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2012 Benjamin Franklin Award Finalists Named

By Bio-IT World Staff 

February 28, 2012 | has announced the finalists in the 2012 Benjamin Franklin Award.  

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. Winners are chosen by voting members of  

The 2012 winner will be announced at the Tenth Anniversary Bio-IT World Conference and Expo on April 25 in Boston. For more details, visit   

2012 Finalists:  

Helen Berman, Rutgers University 

At a time when the concept of data sharing was in its infancy, Helen was a champion of the open access of scientific information. At her instigation, the Protein Data Bank (PDB) was established with only 7 structures in 1971. As head of the Research Collaboratory for Structural Bioinformatics (RCSB), Helen became the Director of the PDB in 1998, and developed the RCSB PDB into a vital and key resource for biology. Her passion for making structural data accessible and understandable by a broad community has driven the development of other bioinformatics resources.  These include the Electron Microscopy Data Bank (EMDB), a global deposition and retrieval network for cryoEM map, model and associated metadata; the Nucleic Acid Database, a resource for information about nucleic acid structure; and the Structural Biology Knowledgebase (SBKB), a comprehensive resource that integrates the results of structural biology and genomics efforts with other publicly available  biological information to facilitate further research. 


Carole Goble, University of Manchester 

Carole is widely recognized as a visionary in the development of software to support automated workflows in biology. She has been a leader of the myGrid and Open Middleware Infrastructure Institute consortia, which have generated a large number of highly innovative open resources for e-research in the life sciences including the Taverna Workbench for developing and deploying workflows in the life sciences, the BioCatalogue registry of bioinformatics web services, and the social-networking based myExperiment workflow repository. Goble has also played an instrumental role in the development of semantic-web tools for constructing and analyzing life science ontologies, the development of ontologies for bioinformatics tools, as well as ontology-based tools such as RightField for managing life science data. 


Eugene V. Koonin, NCBI/NLM/NIH 

Eugene is a cofounder of Biology Direct, a new approach to open peer review, when all the reviews become published with the paper, being signed.  He is still an Editor in Chief, and controls review process in the field of computational biology.  He has numerous and varied contributions to both open access in bioinformatics and computational biology, e.g. PSI-BLAST and COGs (Clusters of Orthologous Groups).  His organization of the COG project opened up the field of comparative genomics, allowing many computational and experimental biologists a new avenue of access to enormous repositories of sequence data, as well as allowing investigators to make sense of their research areas in the light of evolution.  He is an editor for several open access journals, e.g. an editorial board member for BMC Biology and an editorial advisor for PLoS Computational Biology [5]. Lastly, Eugene has 83 articles published in BioMed Central journals (all of them open access). 


Heng Li, Broad Institute 

Dr Li Heng has been a fundamental contributor to widely used open source software. He is mostly known these days for his essential contributions to the next generation sequencing (NGS) field with tools like SAMtools, BWA, MAQ, TreeSoft and TreeFam, that have in many cases been adopted as standard sequencing analysis tools. Before his involvement in NGS, Heng developed algorithms for the analysis of gene family evolution, namely TreeBeST, and he participated in the TreeFam and Ensembl GeneTrees databases. He is remarkably active in open forums for bioinformatics like and, always ready to lend a helping hand to new users in the field. Heng has also focused in pure research projects, and as an example, he published a fundamental piece of work in the field of human genetics in the inference of human population history from individual whole-genome sequences


John Quackenbush, Dana-Farber Cancer Institute & Harvard School of Public Health 

One of John's biggest contributions to promoting open access in bioinformatics has been his long-standing leadership in the development of open source, freely available software tools for genomic data. For example, the TM4 Microarray Software Suite was a project that he started with colleagues and collaborators at TIGR over ten years ago. The development of a specific module, MeV, which handled the bulk of the analysis component in the TM4 tool suite, has been a primary focus of the Quackenbush lab, and MeV has grown into its own formidable software suite. More recently, John led an initiative to create a collaborative data research portal, which made available analysis tools to allow investigators to answer questions by combining clinical and molecular assay data. As one of the founding members of the Functional Genomics Data Society (FGED), John has been instrumental in making data both available and useful.  He helped set the MIAME standards, and among them is the MAGE-TAB format, which has impacted countless other data sharing standards.  As the newly elected president of FGED, he has also been advocating for reproducible research, including sharing of the data as well as the software used to analyze it. 


Bruno Sobral, Virginia Bioinformatics Institute 

Bruno is the Director of the Cyberinfrastructure Division of Virginia Bioinformatics Institute (VBI). He was the founding executive and scientific director and professor of VBI. In addition to the numerous publications in the area of bioinformatics and genomics, Bruno is the brain behind Pathosystems Resource Integration Center (PATRIC). The freely available PATRIC platform provides an interface for biologists to discover data and information and conduct comprehensive comparative genomics and other analyses in a one-stop shop. Bruno also has contributed to the development of Biological Pathway Exchange (BioPAX) language and Pathogen Information Markup Language (PIML). 


Janet Thornton, European Bioinformatics Institute 

Janet is Director of the European Bioinformatics Institute and Scientific Coordinator of the BioSapiens project. She has made a diversity of contributions to open access in bioinformatics including many software tools and databases, e.g. CATH: A Hierarchic Classification of Protein Domain Structures, the Enzyme Structures Database, the Atlas of Protein Side-Chain Interactions.  She has also published extensively in open access journals.  As director of the EBI she has made substantial contributions to the open availability of data and tools for the broader community. 

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