LabArchives. This is a web-based electronic laboratory notebook system, which is used in this course for recording data and preparing the laboratory reports. You will login via the University of Utah portal.
SciDAVis This is a free, open-source program for graphing and analyzing data, which we will use extensively for this class. The most recent public release version (2.8) is available for download from: https://sourceforge.net/projects/scidavis/files/SciDAVis/2/2.8/.
For those using Macs there is a version with a small tweak available on the course Canvas page. This version fixes a problem that arises when the program is launched in the MacOS "dark mode".
The most recent (but not very recent) documentation for SciDAVis is found at:
https://highperformancecoder.github.io/scidavis-handbook/
A detailed tutorial is provided in the lab manual for this class.
PyMOL We will be using this program to look at protein structures.
This is an open source program, but the compiled versions are commercial products. Educational versions are available to students and instructors at no cost, but this requires registration to access the files:
http://pymol.org/educational
The education versions for Macintosh and Windows are available for download on the course Canvas page.
The PyMOL wiki is an excellent source of documentation for the program.
ImageJ A public domain program for analyzing and manipulating images, and an all-time great among free scientific software! We will use it for analyzing gel electrophoresis experiments. Slightly enhanced versions, with special macros, will be provided on the Canvas web page.
ChemAxon Marvin Suite A software package for drawing and analyzing molecular structures. Marvin Sketch, a component of ChemAxon, has much of the functionality of ChemDraw and is available to students and instructors at no cost.
Other Resources
The Protein Data Bank (PDB).This site provides access to the three dimensional structures of thousands of proteins and nucleic acids. When new structures are published, the authors are expected to deposit the atomic coordinates in this database so that anyone can examine the structures.
Chromatography Handbooks Many of the chromatography media most commonly used for biochemistry were developed by Pharmacia Fine Chemicals, now a part of Cytiva. For many years, Pharmacia published free handbooks on the use of these materials, and updated versions are available for download from Cytiva. The handbooks for size exclusion (gel filtration) and ion exchange chromatography are particularly useful: