Here are some of my current and recent projects and activities:
- Preservation of knowledge & data – I'm part of the
Caltech Digital Library Development team, have been active in
community efforts such as Data Together,
and researched decentralized
- CASICS – Comprehensive and Automated
Software Inventory Creation System, a way to catalog software
by leveraging ontologies and machine learning. This has produced
numerous reusable software modules:
Python module that infers whether a given short string of
characters is likely to be random gibberish or something
- Dassie, a database
of the subject term hierarchies found in
of Congress Subject Headings (LCSH).
- Spiral, a
library of functions for splitting class names, function names
and other identifiers found in source code files.
- SBML – A community standard
format for exchanging computational models in biology. In addition
to SBML specifications, some of the notable open-source software
I co-developed include the following:
a program to convert certain classes of MATLAB ODE-based models
into SBML. It does not require MATLAB. Some of
its innovations include a Python-based parser for MATLAB.
- SBML Test Suite.
This includes a Test Runner written in Java with the
SWT GUI widgets and
bundled as a self-contained desktop app.
- libSBML, an
API library for reading, writing, manipulating, and validating
SBML files and data streams in
many languages including C++, Java, MATLAB, Python, R and
- COMBINE – The COmputational
Modeling in BIology NEtwork, a community group to help
coordinate the development of standards and resources for
computational modeling in biology.