Version 1.1

This code was used for Kazakiewicz D, Karr JR, Langner KM & Plewczynski D. Combined systems and structural modeling repositions antibiotics for Mycoplasma genitalium. (In submission).

DREAM8 whole-cell parameter estimation challenge (Karr et al., 2015)

Code used for DREAM8 whole-cell parameter estimation challenge.

A complete example of how to score the challenge, including generating sample submissions is available here.

See also:

• Whole-cell parameter estimation DREAM challenge
• Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA & Meyer P. Summary of the DREAM8 parameter estimation challenge: Toward parameter identification for whole-cell models. PLoS Computational Biology 11, e1004096 (2015).

Synthetic gene network simulations (Purcell et al., 2013)

Code used for synthetic gene network simulations in: Purcell O, Jain B, Karr JR, Covert MW & Lu T. Towards a whole-cell modeling approach for synthetic biology. Chaos 23, 025112 (2013).