> I enjoyed following the graph drawing thread a few weeks ago. A serious > attempt at "better than graphviz" could be fun and worthwhile.
I was going to reply to that thread as well but didn't get to it. There is a great need for something like this in bioinformatics. Down the road a bit, we will want something like it for the startup business which I am in. We are developing bioinformatics software and one of the things on our to do list is a module for graphing protein-protein interactions. Have a look at this paper: http://bit.ly/2yfXTip I painstakingly created figure 1C in Cytoscape. I was unable to make similar graphs, much less the more sophisticated ones I would like to create, for subsequent publications because it just took too much time. Of course I wanted to automate the process. I tried scripting Cytoscape but found that to be too tedious and unreliable. I looked into creating a Cytoscape plugin but it was too much work and I would have had to learn Java. Most of my programming experience, so far, has been Perl and R. I researched a bunch of different options and then turned to a GraphViz library for R but found that it was too limited. Finally, I wrote some custom R code to create GraphViz code. This got me the farthest but I would really like to have something nicer than GraphViz to work with. Figure 1C is combining raw gene expression profiling data with Gene Set Enrichment Analysis (GSEA) to indicate the activity of various transcription factors. The raw data and GSEA scores are then graphed in the context of the most significant transcription factors and their known target genes. This can be a very powerful way of looking at the data under the right circumstances. The more common situation is looking at a combination of expression profiling data with mutation calls from sequencing in the context of known protein-protein interactions. There are some commercial options which do some of this but they are not very good and not really open enough to allow for accessible and reproducible research. Our model is to charge for participation in our network and for what will eventually become our platform software. The analytical tools and community contributed analytical modules will be open source so you can see exactly what they are doing. Moving forward, something which has been an idea for a long time but not yet done satisfactorily, as far as I know, is to show proteins as either logic gates or analog circuits. Proteins are viewed, in many cases, as forming signal networks. It would be good to be able to show an animation of how the signal flow over the network changes with different environmental signals. Alternatively, hold the environmental signals constant and show what happens to the signal flow if you add/remove a mutation in one of the proteins. So that's a step or two beyond what GraphViz does but I think it's a logical direction to go for further development. James -- You received this message because you are subscribed to the Google Groups "Racket Users" group. To unsubscribe from this group and stop receiving emails from it, send an email to racket-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
