be effective against viral variants, and Moderna reports on booster shots to combat variants.

CRISPR for What Ails You

The Wall Street Journal writes that CRISPR-based therapies could someday be used to treat common conditions like heart attacks.

Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.