BIO systems project
Bioinformatics Project: Defining a System
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 your term project I would like you to identify a defined biological "system" - a set of genes that collaborate towards a shared purpose. We start by looking at biological processes, represented in the Gene Ontology (GO). From there we can find related processes, functions and cellular components. The problem and reason why we need human intuition to work out a systems definition based on this kind of information is that there are more aspects to a system than just the actual function: genes that are responsible for substrate import, biosynthesis of cofactors, signalling, regulation, constructing scaffolds etc. may also be part of the system. On the other hand some genes participate in a central role in making the process possible, but they provide this service to many other systems as well and are actually parts of a distinct but collaborating system. Membrane transporters might be an obvious example.
It is your task to manage this from the perspective of a biological expert and try to define inclusion/exclusion criteria as best as you can. While your "list of genes" is going to be interesting, compiling such lists can be automated. Thus the most valuable outcome of your project how you will address the task of defining your system boundaries.
In practice you should
- define the biological process you are interested in;
- collect all contributing genes as best you can, using a broad spectrum of literature comments and bioinformatics tools that we may have or have not covered in the course;
- develop unambiguous criteria for including or not including such genes in your system;
- provide an annotated list of included genes, and ones that you have excluded; and
- carefully document your efforts and results: the datasources, what procedures have been applied, how the results been accessed, validated and interpreted...
Ideally, your process would be defined at a level where the system that realizes it is comprised of some 20, 30 genes or so, not much more, to keep things manageable.
Contents
Open topic
The function you choose is open. I have posted a list of suggestions. However, you should ensure you don't choose the same process as someone else in the class.
First stage: Choosing a suitable process (5 marks max.)
To define a system, we will start from a biological process in the GO biological process ontology. I have excerpted a table of processes to get you started, explained the procedure in detail and worked it out in one example. You can find all of this here.
Note that you are not constrained to use a process from that table. If you are determined to work on a different human system, you are welcome.
The page also links to an example page on my Student Wiki. The example page illustrates what I expect from you for full marks for this stage.
Second stage: Compiling a list of genes (12 marks max.)
Details to be announced ...
Final stage: Documentation (9 marks max.)
Details to be announced...
Due dates
The function choice is due by the end of week 6.
The compilation of the list of genes is due by the end of week 10.
The documentation is 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. Be especially mindful of your other courses, and their midterm tests.
Just to clarify: "by the end of ..." means Tuesday 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
