Section: Application Domains
Biology and bio-informatics
Because post-genomic data is made available publicly and is easily accessible on the web, biological data often becomes a target for visualization techniques we develop. Protein interaction networks nowadays are easy to find on the web; authors publishing in bio-informatics journals even sometimes provide the datasets they used as a benchmark.
Biology offers a fertile area for research in visualization because of massive data produced from experimentation, and also from a strong demand on the side of biologists. Problems in biology and bio-informatics concern almost all issues cited above:
graph statistics enter the scene when inferring graph structures from biological data, or when interpreting measures/attributes associated with the data;
the nested structure of metabolism naturally makes use of graph hierarchies.
Strong graphical conventions in biology (when drawing metabolic pathways or RNA secondary structures for instance) turn the design of automatic graph drawing algorithms into a real challenge. Part of our research was developed through the ANR AReNa project(See the URL http://www.lri.fr/~denise/AReNa/ ). RNA comparisons required the development of new graph drawing algorithms and graph visualization software   . The Bordeaux environment places us close to biologists and bio-informatics researchers. We also have contributed to the study of metabolism, more recently together with researchers from the INRIA HELIX project in Lyon  . The questions addressed through this starting collaboration this time concern the identification of biological patterns in metabolic or signal networks.
We have direct collaboration with biologists and bio-informatics researchers since the LaBRI team from which our project stems is directly concerned with bio-informatics, placing us close to the actual users (as with SPANGEO). Team members interact with researchers of the INRIA MAGNOME project; these interactions already gave rise to the development of the software application ProViz  .
The ANR project SysTryp already gave us the occasion to reinforce collaborations with researchers from INRA Toulouse (Fabien Jourdan) and Bordeaux (Antoine de Daruvar, Patricia Thébault from CBib). SysTryp focuses on the relationship between metabolism and cellular differentiation in the protozoan Trypanosoma brucei, by collecting high resolution mass spectrometry data and reconstructing networks based on this data (see section 8.1 ).