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University of Utah
Interactive Computer Simulations
PhET (Physics Education Technology)
is a program at the University of Colorado that is developing interactive simulations designed to help in the teaching of science and mathematics. We will use some of these simulations in this course.
An online encyclopedia of mathematics created by Eric W. Weisstein and sponsored by Wolfram Research Inc, the makers of the Mathematica computer program. MathWorld covers a wide range of mathematical topics, from the basic to the very advanced.
On-line calculus tools
The manipulations for differentiating and integrating (at least some) functions can be formalized in computer code, and there are computer programs that are remarkably effective at "doing calculus". One of the best, if most expensive, of these programs is
, a product of Wolfram Research, Inc. Portions of Mathematica are available as free online tools for determining derivatives and integrals:
Using these tools can be a little bit tricky, since they require that you write things in a syntax that the program understands. In general, the arguments of functions should be enclosed in square brackets (like f[x]), and the standard functions (like logarithm, sine and cosine) should be written with the first letter capitalized and are often abbreviated, such as Log[x], Sin[x] and Cos[x]. Also, Log[x] represents the natural logarithm (base e), not the common logarithm (base 10).
Also, as with all powerful tools, caution is advised! The programs will probably produce the the correct solution for the problem you specify, but you should always make sure that the result makes sense. If the result doesn't make sense, first check to make sure that you correctly specified the function to be integrated or differentiated. If the result still doesn't make sense, consider the possibility that you have discovered a bug in the program!
Data Graphing Software
(Scientific Data Analysis and Visualization) is an open-source (free) program for plotting and analyzing data. It has much of the functionality of commercial programs such as KaleidaGraph, if a somewhat more rudimentary interface. Although the development of this project seems to be rather slow, the current version is quite functional. The latest versions, 1.23 as of July 2018, can be downloaded from
Versions for different flavors of Linux are available at:
I have written a short SciDavis tutorial, which is largely based on a chapter from a lab manual for another course that I teach. Athough the tutorial is focused on a particular data set, it should be helpful in a more general setting.
The tutorial can be downloaded
is a general-purpose graphing program with powerful curve fitting tools. This is a commercial program that is available in versions for both the Macintosh and Windows. A
free demonstration version
is available from the publishers, Synergy Software. The demo version is fully functional, except that it cannot save or export documents or graphs, a feature that you will need in order to save your work in LabArchive. Graphs can be printed, but have a banner printed across them. Fully functional versions of KaleidaGraph are available in the open-access computer lab in the S. Biol. Building and on some of the computers in Marriott Library.
KaleidaGraph is also available for remote use by University of Utah students. 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. For information, see
Remote Software Access
Other Scientific Software and Resources
. This is an open source program for analyzing molecular structures, including proteins and nucleic acids, with versions for Windows, the Macintosh and Linux. The compiled versions are commercial products, but educational versions are available to students and instructors at no cost. This requires registration to access the files:
The PyMOL wiki
is an excellent source of documentation for the program.
The Protein Data Bank (PDB).
This site provides access to atomic coordinates representing the three dimensional structures of thousands of proteins and nucleic acids, which can then be viewed in programs such as PyMOL. When new structures are published, the authors are expected to deposit the atomic coordinates in this database so that anyone can examine the structures.
A public domain program for analyzing and manipulating images, and an all-time great among free scientific software! 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.