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 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. See Fox et al., 2022 (PMID: 35794472) for details.

We also have an extended network model that harbors reactions annotated in multiple C. elegans strains (Fox et al., 2022):

	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

eFPA-related Models, Datasets, and Code (?) Models, datasets, and scripts used in the development and applications of enhanced Flux Potential Analysis (eFPA). This is an ongoing project with a reference paper under review.

The following files cover the metabiolic models, datasets, and code used during the development of enhanced Flux Potential Analysis (Li et al., in review):

	Link to file
S. cerevisiae model (?) Model and distance matrix for the yeast metabolic network model v8.3.5 (takes about 24 MB of space).	yeastGEM_8.3.5.zip
H. sapiens model (?) Model and distance matrix for the human metabolic network model human 1 ((takes about 352 MB of space)).	human_1.5.0.zip
C. elegans model (?) Model and distance matrix for the worm metabolic network model iCEL1314 (takes about 9.5 MB of space).	Celegans_iCEL1314.zip
Full dataset (?) The full collection of input, output, and scripts for the eFPA project (takes about 9 GB of space).	eFPA_raw_data_full_11172022.zip

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.