Team:USTC-Software/Lab1


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Metpredictor

A Metabolic network software based on gene expression and meabolic network modeling。

Inspiration

Since we’ve been doing the similar projects with even same names, we want to have a change this year. Not only doing same things is quite boring, but we wish to do something that is really in need. After visited a synthetic biologist in our school, chatted a lot, we came up with an idea. Our professor mention that a software can help him a lot is one can tell him what changes will happen to the various ingredients after he changes the metabolic pathway, especially the coenzymes. Considering it’s absolute more interesting than making a search engine, we set our project as it.

Generally, our project focuses on the proportion of the coenzymes after adjusting the metabolic pathway. Giving the variation range of the concentration of the coenzymes will greatly lessen the pressure of synthetic biologists while doing experiments and reduce the time or money cost of many trials.

Project

Method

This is method description.

Function

  1. By analyzing and modeling the gene expression and metabolic network, our software can get the range of the concentration or proportion of the intermediate reactant after changing or adjusting a metabolic pathway.
  2. Compared with other metabolic prediction software, we more consider whether the concentration of coenzymes, for example NADH/NAD+ is in the best range.
  3. Even included some data visualization work so that it’s convenient for the experimenter to analyze the bacteria and optimize the experimental design.
  4. Recognizing the database of metabolic network or packages of the prediction tools are still not robust or complete for us to use, we first do several work of database integrations.
  5. To make our software more usable, we design a set of algorithms, creating a recommendation system.
  6. We managed to create a platform where the synthetic biologist can easily share their ideas and issue their results.