It's been a while since I last posted. Been busy with a conference that I had to attend. Still suffering from jet lag, but at least the headache has gone.
In the first week back to work, I got on to cleaning up the simulator code. Removed libraries that duplicated functionality already existing in jQuery and jQuery-UI. The reason for this was that these libraries were anyways required for bui, hence it would make sense to use their functions. jQuery is really awesome, makes selections so simple and we can concentrate on getting stuff done rather than fiddling with the DOM.
Another important change is that the 2 Boolean Network importers have been unified using libSBGN.js. Quite a nice library, well documented and clean. Thanks Lian.
Upcoming Tasks:
1. Layout: The d3.force layouter requires the edges to be straight, whereas in graphviz the edges can be curved. This restriction results in overlapping of edges with nodes and also with other edges. I found a nice thread that listed various js graph layout libraries
http://stackoverflow.com/questions/7034/graph-visualization-code-in-javascript
2. More importers: There are a few formats for which importers need to be written. GINML, SBML-LRG, BLIF? These formats are much more complex than the ones being used currently. Writing these importers will take time.
3. SBGN Logical Operators: The graph that is currently displayed in bui from the Boolean Network file formats only have the chemicals as nodes, if we have to conform with SBGN, then the AND/OR/NOT nodes also need to be displayed. For this the update rule needs to be parsed. Have to start searching for a expression parser library for js.
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