Input files for 3 case studies

Last modification: 13 June 2011

M Dobrzynski, Jordi Vidal Rodriguez, Jaap A. Kaandorp, and Joke G. Blom (2007) Computational methods for diffusion-influenced biochemical reactions, Bioinformatics 23(15):1969-77 (link to journal site)
Centre for Mathematics and Computer Science (CWI), Amsterdam, The Netherlands

For questions and comments please email MD

Input files for 3 case studies:
  1. gene - simple gene expression (tar.gz file),
  2. rev - reversible reaction of two molecules, one fixed, other diffusing (tar.gz file),
  3. chey - diffusion of phosphorylated CheY through the cytoplasm in E.coli chemotaxis (tar.gz file).
After unpacking, every directory will contain three sub-directories:
  1. smoldyn - input files fo Smoldyn,
  2. mesord - input files for MesoRD,
  3. gmp - sources and input files for GMP.

To unarchive files with code type: tar zxf name_of_the_file
Archives contain directory structure.
Created by MD.