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.

Open topic

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.

First stage: Vision

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. Add a category tag of [[Category:BCH441 2013 Open Project I (in progress)]] to your page so your classmates and I can find it.

As for scope and contents, you may want to consider the following ...

• Don't write more than a paragraph, but make it clear what you want to do and why this is interesting and/or useful.
• Don't provide an extensive review of literature, but make it clear that you understand how your vision is neither too narrow nor too broad. Addressing a solved problem (e.g. sequence alignment) would be too narrow (but a good tutorial for a complex workflow may be oK). Addressing an (as yet) unsolvable problem (e.g. cure cancer) would be too broad (but an exploration of a well defined step, or what is missing in the field would be oK). Add one citation that gives you confidence that what you are planning is doable! and make sure to explain in your vision why you think so.
• Don't attempt to do too much, but keep in mind how much available time you have this term. Many students have found their projects inspiring and greatly enjoyed devoting significant time to it, that's great. But if you get stressed out because the implementation turns out to be harder than you thought, that's bad. This should be fun. That said, a solid analysis of a problem is useful even without implementation. If it's a cool idea, you can come back to it over the winter break and perhaps form it into something publishable.
• Don't burden your concept with details of algorithms and databases – these may change anyway as you refine the idea – but by all means, add links for clarity to appropriate resources and references.
• Don't be too invested in any single strategy, but keep in mind that things might not work as expected and give some thought to fallback approaches.
• Above all, don't focus too much on the process and methodology, but be very clear about your objectives. Software development starts from a "requirements analysis".

Marking will consider quality, usefulness, creativity and originality of the contribution in the general field of bioinformatics or computational biology (unless we have discussed that your project will be in a different field.)

When you are done, hopefully before the deadline, please change your category tag to [[Category:BCH441 2013 Open Project I (submitted)]]

We will go through a round of peer feedback immediately following the deadline. Please see here for details.

I will review your proposals and move them into one of two categories:

• [[Category:BCH441 2013 Open Project I (review requested)]] means I propose significant changes to scope or focus of your project. You may discuss with me, change your project, or simply change the category and move on ... this is your project after all.
• [[Category:BCH441 2013 Open Project II (in progress)]] means you should move on and develop your outline.

 

Second stage: Outline

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. You can put this on the same page of the Student Wiki as your concept.

Final stage: Implementation

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.

Evaluation

1. Evaluation will be done with contributions from your peers; details will be announced at a later time.
2. 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.
3. Time management is up to you. However there are three stages of the project and three deadlines.

Due dates

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.

Late submissions

The time of submission is implicit in your edits on the Wiki and can be identified in the history tab of a page: I will mark the last edit before the submission deadline. However, if you want me to consider a later edit instead (i.e. "late submission" with the appropriate penalties), send me an eMail to that effect.

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 submitted:

Received 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