The final course to be completed for the CCB Certificate in Computational Biology is MATH 5840 or CSC 5840 which is taken after all other coursework is completed. The catalog course title is Independent Study, but we require specifically that you complete a complex programming project with the following objective.

Each student must generate, document, and present original computer code that demonstrates an ability to build complex software systems that address a significant biological problem.

This will be done under selected faculty supervision, approved by CCB. Each student will select two advisors: one who will serve as the biology expert for the problem being solved (and may provide the problem), and one who will will serve as the computational and mathematical expert for the solution. Both advisors will participate in helping the student to organize the scope of the work, the report, and the presentation.

Note: you will not be able to choose your project on your own. The work you do depends upon what your advisors want you to do. You must follow the steps below to find a project. This must be completed before you can register for the independent study, so you must begin discussions with potential advisors at least a month before the beginning of the semester you wish to enroll.

Here are the steps each student must execute prior to the beginning of the semester that the course is taken.

1. Select advisors. This will require some exploration and discussion of possible topics, so you want to do this as early as possible (at least one month is recommended). The list of approved advisors will grow; for now, here are faculty whom you can contact to be your advisor:

   Bioscience	Computer science/Mathematics
   Mark Duncan, HSC Robert Hodges, HSC Karen Newell, UCCS Jim Sikela, HSC Brad Stith, UCD Vasilis Vasiliou, HSC	Steve Billups, UCD Bill Briggs, UCD Krys Cios, UCD Harvey Greenberg, UCD Larry Hunter, HSC Dennis Lezotte, HSC

2. Prepare a proposal (with help of advisors) that contains the following:
   1. Title of project and names of advisors, with signatures
   2. Statement of project goal and its biological significance
   3. A list of specific aims that the project intends to achieve. Each aim must have associated evaluation criteria for measuring progress toward the aim. The possible point scores for all evaluation criteria on all specific aims combined must total 100. (The grade will be based on how much is achieved.)
   4. List of deliverables, concluding with a written report, complete software documentation, and a 20-minute presentation. These will be staged, allowing re-evaluation at each stage, or plateau, to see if the goals need to be revised. If so, the advisors must approve any change.

3. Have the proposal attached to the form for Independent Study that is a contract between the student and the University, and submit it (with student and advisors' signatures) to the CCB Administrative Assistant. (This will remain on file.)

4. Register for either MATH 5840 or CSC 5840.

Once registration is complete, the date of the presentation will be set to be between 10 and 11 AM on the last Friday of the semester. (Exceptions, due to schedule conflicts, can be accommodated by the CCB Director.) The presentation will be advertised as a CCB event, and the public will be invited.

During the semester each student will be expected to meet at least one hour per week with at least one of his/her advisors and at least once per month with both advisors.