August 1, 2007 (Vol. 27, No. 14)
Strong Points: Useful program for studying cellular networks
Weak Points: Nothing significant
Turn the clock back to the 1960s. You’re interested in DNA replication, so you begin purifying proteins that function in replicating DNA. Around the replication fork, there are about 20 such factors in prokaryotes. To see if you have the right mix and all the factors, you throw them together in a tube and measure the progress of the reaction. You have to do some mixing and matching and purifying to ultimately find what gives replication characteristics most like what is known to happen in the cell. When you are able to finally mirror cellular replication, you can feel confident you have identified all the relevant factors for the process. Next, fast-forward to the present day and apply the same procedure to identifying genetic networks of interaction known to exist inside of cells. This is a new age, however, so instead of mixing and matching proteins, you mix and match methods in silico to mimic cellular functions. If that makes sense, then you understand the philosophy that gave rise to Ingeneue, a downloadable software package available at this site.