Automated layout algorithms for cellular pathways?

Question

[justp]

I'm new to bioinformatics. I'm trying to learn more about algorithms that are used for pathway layouts and how that works. For example if one has an xml, gpml, or csv files with gene names and attributes (including cellular location) and interaction (gene1 activates gene2), but not specific node location/position information (e.g. x or y coordinate information), what would help one align everything properly? I'm not really working on this myself, but I wanted to know more about how this works. I've been told by others that this is possible, but I myself have no knowledge about this. I would like to learn more about this process and how I could implement it with some potential side projects.

Thanks!

Answer 1

[Alex Reynolds]

Investigate Graphviz and the DOT format. The gallery can give you some ideas about how layout can be directed.

[justp]

Thank you for the suggestion. I've looked at the DOT format, but it seems that I would have to manually type out everything or either create a script for Excel that writes everything into the DOT format. I'm not sure how this solves my problem, unless there's some algorithm I can implement using the DOT language?

[Jean-Karim Heriche]

Several programs/libraries allow you to automatically layout the nodes then manually adjust their positions. Look for example at Cytoscape or the igraph library.. You can of course always add node coordinates to the file if the format can then be imported in your graph drawing program. You could also write a script to draw the graph as you'd like. By the way, using Excel for bioinformatics data is a bad idea (see this paper and this one).

Answer 2

[Jean-Karim Heriche]

The wikipedia page on graph drawing is a good starting point. In addition to software listed on the wikipedia page, you can also have a look at the igraph package for R.