BIO systems project

Bioinformatics Project

   

This course gives you a broad overview of bioinformatics principles, but you should also strive to explore one aspect of the field more deeply.

For this term project I would like you to identify an article published less than a year ago that applies bioinformatics to an important biological question. You should define the workflow of the analysis - what are the datasources, what procedures have been applied, how have the results been presented, validated and interpreted. The result should be a cookbook-style description of the methodology. Then you should apply the method to some data of your own.

Open topic

The topic is open. You can work on a process that is closely related to the course material or more distant. I will provide feedback on the suitability of the article, if asked, keeping in mind the marking criteria detailed below.

First stage: Choosing a suitable process (5 marks max.)

1. Choose an article and post its PubMed ID on the student Wiki. Make sure the article is not older than one year, and that no one else has chosen the article.
2. Start a subpage in your Student Wiki user space where you link to the article. Use the following syntax: {{#pmid: 16011803}}.
3. Write a one-sentence abstract of the process you are working on. It does not have to be the full process described in the article, but can be limited in scope or depth. However it must be independently useful and non-trivial. A BLAST search won't be enough.
4. Write a sentence on how the results are useful.
5. Write a bulleted list of procedures that your process uses.
6. If you think you can improve on the published method, by all means do so. Explain your plan in one or two sentences.
7. Add a category tag of [[Category:BCH441 2014 Bioinformatics Project]] to your page so it can be easily found.
8. If you would like to deviate from this template, coordinate with me.

Marking will consider suitability and usefulness of the process for this project, how well you were able to abstract the procedures, and how well you succeeded to implement the process in your example.

 

Second stage: The process (14 marks max.)

The second stage of the project is your detailed analysis of the process. Describe the steps of the process in enough detail that someone new to the field could execute it following your instructions. Make sure you define input data, algorithms, output, how to present the results, what controls to run, how the results should be interpreted. Don't forget to execute the process in an example and documenting this.

Develop this on the same page of the Student Wiki as your concept.

 

Final stage: Review (3 x 3 marks max.)

Finally, provide some review feedback. I will assign each student three projects for review. Access the project page and write approximately a paragraph of critique on the Discussion page. Discuss whether the process was easy to follow, completely described, and, in your view useful (for what purpose). As a metric for completeness, imagine you were a project student in the lab and had just been handed the project text as instruction to perform an analysis on new data. Would it contain all you need to know to proceed?

 

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 article choice is due by the end of week 4.
The project implementation is due by the end of week 10.
The project reviews are due by the end of week 12.

 

Late submissions

The time of submission is recorded with your edits on the Wiki and can be identified in the View history tab of a page: I will consider the last edit before the submission deadline for marking. 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 the bulk of your project 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