Modeling and simulation of biochemical networks has become an essential activity to aid in the understanding of cellular behavior and to facilitate quantitative interpretation of modern experiments. A new approach, """"""""systems biology"""""""", is being advocated which combines modeling, simulation and quantitative experiments. The novelty of systems biology is that experiments, mathematical modeling, and computer simulation are practiced in a cooperative way, the results of one being used for subsequent iterations of the others. Arguably, to fulfill the promise of systems biology there is a need for software tools to be able to appropriately connect models to experiments. We propose to address this, and other systems biology needs, with continuing development of our software COPASI, which is the successor of the widely used Gepasi. This project will also provide support to the vibrant community of COPASI users/biomedical researchers. We will address this with the following Specific Aims:
Aim 1 : Enable COPASI with new functionality to provide advanced model analyses. This will include adding algorithms for nonlinear dynamical analysis, model complexity reduction, improved parameter estimation and methods for closing the loop of experiment-model-experiment, and parallelization of certain algorithms.
Aim 2. Improve and extend interoperability and standards compliance. COPASI will be equipped to facilitate users to create and maintain models according to the MIRIAM standard, and with methods to act as a client and provider in the SBW environment. SBML support will continue and be enhanced.
Aim 3. Software maintenance. A testing plan will be established, including appropriate testing suites and procedures;bug reports will be collected and fixed;suggestions for improvement will be collected from users and followed.
Aim 4. Support the modeling community. Providing online support tools, such as a user forum, FAQ and Wiki. An Annual COPASI User's Workshop will be held.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM080219-04
Application #
7924780
Study Section
Special Emphasis Panel (ZRG1-BST-D (51))
Program Officer
Lyster, Peter
Project Start
2007-09-01
Project End
2012-08-31
Budget Start
2010-09-01
Budget End
2012-08-31
Support Year
4
Fiscal Year
2010
Total Cost
$509,951
Indirect Cost
Name
Virginia Polytechnic Institute and State University
Department
Type
Organized Research Units
DUNS #
003137015
City
Blacksburg
State
VA
Country
United States
Zip Code
24061
Mendes, Pedro (2018) Reproducible Research Using Biomodels. Bull Math Biol 80:3081-3087
Parmar, Jignesh H; Quintana, Julia; Ramírez, David et al. (2018) An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Mol Microbiol 110:357-369
Gupta, Abhishekh; Mendes, Pedro (2018) An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. Computation (Basel) 6:
Bergmann, Frank T; Hoops, Stefan; Klahn, Brian et al. (2017) COPASI and its applications in biotechnology. J Biotechnol 261:215-220
Verma, Meghna; Erwin, Samantha; Abedi, Vida et al. (2017) Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa. PLoS One 12:e0168133
Millard, Pierre; Smallbone, Kieran; Mendes, Pedro (2017) Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Comput Biol 13:e1005396
Dacheux, Estelle; Malys, Naglis; Meng, Xiang et al. (2017) Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Res 45:6981-6992
Meng, Xiang; Firczuk, Helena; Pietroni, Paola et al. (2017) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Res 45:1015-1025
Swainston, Neil; Smallbone, Kieran; Hefzi, Hooman et al. (2016) Recon 2.2: from reconstruction to model of human metabolism. Metabolomics 12:109
Millard, Pierre; Portais, Jean-Charles; Mendes, Pedro (2015) Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Syst Biol 9:64

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