Team:SCUT/Model/Tips for other teams

Outline

In the process of searching for data, we have met a lot of difficulties. On the one hand, the parameters for the pathway we want are difficult to find. On the other hand, even when we find the paper we need, the data on the paper is too many to figure out what is we exactly want. However, after numerous times of searching, we find that there exists a wonderful database, the BioModel Database [1]. It is a useful library for those who want to find the data and models for biology. Besides, the data is showed in a brief way, which is easy to read and use. So we highly recommend other iGEM teams to browse this database when you need to find the models for your project.
The other powerful tool we want to share with you is the JWS online[2], an online lab for the models that have already uploaded to it. It can give you the results you want in a few seconds, which can help you immediately grasp the features of the model. We also use the results on it to exam the correctness of our code by finding if there are any differences between our results and theirs. For example, we use the results of the online lab to compare with our results of glycolysis subsystem. Since the glycolysis model is the most complex one, it is difficult to exam the code row by row. With the help of the online lab, we can easily test whether there are bugs of our code, which has saved us a lot of time. The only limitation of JWS online is that it cannot combine different models in it to construct a more powerful system. However, it is still powerful, isn’t it?

Figure 1 the figures of our code and the corresponding online model. (a) is part of the results of our code, (b) is the corresponding figure.

Reference

[1] http://www.ebi.ac.uk/biomodels-main/, BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic
[2] http://jjj.mib.ac.uk/database/, JWS online