README.md

In artedison/ensRadaptor: Metabolic model creator for ensemble method

ensRadaptor

ensRadaptor makes conscutrucing biological ODE model easier. It works as a interface to ens mehtod1, a MCMC based fortran program for rapid ODE system parameterization. ens models biochemcial systems with partial obervation and fit the ODE to experimental measurement. Although ens is fast, it has diffcult input and output format, among which considerable information are repeated or not useful for users. Learning the ens grammar oftens takes long time. ensRadaptor is designed to simplify the model construction process and provide easy visualizations. ensRadaptor takes in descriptions of the metabolic systems and experimetnal measurement, and it output input files to the ens program. ensRadaptor adopted a format based approach (link). For explanation on input and output of ens program, please refer to documents (link) or contact Bernd Schuttler. For any questions about ensRadaptor, please contact Yue Wu

Examples

For examples on using ensRadaptor, please refer to the script in the folder ./tests/workflowtest_open/

script.input.standalone.R: model contruction

script.output.standalone.R: ens result visualization. To produce the input files for this script, the user need to run the ens program based on the files produced by script.input.standalone.R. Specifically, the user can upload the folder 'input' to an HPC environment, run submit.sh, and start another accumulation runs from there. The accumulation run output ens.o01 and ens.o02 will be used in script.output.standalone.R. Example output figures can be found here.

Install

install_github("artedison/ensRadaptor")

You might need to do Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true") before installation.

Reference:

1. An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa D. Battogtokh, D. K. Asch, M. E. Case, J. Arnold, H.-B. Schüttler Proceedings of the National Academy of Sciences Dec 2002, 99 (26) 16904-16909; DOI: 10.1073/pnas.262658899

artedison/ensRadaptor documentation built on Dec. 8, 2020, 5:31 p.m.