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Network Biomass
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Walhout Lab web page:
walhoutlab.umassmed.edu

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

General Instructions

Finding your way within WormFlux is really easy:

Currently, only orange buttons are active on the left-hand menu. Grey buttons will be activated when the indicated tools are ready. These tools will be available only to authorized users with log-in information. If you would like to use these tools once they are made, please send us an email following the account request link.

Metabolic Network Model

The current network model is available in different formats in the Download page in the upper menu. The biomass parameters in the model (regarding both bacterial biomass composition and worm biomass composition) are adjustable using the Biomass tool in the left-hand menu.

Database

WormFlux database consists of annotated items that are presented in separate pages. These pages present genes, enzymes, reactions, metabolites, and pathways in the current model. Additionally, current annotations on all analyzed protein-coding genes are presented. In total there are 20,344 gene pages, 623 reaction pages, 887 metabolite pages, and 100 pathway pages.

Flux Balance Analysis (FBA)

The FBA tool in WormFlux performs flux balance analysis, where, an objective function (typically the flux of a selected reaction) is maximized or minimized, while some reaction constraints are met (e.g., reversibility, uptake rates, etc.), and a steady state mass balance is satisfied for all metabolites. While the optimized objective function value is unique, typically, there are alternative flux distributions that can achieve the same value. Our tool calculates a flux distribution that has minimum total flux possible (in absolute values) and reports this particular distribution. This method is known as parsimonious FBA (pFBA).

Details of flux balance analysis can be found elsewhere (e.g., this paper). You can use the FBA tool following guidelines (indicated by ?) in the webpage. Here are some useful hints:

More

The details of annotation and model reconstruction are provided in the pdf file below.

  • iCEL1273.pdf
  • The information and tools provided in this website are to be used for academic purposes only. Potential users of the flux analysis tools (grey buttons 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.