Berkeley Bioinformatics Open-source Projects

Here's the BBOP folks...

Suzanna Lewis

Principal Investigator

MS. Biology
MS. Computer Science

I am a scientist at LBL and head the BBOP group. Basically this means I write grants and everyone else does the work.
I believe that the only way to develop effective software is through user-centered design. We have biologists on our development team so that the software designers get to know their needs (and can hear them swearing when something doesn't work).
I am interested in the management of large-scale biological data: describing it rigorously using ontologies; designing databases that are flexible enough to be easily maintained; quickly searching and accurately retrieving data; and presenting it effectively to researchers and biologists.

Chris Mungall

Bioinformatics Scientist: Gene Ontology, OBD, Chado,

B.S. Artificial Intelligence. University of Edinburgh

I lead the software and databases group within the Gene Ontology consortium, and am the lead developer on the OBD resource for the National Center for Biomedical Ontology. I am also involved in other projects such as the OBO Foundry and GMOD.

I previously worked as a bioinformatics specialist for the HHMI where I designed a number of genomics resources such as the Chado database (with David Emmert and others). Prior to that I was at the Roslin Institute (home of Dolly) in Scotland. I studied Artificial Intelligence at the University of Edinburgh.

My research interests center around the representation of biological reality, and the use of these representations to progress science and biomedicine. My old work page can be found here

Nicole Washington

Software Developer: Phenote, modENCODE

Ph.D. Molecular and Cellular Biology. University of Arizona.
B.S. Biology. Harvey Mudd College.

I'm interested in the intersection of computers and biological research by making useful tools for real-life bench biologists, that they actually use.

I'm the "data wrangler" for the Drosophila groups affiliated with the modENCODE project. I'm also involved in heavily testing the GMOD gbrowse browser. I also work on the Phenote project - I work with the biologists to get to know their needs, and turn them into requirements for writing the software. I also get my hands dirty once-in-awhile in the codebase. For OBD, I'm testing out the usefullness of a ontology-based datastore for all the annotations in the NCBO project, and beyond.

Before joining this group and learning the rigors of ontologies, I spent my time staring through a microscope at worm sperm in my Ph.D. at the University of Arizona.

Non-science interests: cycling, gardening, movies, life, whatnot

Seth Carbon

Software Developer: Amigo

BS Mathematics. UC Santa Cruz

Currently, I'm primarily working on AmiGO and AmiGO2 for the Gene Ontology Consortium. I am tangentially nibbling on a few other things too.

Before coming to Berkeley BOP, I've worked as an English teacher and programmer for the USGS SF Bay sedimentation group.

I'm new around here, so if you know any killer restaurants in the Berkeley/SF area, please let me know. Please.

My personal pages can be found here.

Ed

Software Developer: Apollo

E.O. Stinson

Software Developer: modENCODE

MS Bioinformatics. Notre Dame
BS Computer Science. Something

I'm working as a developer on the modENCODE project. I was also a lead developer on the VectorBase project, and so my recent experience is almost exclusively based on the development of web-based repositories for genomic information.

You can find various other information about me by following the links here.

Nomi Harris

Software Developer: OBO-Edit

MS Computer Science. MIT
BS Computer Science and Molecular Biology, Princeton

Nomi Harris has been part of the BBOP group (in its various incarnations) for over ten years, with a brief hiatus at a startup company. Her research interests center around visualization tools for biomedical information such as genome analysis results.

Nomi joined the Human Genome Informatics group at LBNL in 1995, where she developed Genotator, one of the first sequence annotation workbenches. She then became part of the Berkeley Drosophila Genome Project. From 2002-2006, she was the project manager for the Apollo genome annotation and curation tool. Currently, she is the project manager for OBO-Edit, an ontology editing tool that was written by John Day-Richter for the Gene Ontology project.

Nomi has been on the organizing committee for many bioinformatics and computational biology conferences, including the Bioinformatics Open Source Conference (BOSC) and the Annual Conference on Computational Genomics. Her publications list is here.

Amina Abdulla

Software Developer: OBO-Edit

MS Computational Biology, Carnegie Mellon University
MS Bioinformatics, University of Mumbai
BS Mathematics, University of Mumbai

I'm one of the lead developers for OBO-Edit. My research interests revolve around machine learning techniques for data mining and reasoning tools.

E-mail: ASAbdullah@lbl.gov, aabdulla@berkeleybop.org

Rob Bruggner

Software Developer: OBD

MS Molecular Biology. Notre Dame
BS Computer Engineering. Notre Dame

I'm an OBD developer. Documentation can be found here.

Previously, I was a lead developer / architect for the genomics resource VectorBase.org. Stemming from this, I'm interested in manipulation, storage, and automated analysis of large quantitites of genomic data.

In my spare moments, I can usually be found playing ultimate frisbee or building stuff.

Amelia Ireland

Software Developer: Amigo

MA Natural Sciences University of Cambridge, UK
Diploma, Computer Science, University of Cambridge, UK

I'm on loan to BBOP from the GO Editorial Office at the EBI for a year to help with the development of AmiGO and other GO-related projects.

and some BBOP affiliates...

Karen Eilbeck

Sequence Ontology

Ph.D. Biochemistry, University of Machester, UK
MSc Bioinformatics, University of Manchester, UK
BSc. Biological and Biochemical Science, University of Salford, UK

I spent nearly 3 years working for the BDGP - with Suzi and Chris, before moving to Utah. I am now a Research Assistant Professor in the Human Genetics Department at the University of Utah. I curate the Sequence Ontology for the Gene Ontology Consortium and am the PI on an NHGRI grant for the development of software to facilitate the use of SO.

When I am not at work, I am usually running, camping, or planning a trip to go camping.

and some BBOP alumni...