Home - HelikarLab/cobra-app GitHub Wiki

Welcome to the cobra-app wiki!

For development-related documentation, please read the README at https://github.com/HelikarLab/cobra-app.

1. Overview
2. Background

Overview

Today, Cell Collective (CC) supports only Boolean Modeling. Models are represented by internal and external components and the components interact with each other as described by the regulatory mechanism for each component. We want to expand CC to support Constraint-Based Modeling (CBM). Thus, this document is an effort to describe what CBM is and how we could support CBM within Cell Collective in such a way that it parallels current software usability.

Background on Constraint-Based Modeling

Constraint-Based Modeling is based on the principle of applying constraints to a matrix to create a solution space that has some sort of relevance to a physical problem. The main solving method is to utilize linear programming. The way a model is created is by having a set of reactions and metabolites that are represented by columns and rows respectively in a stoichiometric matrix.