Joshua is a first year Ph.D. student in the Biophysics
Graduate Group at U.C Berkeley. He is currently completing
the rotation phase of the program in several computational laboratories.
He received a B.S. in Biology with a concentration in Biophysics
from Haverford College in 2001. During the intervening years,
Joshua conducted fluorescence microscopy
research at the German Cancer Research Center (DKFZ) in Heidelberg,
Germany and was in residence at Harvard University doing single
molecule
spectroscopy.
Project Contributions:
Computational Engine:
- Implementation of the Heymans algorithm and Hungarian Algorithm
- Supporting classes to convert Pathway Graph into an Enzyme Graph, and to calculate
similarity scores between reactions. Container Classes:
- Simple modifications to some container classes as well as design suggestions GUI:
- Implementation of JUNG graph renderer and GUI layout
Josh England (
)
Josh is a researcher in the field of high performance computing
and networking, currently working at Sandia National Laboratory.
He received a B.S. in computer science from the New Mexico Institute
of Mining and Technology, and has done research while employed
at the Energetic Materials Research and Testing Center in Socorro,
NM, and Integrated Genomics, Inc. in Chicago, IL.
Project Contributions:
Data Input and Container
Classes:
- Parsers for BioCyc data
- Design and implementation of container classes Pathway Graph:
- Construction of Pathway Graphs GUI: Implementation of JUNG graph renderer and GUI layout
Alex Chen (
)
Alex is fourth year undergraduate in the department
of Electrical Engineering and Computer Science at UC-Berkeley.
Project Contributions:
Perl Scripts to find E.C numbers: - Implement
various methods to get EC number for each enzyme(protein), either
by looking through local dat files, or access swissprot database
remotely, or BLAST the sequence to find and use the
EC number of its similar enzyme(protein).
- This code does not directly link into PWComp. It's interaction
is a goal for future releases, however at this time we do not guarantee
its functionality. (Download)