I haven’t updated this blog for a while, the reason being the usual for many researchers working in the US: grant writing. Part of this grant writing involved producing diagrams to illustrate various processes occurring at different scales in prostate tissue. These diagrams describe rather sophisticated intra and extra cellular interactions in the simplest possible manner. Yet these diagrams can be complicated and selecting the right symbols and colours to describe these interactions in a visually appealing but consistent manner can be far from trivial.
As someone with a background in computer science I appreciate the advantage of having a standard notation to describe processes. Software engineers use tools such as UML to describe software modules and how they interact to form complex software systems. This allows other software engineers to understand complex systems with little ambiguity. Now systems biologist will be able to do the same thanks to SBGN, recently discussed in Seed magazine (article that came to my attention thanks to Simon Hayward).
Standarising on a formal graphical notation will allow computational, mathematical and system biologists to better communicate with biologists but only if both communities learn how to speak this language. This will be tricky but if funding bodies and journals start requesting diagrams in this notation, that could ease its introduction. I hope that this (or an alternative formal graphical notation) will eventually emerge successfully. Formal graph notations are easier to read by non experts than mathematical equations or software algorithms but being more precise than informal non-standard ones they represent a more solid foundation in which to build integrative work, combining theoretical and experimental research, and exchanging models between different groups.
Sounds interesting but I don’t really get how to use it. Can you give an example?
Thanks!
I am a cell biologist and have used SBGN (courtesy of Cell Designer) for preliminary construction of a biological network. The challenge now is securing funding to drive the work forward. It is not clear that projects built around SBGN-based diagrams are sexy enough in the current climate. I don’t think funding bodies and journals will be asking for daigrams in SBGN for a long time yet – as most biologists would not know where to start.
David, I rather agree with the previous two responses, and with your last paragraph – this is something that I think will become increasingly needed and which – like road signs – must be standardized. As to how to use it and how to get people to understand it that’s going to take some time – it will probably require teaching grad students and perhaps undergrads the elements before it permeates upwards – at least outside of specialized exclaves (systems biology might be a good place for it to get a foothold).
Kehinde – I wasn’t aware of the celldesigner package, thanks for the information, will try fiddling with the download. Your point regarding funding bodies is well taken, I would hesitate to send in a grant with a diagram that I didn’t think would be clear to the study section (possible instant death!)
Anna, I wish I could come with one example I could add here. The idea though is that by agreeing in some standards it would be easier to exchange information about molecular interaction networks like the ones that both biologists and computational biologists work on.
Kehinde, thanks for the tip for Cell Designer. Downloading it now and hoping to give it a go very soon. Both you and Simon point to the fact that we need biologists to be trained into these formal notations. The need will become more apparent as more and more work is integrative (biologists with comp. biologists). Also it should be possible to make these diagrams both unambiguous and formal but yet visually attractive, right?