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. The Macintosh computers in the Biology Department have version 1.d8 installed, beecause some of the newer versions introduced bugs, at least in the Mac and Linux versions. The newer versions may prefered on Windows.
    Unfortunately, the documentation for SciDAVis is rather limited (and out of date), but a detailed tutorial is provided in the lab manual for this class.

  • Kaleidagraph. A general-purpose graphing program with powerful curve fitting tools, similar to those found in SciDAVis. This is a commercial program that is available in versions for both the Macintosh and Windows. This program was previously used in Biol 3515/Chem 3515, and you can, if you prefer, use it for this class. If you do choose to use this, or another graphing program, please check with the instructor first to discuss how to submit your work on LabArchives.
    Fully functional versions of KaleidaGraph are available in the the Biology teaching laboratories and in the open-access computer lab in S. Biol. 106, and on some of the computers in Marriott Library.

  • 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 is written in Java and should run on any computer with Java "virtual machine" software.

  • 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.

  • Remote access to Macintosh software via Marriott Library. The library operates servers that allows remote users to create a virtual Macintosh screen on your local computer, which can be another Macintosh or a computer running Windows or Linux. This provides access to a wide variety of software, including KaleidaGraph. One limitation, however, is that there is not a simple means of transferring files from the remote computer to your local one. For the purposes of this course, however, you can transfer the files to LabArchives by using a browser within the remote computer.

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 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 these remain available for download. The handbooks for gel filtration, ion exchange and affinity chromatography are particularly useful: