BIO systems project

Open Project

   

What interests you about Bioinformatics? 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 as a Perl or PHP script, or defining an interesting protein domain in depth through a Jalview alignment? 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 in "R"? Or how about editing and improving one or more Wikipedia article(s)? In 2011 we had a student who hooked up VMD input to a Wii... but perhaps you would like to choreograph a modern dance on the topic of evolutionary trees?

In this Open Project, I invite you to think creatively, research some knowledge or viewpoint about the field, acquire a personal position and perspective, and share it with your peers.

1. The topic is open. You can submit anything you want. However, I will provide feedback on the suitability of the topic, if asked, keeping in mind the marking criteria detailed below. What I have written above are merely suggestions off the top of my head. I advise against running off with the first thing that comes to your mind, it may indicate to us that you haven't thought about this sufficiently. I also advise against choosing something obvious, such as e.g. "the topic of week 5 lectures", because it may be trivial, or trite, and indicate to us that you haven't thought about this sufficiently. Perhaps it is best to exploit the power of collective intelligence and to discuss your ideas among yourselves, or on the mailing list. Or you could pick up a current issue of a bioinformatics journal, and get a sense of where the frontiers of the field are at. However, try not to ask me what to do just because you can't come up with anything. If I get the impression that there was nothing that interested you in the whole, wide world of bioinformatics and computational 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 and submit it on a subpage of your User Page on the Student Wiki.
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 on a separate page of the Student Wiki.
4. The third stage is the project itself. Its main deliverable would typically be something in electronic form that you can submit on the Wiki; please note that all contributions on the Student Wiki are implicitly available under a Creative Commons license (attribution, share-alike). If it is something more ephemeral however, or made in a different medium, coordinate with me.
5. Marking will be assigned to your peers; details will be announced at a later time.
6. Marking will consider:
   1. Quality, usefulness, creativity and originality of the contribution in the general field of bioinformatics or computational biology;
   2. Execution and form;
   3. Timely submission.
7. 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 3.
The outline / project plan is due by the end of week 5.
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 have to do with your normal, expected workload. If you want to, you can submit all phases of your project at any earlier date you choose - and get it done with. Since you will be done by mid-November at the latest, we help you avoid the mad, soul-destroying, end-of-term rush for this deliverable which is worth more than a quarter of your total grade.

Just to clarify: "by the end of ..." means Sunday at midnight. And yes, there will be penalties. Your final mark for the stage will be multiplied by the following factor for each day after the deadline on which it is received:

Rceived on the ...

• first day after the deadline: marks times 0.9
• second day: 0.7
• third day: 0.4
• fourth day: 0.1
• fifth day and later: 0