> can you summarize for us, what is done, what needs to be done. so far we have experiences visualizing biochemical networks with tools like Cytoscape, Graphviz, ... we even wrote our own web2py plugin to create force directed graphs http://groups.google.com/group/web2py/browse_thread/thread/d9c5b9ef9ddf2e49/63cec30770d1ef9f?lnk=gst and we have drawn tons of network images by hand, but this is not enough, what we really need is
1) a fast layout algorithm that creates good layout for biochemical graphs (better than force directed, ...) 2) a js library that renders these layouts in a standard compiant way in SVG, - so far the only standard for drawing biochemical networks out there is SBGN (http://sbgn.org/Main_Page see here for some examples) and we intend to use that - SVG images because the can be displayed in a browser (http:// slides.html5rocks.com/) - SVG images can be edited with (e.g. Inkskape) and that is crucial since no layout algorithm will generate images good enough for publications, wikipeda, ... 3) a communication layer that calls our new layout algorithm (and possibly others that are available) and uses the js lib to show the result in a browser, this is where web2py could act as the communication layer 4) an extension to the js library 2) so that the images can edited on the web (this will also have to communicate to 3) somehow) - this lowers the border for people to create standard compliant images 5) an extension to the communication layer 3) so that it access all kinds of databases that contain biochemical reaction networks and visualizes them (we have plenty of experinces with that, but it is hard work every time you want to do something like that) you probably see that all the ideas depend on each other and that some of the steps can be unified/done by one developer so far a lot of people are interested in 1) and also some in 2) but for 3) we there was nobody really showing much interest The development will start from scratch but we a optimistic that we will have some good results within the two month with a team of 3 students and about 6 mentors Finally I should mention that we have a experience in using web2py (http://pymantis.org/ http://semanticsbml.org/semanticSBML/ http://sysbio-goods.org/ ...) and other tools and programming languages (some of the tools developed in our group: http://www2.hu-berlin.de/biologie/theorybp/index.php?goto=tools)
