Software projects¶
Modern life sciences research increasingly relies on information technology: data storage, custom algorithms, advanced search and query mechanisms, streamlining recurring tasks, presentation and visualization interfaces. I’m most interested in applying modern and sophisticated computational solutions to diverse biological problems. I have lead the development of several software projects, some with teams, others as sole developer. Here is a quote that best capture my philosophy:
One of the big insights in the last few years, through work by the internet search engines but also tools like Udi Manber’s glimpse, is that data with no meaningful structure can still be very powerful if the tools to help you search the data are good [...] Expect more liberation as searching replaces structure as the way to handle data – Rob Pike
Data Management¶
Currently I oversee the operations of various bioinformatics resources:
- 2010-2011: Director of the Center for Translational Informatics
- 2010-2011: Director of the Bioinformatics Consulting Center
- 2006-2011: Bioinformatics Director of the Genome Cartography Project
- 2005-2011: LionDB Data Sharing Manager
Data Analysis Software¶
I have extensive software development experience having served as primary or lead developer on the numerous web-enabled software tools:
- 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 (funded by NSF, served as Co-PI between 2004-2005). A collaboration with Anton Nekrutenko, James Taylor and Ross Hardison (2005)
- 2004-2011: LionDB Lead developer of LionDB, a laboratory data management system in continuous operation since September, 2004 it serves the data exchange needs of the life science researchers at Penn State. A collaboration with Naomi Altman and Craig Praul (2004).
- 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.