BMMB 597C
Computers for Biochemists & Molecular Biologists

This course is taught by B. Tracy Nixon (btn1@psu.edu). Prior versions were offered beginning in the Fall of 1995. It is being offered again in the Fall of 2004, with some changes.

• Meet in the Microbiology Computer Lab, room 122 South Frear Building, on Tuesdays and Thursdays, 4:40 to 5:30, and Friday 3:35 until 5:30. Mutally convenient alternate times for class sessions can be determined on the first day of class. Students may use the computer lab at various other times to work on their projects, but much of the work can be done at your convenience at many other sites. How to work remotely will be explained during the course.
• For the data analysis portion of the course, the book Data Reduction and Error Analysis for the Physical Sciences by Philip R. Bevington, D. Keith Robinson, 2nd Edition may be helpful. It is a classic, that you may want to purchase from Amazon or other bookstore.

Statement on Academic Integrity

The computers in the lab have had software installed from an Instructional Lab Grant  (#97597) issued by Microsoft Corporation to me to enhance the course. In addition, various programs are installed for use in the class. These include

Rasmol, KinMage	CHIME	NONLIN	WinNonlin	UltraScan	KinTekSim	Clamp	SwissPDBView	GNOME, etc	CNS_SOLVE	"O"
3D Viewers	3D Viewer as Browser Pluggin	nonlinear regression with rigorous error analysis	NONLIN for global fitting of Equilibrium Centrifugation Data	Sedimentation Velocity & simulation (Linux - subsitute for WindowsNT)	Kinetics simulation and global fitting	BiaCore global fitting	3D Structure viewer, PDB file manipulator, refinement, ...	processing of SANS, SAXS and WAXS data for solution structures of macromolecules	Refinement of structure models using X-ray crystallographic data	Refinement of models based on X-ray diffraction (Linux - subsitute for WindowsNT)

To make best use of the material found in this self-help course, you may benefit from:

1. An ability to create ASCII text (Dos text in many word processers) - the DOS editor EDIT is one such program; others exist.
2. An HTML Editor such as the free software AOLPress from America On Line; RasMac (Mac's) or RasWin (PC's and Unix's); Chime pluggin, KineMage plus Pkin, and Swiss PDB Viewer for viewing 3D models of macromolecules, and other software presented in the lessons. See the listed URL's under the Lessons section for where to get these programs.
3. A spread sheet program, such as Excel or one of many others commonly available will also be useful..

We will learn to to use these programs with real data, and learn how to avoid or solve problems associated with individual cases, so that your future molecular biology or biochemical work can be quantitative when desired, and well presented. See the Purpose link below for more details. Many of the lessons will make use of software we have here at Penn State - sorry if that complicates things for anyone making off-campus use of the material.

Purpose	Bookmarks (woefully outdated - Let's rebuild as part of the class)	Grading Policy	Lessons	Student Pages
			2004 (in progress)	Students - 2004
			2003, 2001, 2000 , 1999	Students - 2001