Biochemistry: This step included individually understanding the different biochemical reactions that are taking place in the liver. These reactions were then created into a biosystem which is looking at the interactions between the different individual biochemical reactions that occur in the liver. The "Model Scope Research: Escher Maps" page goes into more detail of the biochemical reaction pathways that were included.

Data Extraction: This step included looking at protein databases such as SABIO-RK and UNIPROT for fluxomic, metabolomic and kinetic data of different chemical reactions that occur in the liver. This step was expedited using some webscrapping techniques described in "Data Extraction: Helium and Beautiful Soup".

COBRApy: This is a python software package that allows for the backbone biosystemic interactions of the biochemical pathways in the liver using the stiochiometry of the reactions. This package also allows for Flux Balance Analysis (FBA) using Linear Programming (LP) which is a way to optimize the flux (or flow) of the mass through the reaction in the liver by using the fluxomic parametrized values extracted from the data bases as a validation point. In order to do this Flux Balance Analysis, the package takes into account the steady state assumption (S*v = 0) which states that the kinetics are not changing over time which allows for the optimized flux values to be outputted. Examples of this are given on "Model Construction".

MASSpy: This is another software package that was used to create the dynamic (changes over time) aspect of this project. This was done using quadractic programming which optimized the metabolomic and kinetic data compared to the data that was extracted. This was then simulated over time using Ordinary Differential Equations (ODEs). "Model Construction" gives the results from this process.

Ensemble Modeling: This is the process of simulating multple models which allows for making sure that there is no bias in the results that we obtained. This idea similar to doing experiments multple times to make sure the results are valid.

SIMULATION: The process of using a model to predict the behavior of the system (in our case, Liver) being studied.

MODELING: The process of making the model (in our case, Liver).

Leader: Sicily Rose Panattil