Additional Resources

This list organizes two types of extra resources for your consideration. Everything here is optional but valuable.

First, we have a set of links to software tools supporting design and analysis of biomolecular and genetic systems. Learning to use these tools is a great way to gain understanding and also demonstrate to others (e.g., future co-founders or employers) that you can do useful things with state of the art software. Second, we have a set of links to background reading in case you wish to learn more about the details of biology. We will periodically update this post with new resources, so check back!

Biomolecular Analysis and Design Tools

  • Benchling: Useful online tool offered by for-profit company started by iGEM students from MIT. Supports tracking of DNA parts and analysis and layout of DNA sequences, primarily at the scale of plasmids (vectors)

  • PDB Structure Viewer: In-browser structure viewers from the Protein Data Bank (every molecule at PDB can be viewed in browser).

  • Meta Link: Many molecular graphics analysis and design tools curated by the Protein Data Bank.

  • PyMol: Professional grade molecular structure viewer.

  • FoldIt: Protein folding computer game (based on software engine used to design proteins, like KumaMax example).

  • eterna: Tool, game, and community for analysis and design of RNA molecules

Extra Learning Resources

  • Molecular Biology of the Cell: 4th edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. This is the go-to molecular biology textbook used by advanced undergrad classes and graduate students. Older editions are ok because foundational biology topics are generally unchanged. Topics include: molecular biology, DNA, RNA, protein, translation, transcription, and others. Available from amazon here.

  • The Molecules of Life: Physical and Chemical Properties by John Kuriyan, Boyana Konforti, and David Wemmer. This textbook is for advanced undergraduates interested in exploring more in-depth material on the biochemical structure of macromolecules, energetics of protein folding, and other biophysical concepts. Chapters 1-4 are especially relevant to topics discussed in class. Link to Stanford Libraries catalog. Unfortunately I can’t find a full online version, but the Google books preview is here.

  • Allen Institute’s Cell Explorer: Resource for looking at mammallian cells as they are being observed via microscopy, studied, and figured out.

  • Lehninger: Principles of Biochemistry </em>by David L. Nelson; Michael M. Cox. Ebook

  • The Machinery of Life by David S. Goodsell. An electronic copy of the book is available for free from Stanford Library and you should be able to access from here.

  • Cell Biology by the Numbers by Ron Milo: order of magnitude estimations in biology free download and website from here.

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