Discussion_Limitations

Discussion & Limitations & Results

Systems biology studies generate many data files for the simulation of biological systems. Such data files can be saved and manage into fully-featured COMBINE archives. These are standardized containers for data files related to a simulation study[1].

At the end of our project, we have built a fully-featured COMBINE archive of the Bachmann model in the web platform CombineArchiveWeb. We have used a similar files structure as described by Bachmann et. al. This structure is presented in the section Structure of COMBINE archive. We could upload all files from our repository, but report XML files for validations. On this step, the CobineArchiveWeb interface throws the following error: "Unknown Error: Cannot upload file". We have made a new issue (146) in our GitHub repository and the repository from the WebCAT. After the creation of this COMBINE archive, we selected the option Simulate. This simulation shows the species and its behavior in the reactions. We note that this visualization is only the Default simulation. However, we have tried a previous simulation without the Default folder, which functioned too, showing the result of one of our simulations. This point is registered in another issue (147) in the GitHub of the developer of CombineArchiveWeb.

References

[1] Scharm, M. and Waltemath, D. A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5, 2421 (2016). https://doi.org/10.12688/f1000research.9379.1