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Working out Classic Examples of Metabolic Networks Structural Analysis with Wolfram Language

Liang, K. K.

2019-06-18 bioengineering
10.1101/672881 bioRxiv
Show abstract

Metabolic reaction networks usually include a large number of enzymatic reaction steps. Nowadays, people desire to work on larger and larger metabolic networks, in the research fields of for example systems or synthetic biology. With the growing sizes of the metabolic networks considered, it is more and more tedious and cumbersome for a human to perform routine processing and analysis of the networks. Computer programs that automate metabolic analysis will be beneficial. In this work, the use of Wolfram Language to automate metabolic analysis is demonstrated. Although there are many different analyses to perform in a metabolic network analysis project, the analysis of metabolic network structure may be the most common first step and one of the most troublesome tasks. Therefore, instead of demonstrating a lot of different analyses, the structures of a few important examples from one chapter in the classic textbook by Professor Gregory Stephanopoulos are analyzed with a program written in Wolfram Language and the models are book-kept in JSON format.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.