On to the second week of GSoC, started with editing the ServerInstallation page of the wiki. Modified it to support Ubuntu. The installation scripts present in the server repository are a bit outdated and need to be modified to run on the latest Debian/Ubuntu systems.
Then I moved on to studying the source code of BooleanNet import module. It has been written in javascript and converts BooleanNet files to jSBGN objects which consists of nodes, edges and update rules. The layouting is done by graphviz currently(on the server side) which generates an SVG of the network. The simulator runs on the client side and consists of code to modify the SVG's at every iteration.
I also looked into R's BoolNet. It's file format closely matches BooleanNet's and the existing function for importing BooleanNet only has to slightly modified to support BoolNet. I'll start writing code for this next week.
I had a discussion on the biographer-dev list about how to incorporate libscopes in the boolean network simulation module. It was decided that libscopes can be used for simulating SBGN PD networks and the simulation code would utilise libscopes API. Hence the boolean network simulation for PD has to be executed on the server side. For the libscopes API ctypes seems a better option as it has lesser overhead and provides a more direct route.
Finally, the remaining task for this week is to analyse the biographer-ui.
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