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.
Mathematics
MathWorld. 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 Mathematica, a product of Wolfram Research, Inc. Portions of Mathematica are available as free online tools for determining derivatives and integrals:
Derivatives 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
SciDAVis (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 laatest version (as of August 2022, 2.8, is available as pre-compiled binaries for both MacOS and Windows, which can be downloaded from
https://sourceforge.net/projects/scidavis/files/SciDAVis/2/2.8/.
I have written a short SciDavis tutorial, which is largely based on a chapter from a lab manual for another course that I teach. Although the tutorial is focused on a particular data set, it should be helpful in a more general setting.
PyMOL.
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.
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.
ImageJ 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.
Zosimos Is an online tool for drawing chemical structures. It is based on the 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.