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, Python or PHP script, an R/Bioconductor workflow, or simulating (part of) a metabolic pathway? Are there interesting databases or services that are missing from the syllabus? 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 at our feedback sessions. I advise against running off with the first thing that comes to your mind - discuss your ideas with your peers, 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:

5.1 Quality, usefulness, insight, creativity and originality of the contribution;

5.2 Execution and form;

6. There are three stages of the project and three firm deadlines.

The concept / vision is due in class in week 4.
The outline / project plan is due in class in week 7 (after reading week).
The final submission is due in class in week 11.

Please get your deliverables done early! They are due in class and even though you may be able to convince me to grant an extension, not having them available for feedback is likely to impact negatively on your marks.

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:BCB420 2014 Open Project I]] to your page so I can find it for reference.

For Wednesday in class, print out your vision on a "mini poster" of approximately two pages (landscape) in size, with as large a font as you can use. You will tape your mini poster to the classroom wall, we will discuss and review the concepts and I will mark them.

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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 have reviewed it and understand how your vision is neither too narrow nor too broad. Addressing a solved problem (e.g. finding differentially expressed genes) 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 summer and perhaps form it into something publishable.
• Don't burden your concept with details of algorithms and databases and other implementation details – these may change anyway as you refine the idea – but by all means be specific in your goals.
• 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, insight, creativity and originality of the contribution in the general field of computational systems biology (unless you can convince me that your project will be in a different field without detracting from the academic objectives of this course.)

max. 6 marks

 

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 vision. Add a category tag of [[Category:BCB420 2014 Open Project II]] to your page so I can find it for reference. It will again be presented on mini poster, discussed, and marked in class.

For Wednesday in class, print out your outline on a "mini poster" of approximately two pages (landscape) in size, with as large a font as you can use. You will tape your mini poster to the classroom wall, we will discuss and review your outlines and I will mark them.

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As for the details of your outline, you may want to consider the following ...

• Make sure your steps are defined. Don't be vague. State clearly what data, resources, algorithms etc. you are going to use.
• Make sure your steps are complete. From the first step of your project (perhaps: accessing source data) to the last step (usually: interpreting results) there should be no gap or uncertainty in your project. But if there is, a clear definition of alternatives is needed. In no case should the project turn out to be simply not feasible as it progresses. Remember: fallback approaches were a part of your vision requirements.
• As a corollary:
  • Your vision had objectives: make sure your project steps fulfill your objectives.
  • Any project must have an endpoint. If there is no endpoint, it is not a project but an activity. Make sure your endpoint is defined.
  • Don't forget to include positive and negative controls if your project has an experimental aspect.
  • Don't forget to consider testing and validation if your project includes code development.
  • Don't forget to provide references and citations, if your project relates to problems or solutions you have learned about in the literature.
• Make sure your steps are relevant. Your outline should implement your project vision. If your vision has changed significantly, you might want to mention this in one or two introductory sentences.
• Find the right balance of detail and conciseness in your steps. Break down the project into distinct chunks that should not be longer (as a rule of thumb) than what you can accomplish in a day, or shorter (as a rule of thumb) than what you can do in an hour.
• Finally, consider that your mini-poster should be able to stand for itself, without narration.
• Feel encouraged to include a Gantt chart, to convince yourself that your project is still feasible in the required timeframe. (Although I don't require this.)

Marking will consider how well the project steps and especially the deliverables have been defined, whether they steps are complete, whether they implement your vision, and whether your outline is well written and formatted and easy to understand for me as a good-willed but uninformed layman.

max. 14 marks

 

Third 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. Add a category tag of [[Category:BCB420 2014 Open Project III]] to your page so I can find it for reference. Also, please note that all contributions on the Student Wiki are implicitly available under a Creative Commons license (attribution, share-alike). If your project is something ephemeral that cannot be well presented on the Wiki however, or created in a different medium, coordinate with me. Again, final presentations will be in class – please prepare an abstract for your mini poster and make sure your actual submission is accessible on the Web.

max. 10 marks