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Elementary Flux Mode Workshop

What is being modeled?
Biochemical pathways, cellular- and microbial community-level metabolism
Description & purpose of resource

Hands on workshop for learning or teaching genome-enabled, metabolic modeling.  Materials include presentations, step-by-step guides, example metabolic models and completed exercises.

Spatial scales
molecular
cellular
Temporal scales
10-3 - 1 s
1 - 103 s
This resource is currently
mature and useful in ongoing research
a demonstration or a framework to be built upon (perhaps with a sample implementation)
Has this resource been validated?
No
How has the resource been validated?

Material has been used for educating 4 classes of graduate students in elementary flux mode analysis.

Can this resource be associated with other resources? (e.g.: modular models, linked tools and platforms)
No
Key publications (e.g. describing or using resource)

Beck, A.E., Hunt, K.A., Carlson, R.P. (2018) Measuring Cellular Biomass Composition for Computational Biology Applications. Processes 6(5), 38. 10.3390/pr6050038

Hunt, K.A., Jennings, R. deM. Inskeep, W.P., Carlson, R. P. (2018) Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PLoS Computational Biology, 14(9):e1006431. 10.1371/journal.pcbi.1006431

Carlson, R.P., Beck, A.E., Phalak, P., Fields, M.W., Gedeon, T., Hanley, L., Harcombe, W.R., Henson, M.A., Heys, J.J. (2018) Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross feeding microbial consortia. Biochemical Transactions. 46: 269. 10.1042/BST20170242

Beck, A.E., Bernstein, H.C., Carlson, R.P. (2017) Stoichiometric network analysis of cyanobacterial acclimation to photosynthesis-associated stresses identifies heterotrophic niches. Processes 5 (2), 32. 10.3390/pr5020032

Carlson, R.P., Beck, A.E., Phalak, P., Fields, M.W., Gedeon, T., Hanley, L., Harcombe, W.R., Henson, M.A., Heys, J.J. (2018) Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross feeding microbial consortia. Biochemical Transactions. 46: 269. 10.1042/BST20170242

Beck, A.E., Bernstein, H.C., Carlson, R.P. (2017) Stoichiometric network analysis of cyanobacterial acclimation to photosynthesis-associated stresses identifies heterotrophic niches. Processes 5 (2), 32. 10.3390/pr5020032

Taffs, R., Aston, J.E., Brileya, K., Jay, Z., Klatt, C.G., McGlynn, S., Mallette, N., Montross, S., Gerlach, R., Inskeep, W.P., Ward, D.M., Carlson R.P. (2009) In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Systems Biology 3:114.

Carlson, R.P. (2009) Decomposition of complex microbial behaviors into resource-based stresses. Bioinformatics. 25: 90-97.

Carlson, R.P. (2007) Metabolic systems cost-benefit analysis for interpreting network structure and regulation. Bioinformatics. 23: 1258-1264.

DOI link to publication describing this resource

graduate course publication based on material in workshop:

 

https://doi.org/10.1186/1752-0509-3-114

https://doi.org/10.1111/1462-2920.13444

https://doi.org/10.1371/journal.pcbi.1006431

Link to resource
http://www.chbe.montana.edu/biochemenglab/EFMAworkshop.html
Collaborators
Ross Carlson
PI contact information
rossc@montana.edu
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