BioInfo SIG: BioLingua: A Biologist's Computational Workbench



  • Monthly Meeting of the Bioinformatics SIG



    Jeff Shrager, JP Massar, and Mike Travers - The BioLingua Development Team

    Presentation Overview

    BioLingua is a biological programming environment developed through a close collaboration between biologists and software engineers. Its design flies in the face of the common principles of current bioinformatic engineering: Rather than access remote databases, we warehouse data and knowledge locally in order to permit efficient analysis; rather than provide push-button interfaces to complex tasks, we provide a live programming language (BioLingua) designed for convenient use by biologists themselves; rather than operate in a world of flat files (or flat databases) BioLingua operates in live knowledge framework that integrates the data and knowledge relevant to specific biological communities; rather than let users work in their own little worlds, we provide an integrated community code and knowledge repository; and rather than offer a morass of tools that do not smoothly talk to one another, we use a combination of programming language constructs and framework objects to integrate tools with one another. The result is a completely new concept in computational biology where Biologists, not programmers, are the users, and our goal is to serve their computational needs, rather than the computational needs of the "pet programmers" who often work for them. BioLingua is not merely a vision; It is a real, running, system, live on the web and being used (in Alpha) by a number of biologists around the world. In this talk we'll cover all aspects of BioLingua, from its inception through its current state, and including plans for the near and not-so-near future.


    About the Presenters

    Jeff Shrager is the PI of the BioLingua project. He is a Research Fellow at the Carnegie Inst. of Washington, Dept. of Plant Biology, and Consulting Associate Professor of Symbolic Systems at Stanford.

    JP Massar is the BioLingua core engineering lead. He is a symbolic systems and bioinformatics engineer.

    Mike Travers is the lead knowledge representation and interface designer and engineer on BioLingua.

    Jeff comes from CMU, whereas JP and Mike both hail from MIT.


    Event Logistics:



    Hanson Bridgett

    333 Market Street, 21st Floor

    San Francisco, CA, 94105

    Note: Location provided courtesy of Hanson, Bridgett, Marcus, Vlahos, Rudy, LLP.


    6:30 - 7:00 p.m. Registration and Networking

    7:00 - 9:00 p.m. Presentation



    $15 at the door for non-SDForum members

    No charge for SDForum members

    Please call 408.494.8378 for student memberships

    Registration NOT required

    More on the BioInformatics SIG....