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Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
Walhout Lab web page:
walhoutlab.umassmed.edu

Email for WormFlux:
lutfu.yilmaz@umassmed.edu
Metabolic Network Modeling of C. elegans

Metabolic Network Model

You can download the current metabolic network model in the following formats:

Link to file
SBML (?) Systems Biology Markup Language, Level 3, Version 1 iCEL1314.xml
JSON (?) JavaScript Object Notation format iCEL1314.json
MS Excel (?) Spreadsheet created in Microsoft Excel iCEL1314.xlsx
mat (?) MATLAB structure for use with COBRA toolbox. iCEL1314.mat

WormPaths and Pathway Enrichment Analysis (PEA)

The following files cover gene annotations in WormPaths and PEA:

Link to file
Categorized genes (?) List of WormBase IDs and gene names for model genes that are assigned to pathways or categories. iCELgenes.csv
Pathways and categories (?) Pathways or categories for gene annotation at four levels of resolution. CategoriesAtFourLevels.tsv
Gene sets (?) Sets of genes assigned to each pathway or category at the four levels of annotation. GeneSetsAtFourLevels_WBID.xls

pan-iCEL Model (?) An expanding network that covers metabolites detected and reactions annotated in not just N2, which is the strain the iCEL model is based on, but also other strains being studied. This is an ongoing project and a reference manuscript is underway.

We also have an extended network model that harbors reactions annotated in multiple C. elegans strains:

Link to file
SBML (?) Systems Biology Markup Language, Level 3, Version 1 pan-iCEL v1.0.xml
JSON (?) JavaScript Object Notation format pan-iCEL v1.0.json
mat (?) MATLAB structure for use with COBRA toolbox. pan-iCEL v1.0.mat
The information and tools provided in this website are to be used for academic purposes only. Potential users of the flux analysis tools (FBA button in the vertical menu) are asked to show proof of working at an academic institution during the creation of their accounts. These mathematical tools are powered by the commercial software Gurobi.