Links to some useful computational resources for teaching contemporary biology

    Computer Visualization


  • Computers are awesome tools for allowing us to see what is difficult or impossible to see.

  • The Inner Life of a Cell demonstrates this. It is a purely conceptual or artistic product which powerfully conveys a sense of the molecular world, but it is not a quantitatively accurate model, and can just as pwerfully produce miconceptions if students assume that it is precisely accurate.

  • This movie Science In Silico from Seed magazine presents real quantitative models that are being used to further our understanding in various fields of science.

  • In many cases the research groups that have produced computational models as part of there research efforts make these models available to the public through education and outreach.




Introduce students to the molecular world with The Molecular Literacy Project from the Concord Consortium

The major repository of biomolecular structures: RCSB Protein Data Bank - Database of protein structures.

The Molecule of the Month at the Protein Data Bank under the "General Education" item includes a large number of examples that demonstrate the link between protein structure and function.

A similar resource can be found at Molecules in Motion.

The structure viewer that I would recommend learning is . This site also has a gallery of Science In Silico from Seed magazine.

Standardized tools are being developed to allow model exchange and interoperability: Systems Biology Markup Language, Modeling Tools, and Model …

Web-based repositories are ever-growing:




A college-level tutorial on using Vensim to model chemical reactions: NCSI Computational Chemistry Lesson on System Dynamics