jkarr

5 ms·

1.
by jkarr 14y ago
A variety of reasons really. In no particular order: - Still has good math support, rapid development - Better OOP support - More libraries -- everything from web development to scientific computing to GUIs to databasing - More reliable, le
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by jkarr 14y ago
We used a combination of representing copy numbers of molecular species and representing individual molecules of a few specific types: DNA polymerase, RNA polymerase, ribosome, FtsZ
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by jkarr 14y ago
We used a combination of tracking concentrations and individual molecules. For specific macromolecules like DNA polymerase, RNA polymerase, ribosomes, etc we kept track of the position of each individual molecule. For other things like gluc
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by jkarr 14y ago
Agreed. MATLAB its set of downsides. On the plus side development is rapid and since 2008 it has good support for classes. We're starting to move toward python for future work. I think MATLAB itself isn't so bad, so much as the way its typi
5.
by jkarr 14y ago
All of the source code is available at http://simtk.org/home/wholecell . http://wholecell.stanford.edu provides a searchable interface to our training set database.
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by jkarr 14y ago
All of the supplementary material is available at http://simtk.org/home/wholecell . http://wholecell.stanford.edu provides a search interface to all of the training data.
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by jkarr 14y ago
The model is "M. genitalium" in the sense that it attempts to predict M. genitalium's phenotype from its genotype. In order to build the model we needed to use data from many additional organisms. In that sense, the model represents a hybri
8.
by jkarr 14y ago
We used MATLAB. We organized the training data into a database (referred to as the "knowledge base") which was implemented in MYSQL with a web-based UI implemented in PHP. The various other scripts in shell and Perl were used to run the mod