Computational Biology

CS795 Geometric Algorithms for Bioinformatics (Fall2009)


  • Instructor: Amarda Shehu amarda\AT\
    Place and Time: ENT #276, R 7:20 - 10:00 pm
    Office Hours: T 4-6 pm


  • This class belongs to the AI/Database area. It presents geometric algorithms developed for modeling and simulating physical and biological systems. The course will first focus on algorithms for purely kinematic (robotic) systems, with an emphasis on planning motions with geometric constraints. This treatment will allow a seamless transition to algorithms for simulation of motions of biological molecules with energetic constraints.
    Algorithms will be presented in the context of applications: (i) simulating realistic motions of robotic kinematic chain for greater autonomy; (ii) computing functionally-relevant motions of protein chains for the design of novel therapeutics; (iii) computing inter-molecular associations and assembly for the engineering of molecular machines.


  • Material will be disseminated in the form of lectures, which, in addition to building background in robotics and structural computational biology, will cover latest research articles in these fields as well. Students will be tested on the comprehension of the basic background material through individual programming assignments. Extra credit in the programming assignments will allow students that are interested in advanced topics and research to demonstrate their abilities. Extra credit will not account for more than 10% of the total grade on an assignment. No late deliverables will be accepted.

    Students will be asked to participate in class discussions of research articles. Each student will also be responsible for summarizing and presenting in class a chosen research article. The choice will normally be a follow-up of articles covered in class and should reflect the student's topic interests for the final project. Regarding the final project, students can choose from a list of topics suggested and covered in class by the instructor or even suggest their own. Students can also choose whether they prefer to be part of a team of no more than 3 students or work individually. If working in a team, students will be asked to document their individual contribution to the project. The grade on the project will combine both the overall project and the individual contribution.

    The final project will provide students an opportunity to present and defend research on a topic of their choice. Final deliverables include source code/executable and a written manuscript, which tests students in their ability to motivate the importance of the topic they have chosen, deal with the technical aspects of implementing the approach, and present their findings. Comments will be provided by way of an intermediate progress report, which will consist of a short, 2-3 page writeup summarizing progress to date. Students that are interested in conducting research with the instructor should consider this project as a good opportunity to showcase their ability to conduct research.

Tentative Grade Breakdown

  • Participation in Class Discussions: 5%
    Individual Programming Assignments: 30%
    Individual Research Article Review and Presentation: 25%
    Final Project Completion and Presentation: 40%