A repository includes the three projects from the Network Analysis and Modeling of Biological Systems class at the University of Maryland, College Park. This class was organized and taught by Prof. Eytan Ruppin.

• Achiles
• ESSbrca: cancer cell model.
• HER2: cancer cell model.
• recon1, recon2: the cell models provided in the class

• findESSGenesFromCancerData.m: a script to extract a list of essential genes from a given cancer data (using threshold score value)
• getHER2fromCancerData.m: a script to extract HER2 cancer type from a given cancer data (assuming the ESSbrca is given)
• findESSGenesFromMModel.m: a script to extract a list of essential genes from a given metabolic model (using FBA)
• getLowExprGenes.m: a script to extract a list of genes that have low expression data by using p-value
• findRxnsWithGenesFromMModel: a script to extract a list of reactions that are related to a given genes but not blocked and essential
• defineHumanMediaNCI60.m: the NCI60 media definition

• finalScript.m: the main script---i.e., used for the class project
• runProjectScript.m: a script that contains our algorithm implementation
• evaluations.py: a Pypthon script to compute the accuracy of a wile-type model and all modified models

This code is licensed under the MIT license. Please see the LICENSE file for more information.