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…
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
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…
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…
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.
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.
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…
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…
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…
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
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…
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…
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.
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.
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…
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…