CSB Open project

Open Project

   

What interests you about Computational Systems Biology? How can you contribute to the field? Would you like to write a tutorial for using a service, database or program you find important? How about implementing a useful task in a Perl or PHP script, an R/Bioconductor workflow, or a simulation of (part of) a metabolic pathway? Are there interesting databases or services we did not cover? Or maybe you would be curious about a particular workflow - is it possible? How can it be done? Can you implement it? Or how about improving a bunch of Wikipedia articles?

In this Open Project, I invite you to think like a computational systems biologist, acquire some knowledge or viewpoint about the field and share it with your peers.

1. The topic is open but I will provide feedback on the suitability of the topic, if asked. I advise against running off with the first thing that comes to your mind - discuss your ideas among yourselves, or with me. However, try not to ask me what to do because you can't come up with anything. If I get the impression that there was nothing that interested you in the whole, wild, wide world of systems biology, that will make me depressed.
2. The first stage of the project is your concept or vision. In a brief paragraph, describe your premise, method, expected outcome and utility.
3. The second stage of the project is your outline or project plan. Describe the steps of your project in detail, list the required resources and tools, clearly define your deliverables.
4. The third stage is the project itself. Its main deliverable would typically be something in electronic form; I strongly encourage attaching a Creative Commons license to your work. Then we could make it available for others.
5. Marking will consider:
   1. Quality, usefulness, creativity and originality of the contribution;
   2. Execution and form;
   3. Timely submission.
6. Time management is up to you. However there are three stages of the project and three deadlines.

The concept / vision is due by the end of week 4.
The outline / project plan is due by the end of week 6.
The final submission is due by the end of week 10.

Please get your deliverables done early, I will be quite resistant to grant extensions for reasons that arise from your normal, expected workload (in particular other assignment due dates and midterm exams). The submission deadline is the Sunday of week in which the material is due, at midnight. Your maximum marks will decay with the half-life of ⁹⁰Y (i.e. 64h). This is awkward, but the problems created by insufficient time management in past years were even more awkward. Don't expect me to remind you that your work is overdue, or that it has deliverables missing.

Concept

Task

Define your project. [...]

Form

Feedback session

Deadline

Vision

Submission