BE/APh 161 - Winter 2014

Biology by the numbers

Bionumbers
http://www.bionumbers.org
This website is a database of useful biological numbers (with references!). It will help you find both key numbers characterizing biological systems as well as the experimental sources for those numbers. This complements the approach we will often take of trying to determine those numbers by thinking them up.
BioTheNumbers
http://www.biothenumbers.com/
Another website of useful biological numbers in ecosystems and how human influence has changed them.
E. coli statistics
http://ccdb.wishartlab.com/CCDB/
This website gives some of the vital statistics for E. coli.

UCSF Chimera
http://www.cgl.ucsf.edu/chimera/
Chimera, developed by RBVI at UCSF is a multi-purpose graphics tool for molecular visualization.
DeepView aka Swiss-PdbViewer
http://spdbv.vital-it.ch/
This viewer has been developed by Nicolas Guex in Switzerland since 1994.
Jmol
http://jmol.sourceforge.net/
This viewer is an interactive web browser applet. It is also used to view structures within the PDB website.
PyMol
http://www.pymol.org/
This viewer was developed by the late Warren DeLano, with binaries now distributed by Schrödinger. It is OpenGL-based and is wrapped in Python for easy scripting. The source code is available without registration.
VMD
http://www.ks.uiuc.edu/Research/vmd/
VMD (Visual Molecular Dynamics) is developed by Klaus Schulten's group at Illinois and is often used as a front end for molecular dynamics simulations and has powerful graphics capabilities.
List of viewers from RCSB
http://www.rcsb.org/pdb/static.do?p=software/software_links/molecular_graphics.html
RCSB provides a lits of molecular viewing software. The list is quite complete, though some of the links are dated.

Sanjoy Mahajan's delightful Street-Fighting Mathematics effectively teaches many of the principles of estimation we use in the course. You can buy it, or download it under the Creative Commons License here.
Peter Goldreich, Sanjoy Mahajan, and Sterl Phinney offered a course at Caltech in the 90s about principles of estimation. Their notes were collated into an online text, Order-of-Magnitude Physics: Understanding the World with Dimensional Analysis, Educated Guesswork, and White Lies.