Careful Curation and Documentation of default parameter file

[WilliamIX]

Currently the default parameter file is somewhat ad-hock using a Mixture of parameter values taken from Cell Biology by the Numbers and some back of the envelope guesses.

All parameters in this file should have citations and/or supporting calculations!

I am thinking we should have a few default parameter files for different organisms/situations: e coli, e coli extract, yeast, and mammalian perhaps? Here is a first pass at a list of parameters:

• Default values of kb, ku, kcat ,ktx ,ktl, kcat. These can be order of magnitude estimates from published data.
• Default values for "strong", "medium", and "weak" for binding / unbinding. these can be order of magnitude estimates based upon binding energy and temperature (for ku) and kb is related to diffusion.
• Specific for machinery: these should include ribosome, polymerase, and endonuclease concentrations, and values for every single tx and tl Mechanism that are rescaled appropriately.

Possible data Sources:

• E. Coli: Many sources, especially Vipul's newest paper.
• Megaterium: Paul Freemont's paper
• Cell Numbers Data base and Cell biology by the Numbers
• Yeast: I think Tom Ellis' group has some good papers with models
• Mammalian: Maybe Elowitz has some papers?

Questions:

• Should we include specific parameters for some synthetic biology parts such as common promoters and RBSs? because we aren't actually collecting data, I suggest NO.
• Is there a way to add different Species.material_types into the parameter defaulting scheme so that different materials can have different default parameters? For example, diffusion of a piece of DNA is probably slower than diffusion of a protein which in turn is slower than diffusion of a metabolite.
• Is there a way to add length into parameter defaulting [in particular for transcription and translation?]. It would be nice if some mechanisms could be length-dependent automatically if length parameters are available.

[WilliamIX]

Leave this as a low hanging fruit for reviewers.