By Bio-IT World Staff
March 5, 2013 | Bioinformatics.org has released the five finalists for the 2013 Benjamin Franklin Award for Open Access in the Life Sciences. Voting is open until Sunday, March 10.
The finalists are:
- Hilmar Lapp, National Evolutionary Synthesis Center
- Aaron Quinlan, University of Virginia
- Alan Ruttenberg, University at Buffalo
- Steven Salzberg, Johns Hopkins University
- Owen White, University of Maryland
Hilmar Lapp, National Evolutionary Synthesis Center
Hilmar Lapp exemplifies a researcher who makes open access to code and data a central focus of his career. While his career began in traditional bioinformatics, Hilmar, beginning in the early part of the last decade, began his involvement with open source software, and subsequently open data. After assuming his present position as Assistant Director for Informatics at the National Evolutionary Synthesis Center (NESCent), he pushed for changes in the everyday practice of both informatics staff and NESCent's visiting scientists and post doctoral fellows—encouraging and frequently requiring that code be shared and data made available. He did this both by initiating work groups in evolutionary informatics (http://www.evoio.org/wiki/HIP) that lead to a continuing series of hackathons at NESCent and elsewhere, and as founding chair of the iEvoBio (http://iEvoBio.org/about) satellite conferences that provided informaticians working in evolutionary biology a chance to meet, share, and demonstrate their ideas and tools in association with the national Evolution meetings. He was also involved in the initial development of the Dryad digital repository (http://datadryad.org/), a repository for data associated with publications in evolutionary biology and related fields. More recently, Hilmar has moved beyond sharing data to encouraging the movement of data out of 'silos' into linked, semantically tagged resources. In addition to his work at NESCent, Hilmar currently serves as President of the Open Bioinformatics Foundation (http://www.open-bio.org/).
Aaron Quinlan, University of Virginia
Aaron Quinlan wrote BEDTools (http://code.google.com/p/bedtools/,
http://bioinformatics.oxfordjournals.org/content/26/6/841.short), a flexible suite of utilities for comparing genomic features, and is releasing this software in a free, open, and robust way (regression tests, bug tracker, distributed source repository, etc.). This high-quality work builds upon common standards and helps reducing the proliferation of data formats. It empowers many biologists to analyze their data by themselves, which is Free Software at its best.
Alan Ruttenberg, University at Buffalo
Alan Ruttenberg is a tremendous force in making data open and efficient on the web. He is not only a fervent advocate of open access, but he also develops standards and tools needed to understand, analyze and reproduce shared data. He was a central developer of the BioPAX, Pathway exchange language for Biological pathway data (http://www.biopax.org/). He is the driving force behind the Neurocommons effort (http://neurocommons.org/, http://bib.oxfordjournals.org/content/10/2/193.short), a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences, and part of the Science Commons endeavor. He has been involved in multiple W3C activities, such as the Health Care Life Sciences Interest Group (http://www.w3.org/blog/hcls/), and more recently he was a chair of the OWL2 working group (http://www.w3.org/2007/OWL/wiki/OWL_Working_Group). He is a coordinator for the OBO Foundry consortium (http://obofoundry.org/coordination.shtml) and is involved in development of several ontological resources such as the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), the Adverse Event Reporting Ontology (AERO) and BioPAX-OBO for representing molecular and cellular pathways. Alan is a pioneer in his work; he encourages everybody, whether they are students, professor, data providers or policy makers to share open data, and provide support in helping them do so on a daily basis.
Steven Salzberg, Johns Hopkins University
Steven Salzberg has made many contributions to open access bioinformatics software, beginning with the pioneering system for bacterial gene finding, Glimmer (http://cbcb.umd.edu/software/glimmer/), and the MUMmer (http://mummer.sourceforge.net/) whole-genome alignment package. His group has built a suite of next-generation sequencing tools including Bowtie (http://bowtie-bio.sourceforge.net/index.shtml), TopHat (http://tophat.cbcb.umd.edu/), and Cufflinks (http://cufflinks.cbcb.umd.edu/), which have been adopted by thousands of scientists around the world, and have collectively been downloaded over 200,000 times. Salzberg has developed open source software for genome assembly as well, launching the AMOS project (http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS) that includes many assemblers and assembly utilities. He has publicly advocated for greater sharing of data, and was the co-founder of the Influenza Genome Project, which sequenced thousands of strains of the influenza virus. Salzberg has also advocated forcefully against both software and gene patents, publishing many commentaries in high-profile journals and on his genomics (http://genome.fieldofscience.com/) and Forbes (http://blogs.forbes.com/stevensalzberg/) blog sites.
Owen White, University of Maryland
Owen White is a long-time supporter of open source development. He has spearheaded or contributed to multiple projects that provide software and computing resources to the research community free of charge. His current projects include The Data Intensive Academic Grid (http://diagcomputing.org/), which provides academic researchers free access to computational infrastructure for large-scale analysis through cloud environments, direct access, and virtual machines; the Open Science Data Framework (OSDF) (http://osdf.igs.umaryland.edu/), which is an open source architecture for the efficient capture, linking, and retrieval of multiple complex datasets and associated metadata, and has been used to store and deliver information from the Human Microbiome Project (HMP) made available through the HMP Data Analysis and Coordination Center website (http://www.hmpdacc.org/). Owen is also involved with the Annotation Engine (http://ae.igs.umaryland.edu/cgi/index.cgi), which provides free prokaryotic genome analysis to the research community giving users access to IGS-developed pipelines and tools and includes is the open source annotation curation and visualization tool Manatee (http://manatee.sourceforge.net/igs/index.shtml), currently in use by hundreds of researchers.