Software

  • 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 page for downloading SciDAVis is here. Several different versions are available for Macintosh, Windows and Linux computers. As of December 2018, the latest stable version 1.23. Version 1.23, for Macintosh and Windows computers, is also available for download on the course Canvas web page.
    The most current 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
    Versions for Macintosh, Windows and Linux computers 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. The program is written in Java and should, in principle, run on any computer with the Java "virtual machine" software installed. There are, however, some issues related to the different versions of Java and their compatability with different versions of ImageJ.

  • 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 GE Healthcare. For many years, Pharmacia published free handbooks on the use of these materials, and updated versions are available for download. The handbooks for size exclusion (gel filtration) and ion exchange chromatography are particularly useful: