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 2017, version 1.21 is recommended.
    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
    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 Java "virtual machine" software. There are, however, some issues related to the different versions of Java, as described below for the case of the Macintosh computers in the Marriott Library
    • The iMac computers in the Marriott Library, including the laptops available for checkout, currently (April 2018) have a version of ImageJ installed on them that is not compatible with the version of Java (Java 8) that is also installed on those computers. The Mac administrators in the library are aware of the problem, and the correct version is currently being distributed, but this can take some time.
      The older version is located at: /Applications/Graphical/Image Plot/ImageJ/ImageJ.app
      The new version will be found at: /Applications/Graphical/ImageJ/ImageJ.app
    • In the meantime, you can download a copy of the new version yourself and copy it to one of the library computers.
      This version is available for download here.
      This version will work with Java versions up to 9 (as found on the library Macs). Simply download it and expand the compressed "zip" file. If the program does not open, or the tools that you are looking for do not appear in the menus, do the following: Close the program (if it is open); move the application file to a different folder and then; move the application back to the ImageJ folder.

  • 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 https://cdn.gelifesciences.com/dmm3bwsv3/AssetStream.aspx?mediaformatid=10061&destinationid=10016&assetid=13101chromatography 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: