It's my perception that introductions to new bio-software are usually confined to low-impact journals. This week there is something strange in the air: Nature Biotechnology introduces V3D, a 3D visualization system for gigabyte-sized microscopy image stacks in real time on current laptops (see en.doge.nous blog), and Plos Computational Biology introduces Smoldyn a modeling software to simulate the diffusion, the membrane interactions, and the reactions of individual molecules inside an entire cell.
Compared to this paper:
Abramoff, M.D., Magelhaes, P.J., Ram, S.J. "Image Processing with ImageJ". Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.