- Pirkko Muhonen, Ranga N. Parthasarathy, Anthony J. Janckila, Kalman G. Büki, H. Kalervo Väänänen. Analysis by ::::siRNA_profile ::::program displays novel thermodynamic characteristics of highly functional siRNA molecules. Source Code for Biology and Medicine, 3, 2008.
- Alexei A. Podtelezhnikov, David L. Wild. CRANKITE: A fast polypeptide backbone conformation sampler. Source Code for Biology and Medicine, 3, 2008.
- Roderic D. M. Page. LSID Tester, a tool for testing Life Science Identifier resolution services. Source Code for Biology and Medicine, 3, 2008.
- Will Stott, Andy Ryan, Ian J. Jacobs, Usha Menon, Conrad Bessant, Christopher Jones. OSPACS: Ultrasound image management system. Source Code for Biology and Medicine, 3, 2008.
- Jacob Frelinger, Thomas B. Kepler, Cliburn Chan. ::::Flow::::: Statistics, visualization and informatics for flow cytometry. Source Code for Biology and Medicine, 3, 2008.
- Lior Shamir, Nikita Orlov, D. Mark Eckley, Tomasz J. Macura, Josiah Johnston, Ilya G. Goldberg. Wndchrm - an open source utility for biological image analysis. Source Code for Biology and Medicine, 3, 2008.
- Zoran Bursac, C. Heath Gauss, David Keith Williams, David W. Hosmer. Purposeful selection of variables in logistic regression. Source Code for Biology and Medicine, 3, 2008.
- Mikael Lund, Martin Trulsson, Björn Persson. Faunus: An object oriented framework for molecular simulation. Source Code for Biology and Medicine, 3, 2008.
- Isana Veksler-Lublinsky, Danny Barash, Chai Avisar, Einav Troim, L. Paul Chew, Klara Kedem. FASH: A web application for nucleotides sequence search. Source Code for Biology and Medicine, 3, 2008.
- István Albert, Juilee Thakar, Song Li, Ranran Zhang, Réka Albert. Boolean network simulations for life scientists. Source Code for Biology and Medicine, 3, 2008.