Assignments CSE 598K (Preview)

Prof. Jesus A. Izaguirre

I. Read 4 Papers
MD Simulation (PM) & Visualization (VMD)

II. Read 4 Papers
Docking Simulation; scoring function (PM)

III. Read 4 Papers
Contest: fastest sampling protocols! (PM, MDSimAid)

IV. Read 4 Papers
Database search & protein-protein interaction

V. Read 4 Papers
Morphogenesis simulations (CompuCell)

Programming:

Some programming in a scripting language and C++ will be expected. Some assignments consist primarily of using existing software.

Every class:

Students are expected to complete assigned reading (typically one paper and chapter from textbook) and to participate on discussion. Each graduate student (and possibly undergraduates for extra credit) will discuss one paper throughout the semester. The presentation should be around 15 minutes, plus 10 minutes of discussion led by the presenter. The student presented is expected to find other papers that cite his paper, using for example Web of Science, and to be able to present developments since the paper was written. The student presenting will make overhead or powerpoint slides, and turn a writeup of 2 to 5 pages discussing the main points of the paper.

Final project:

The final project will be developed throughout the semester individually or in pairs. There will be a final paper and a poster presentation. High quality final papers will be submitted to conference or journal publications.

Undergraduate and graduate grades will be computed separately.