A really neat new web-based metabolic network viewer was presented in today’s PLoS ONE: “Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API.” This is, for me, one of the most useful and intuitive new software systems for biological research. Through an easy to use web interface, you can search for and zoom in on specific metabolic reactions in hundreds of organisms (something that we do a lot in synthetic biology/metabolic engineering when designing new metabolic pathways). Just last week, we were driven to use a metabolic map printed on (gasp) paper in order to find the chemical intermediates of a certain pathway:
Pathway Projector looks literally like Google Maps, with zoomable, draggable interface, solid search feature, and a cute pop-up window when you click on a specific reaction or metabolite with more details and links to websites with other enzyme details:
I think the map metaphor is a really interesting and useful here. The ability to trace your favorite metabolite through the maze of enzyme reactions, zoom in to see more and more detail, and the links to more information are critical, and I think can be very useful for other biological data and eventually synthetic biology pathway design.
However, it is interesting also in terms of how we think about biological information inside of the cell. It is hard to envision the chaotic jumble of proteins and chemicals bumping into each other inside of the cell, but one imagines that it’s not as beautifully diagrammed as it is here. How does the way we draw connections between metabolites and enzymes in metabolic maps or between proteins in protein interaction maps influence our understanding of how biological chemicals interact? How can we incorporate other kinds of information, feedback loops and regulation, speed of reactions, strengths of interactions into the simplified map diagram? What happens when we ignore this kind of information when we build these maps in the first place? What else are we missing? I think these are important questions, especially now as we try to re-create pathways and re-wire the map diagrams in synthetic biology.
