The following papers describe the ChemCell code and modeling problems it has been applied to.
If you wish to cite ChemCell, please use the Journal of Physics paper for now. A better paper has been submitted to Bioinformatics; we will post the reference here, if it is accepted.
If you send information about a paper that uses ChemCell results, I'll be pleased to add info about it to this page. Ditto for a picture or movie for the Pictures & Movies page.
This paper discusses results from network analyses performed with ChemCell:
Sensitivity Analysis of a Computational Model of the IKK-NF-kB-A20 Signal Transduction Network, J. Joo, S. J. Plimpton, S. Martin, L. Swiler, J. L. Faulon, Annals of the New York Acadamey of Sciences, Volume on Reverse Engineering Biological Networks, 1115, 221-239 (2007). (abstract)
This paper gives a brief overview of ChemCell and computational challenges for cell modeling:
Microbial cell modeling via reacting diffusing particles, S. J. Plimpton and A. Slepoy, Journal of Physics: Conference Series 16, 305-309 (2005). (abstract) (pdf)
This paper is about our Genomics:GTL (Genomes-to-Life) project funded by DOE's OBER and OASCR offices, that provided funding and motivation for the development of ChemCell. The author list is the entire project team!
Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling, G. S. Heffelfinger, ..., S. J. Plimpton, ..., OMICS - A Journal of Integrative Biology, 6, 305-330 (2002). (abstract)