The visualizations transforming biology

Ewen Callaway in Nature:

A smart visualization can transform biologists' understanding of their data. And now that it's possible to sequence every RNA molecule in a cell or fill a hard drive in a day with microscopy images, life scientists are increasingly seeking inventive visual ways of making sense of the glut of raw data that they collect. Some of the visualizations that are currently exciting biologists were presented at a conference at the European Molecular Biology Laboratory in Heidelberg, Germany, in March. Called Visualizing Biological Data (VIZBI), the meeting was co-organized by Seán O'Donoghue, a bioinformatician at the Garvan Institute of Medical Research in Sydney, Australia. The gathering attracts an eclectic mix of lab researchers, computer scientists and designers and is now in its seventh year.

…To make cellular model-making more systematic, Johnson developed a tool called cellPACK. To use it, researchers use experimental data to create a series of physical rules (a 'recipe') by which defined cellular components such as proteins, lipids and nucleic acids (the 'ingredients') fill a space. Johnson would like to create a platform such that the models are automatically updated when new data are generated. But despite lots of interest from other researchers, most life scientists find that the tool requires too much time and effort to be very practical. “It's months of research to generate a recipe from scratch,” says Johnson, who plans to release a more streamlined web version of the software later this year. The tool isn't just for making visually striking models, he emphasizes. It can also help scientists to come up with testable hypotheses. His team created a model of the internal structure of HIV and used it to predict how the protein that forms the outer shell interacts with an internal protein.

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