Software

Software development

I have managed the planning, development and launch of multiple bioinformatics resources:

• 2014-2020: Director of the Online Graduate Certificate Program in Applied Bioinformatics
• 2011-present: Director of the Bioinformatics Consulting Center at Penn State
• 2010-2011: Director of the Center for Translational Informatics at Penn State Hershey Medical School,
• 2006-2012: Bioinformatics Director of the Genome Cartography Project at Penn State

Programming

I have extensive software development experience having served as primary or lead developer on the numerous web-enabled software tools:

• GitHub profile
• Google code profile
• Biostar Central

Biostars: Questions and Answers

Built as an open source software it now powers the Galaxy and Bioconductor user support sites:

• Biostars: Bioinformatics Questions and Answers
• Bioconductor User Support

Over past five years Biostar powered sites met the information needs of over ten million users and served over fifty million page views.

Research computing

Research orientied software projects that I have been responsible of:

• 2010-2013: Biostar Central a python based question and answer framework that runs the Biostar website
• 2013: PyBlue micro framework for static website generation with support for bioinformatics reporting
• 2008-2011: BooleanNet, a Boolean network simulation software for life sciences .
• 2006-2011: GeneTrack a bioinformatics software package for storing, querying and visualizing interval oriented data.
• 2006-2007: MiniDB, a data storage system for microarray research. A collaboration with Frank Pugh ( folded into the Genome Cartography Project).
• 2004-2006: Galaxy lead developer of Galaxy between 2004-2006, a web-based data analysis framework
• 2004-2011: LionDB Lead developer of LionDB, a laboratory data management system in continuous operation since September, 2004 it served the data exchange needs of the life science researchers at Penn State.
• 2001-2003: MovieLens I served as lead developer of Movielens between 2001-2003. A movie recommendation site using advanced data mining and novel user interfaces. The site is run by the GroupLens research lab in the Department of Computer Science and Engineering at the University of Minnesota.