Difference between revisions of "BIO systems project"
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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. | 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. | ||
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| + | ====First stage: Choosing a suitable process (5 marks max.)==== | ||
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| + | #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. | ||
| + | #Start a subpage in your Student Wiki user space where you link to the article. Use the following syntax: <code><nowiki>{{#pmid: 16011803}}</nowiki></code>. | ||
| + | #Write a bulleted list of procedures that your process uses. | ||
| + | #Add a category tag of [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2014_Bioinformatics_Project <code><nowiki>[[Category:BCH441 2014 Bioinformatics Project]]</nowiki></code>] to your page so it can be easily found. | ||
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<div class="mw-collapsible mw-collapsed exercise-box" data-expandtext="Expand" data-collapsetext="Collapse"> | <div class="mw-collapsible mw-collapsed exercise-box" data-expandtext="Expand" data-collapsetext="Collapse"> | ||
As for scope and contents, you may want to consider the following ... | As for scope and contents, you may want to consider the following ... | ||
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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.) | 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.) | ||
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When you are done, hopefully before the deadline, please change your category tag to [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2013_Open_Project_I_(submitted) <code><nowiki>[[Category:BCH441 2013 Open Project I (submitted)]]</nowiki></code>] | When you are done, hopefully before the deadline, please change your category tag to [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2013_Open_Project_I_(submitted) <code><nowiki>[[Category:BCH441 2013 Open Project I (submitted)]]</nowiki></code>] | ||
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* [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2013_Open_Project_I_(review_requested) <code><nowiki>[[Category:BCH441 2013 Open Project I (review requested)]]</nowiki></code>] 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. | * [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2013_Open_Project_I_(review_requested) <code><nowiki>[[Category:BCH441 2013 Open Project I (review requested)]]</nowiki></code>] 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. | ||
* [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2013_Open_Project_II_(in_progress) <code><nowiki>[[Category:BCH441 2013 Open Project II (in progress)]]</nowiki></code>] means you should move on and develop your outline. | * [http://biochemistry.utoronto.ca/steipe/abc/students/index.php/Category:BCH441_2013_Open_Project_II_(in_progress) <code><nowiki>[[Category:BCH441 2013 Open Project II (in progress)]]</nowiki></code>] means you should move on and develop your outline. | ||
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Revision as of 19:01, 9 September 2014
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.
Contents
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.)
- 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.
- Start a subpage in your Student Wiki user space where you link to the article. Use the following syntax:
{{#pmid: 16011803}}. - Write a bulleted list of procedures that your process uses.
- Add a category tag of
[[Category:BCH441 2014 Bioinformatics Project]]to your page so it can be easily found.
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.)
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.
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Evaluation
- Evaluation will be done with contributions from your peers; details will be announced at a later time.
- Marking will consider:
- Quality, usefulness, creativity and originality of the contribution in the general field of bioinformatics or computational biology;
- Execution and form;
- Timely submission.
- 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
