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2016 Open Source Awards Finalists Named


By Bio-IT World Staff

February 17, 2016 | Bioinformatics.org has announced the nominees for the 2016 Benjamin Franklin Award. Voting is open now to Bioinformatics.org members. The winner will be announced at the 2016 Bio-IT World Conference & Expo.

The Benjamin Franklin Award is a humanitarian/bioethics award presented annually by Bioinformatis.org to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. This year’s finalists include the founder of the Encyclopedia of Life; the founder of BioRuby; the past president of the International Society for Computational Biology; and leader of the Human Metabolome Project.

Bioinformatics.org members can vote at http://www.bioinformatics.org/franklin/ until Friday, Feb. 19.

2016 finalists are:

Gary Bader, The Donnelly Centre, University of Toronto

Gary Bader is leading a group in computational biology at the University of Toronto and has promoted community efforts for a long time.  As a Ph.D. student, he developed the Biomolecular Interaction Network Database (BIND), one of the first of dozens of molecular interaction databases.  He also plays an active role in the development of open-source biological pathway and network data exchange formats, including PSI-MI and BioPAX; databases such as cPath, Cancer Cell Map, and Pathway Commons; and visualization and analysis software such as Cytoscape.

Benjamin Langmead, Johns Hopkins University

Ben Langmead is one of the most influential and highly cited authors of open source bioinformatics software.  His Bowtie read alignment tool and its sequel Bowtie 2 are widely used, with more than 10,000 citations between them, and they are used within more than 50 other software tools.  Ben also has a series of publications on open source cloud-enabled tools that have collectively pushed back the frontier of what everyday biological researchers can do with large sequencing datasets.  All of Ben's software, and all the software from his lab, are free and open source.  He has also made available a large collection of open teaching resources that have become very popular.

Aaron Quinlan, University of Utah

Aaron Quinlan is a longtime contributor of open source software, going back to the early days of next-generation sequencing.  Open source software tools authored by Aaron and his lab members include Gemini, BEDTools, Lumpy, and many others.

Torsten Schwede, Swiss Institute of Bioinformatics and University of Basel

Torsten Schwede has been a champion in bringing the modeling community together and in making protein models easily accessible to everyone.  In the 1990s, Torsten first started working with others on the SWISS-MODEL modeling platform and repository (SMR, swissmodel.expasy.org).  It is still one of the most widely used modeling servers to date, helping thousands of researchers per month.  In 2007, he established the Protein Model Portal.  Torsten also produced two public access tools: CAMEO, a server that allows developers to continuously evaluate the accuracy and reliability of their predictions; and Model Archive, the first public repository for in silico structural models.

Thomas Wu, Genentech

Thomas Wu developed the GMAP and GSNAP short read aligners in 2005 and made it publicly available to anyone, and he continues to develop and support this software tirelessly.  GSNAP is a complex, flexible and reliable aligner which is supported largely by this one person working at a for-profit institution—a credit to both him and his company, Genentech.

 

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