Difference between revisions of "BIO systems project"
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This course gives you a broad overview of bioinformatics principles, but you should also strive to explore one aspect of the field more deeply. | 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 | + | ;For your term project I would like you to identify a defined biological "function". Then you should collect all genes that collaborate towards that function. This would correspond to a "system". The problem 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. This means you should |
| + | * define the function 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 list; | ||
| + | * 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 function would be defined at a level where it is realized with some 20, 30 genes or so, not much more. | ||
| + | |||
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===Open topic=== | ===Open topic=== | ||
| − | The | + | The function you choose is open. I'll probably provide a list of suggestions. However, you should ensure you don't choose the same function as someone else in class. |
| − | |||
| − | |||
| − | |||
| + | ===First stage: Choosing a suitable function (5 marks max.)=== | ||
| + | Details to be anounced ... | ||
| + | <!-- | ||
#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. | #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>. | #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>. | ||
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#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. | #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. | ||
#<small>If you would like to deviate from this template, coordinate with me.</small> | #<small>If you would like to deviate from this template, coordinate with me.</small> | ||
| − | + | --> | |
<!-- | <!-- | ||
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--> | --> | ||
| + | |||
| + | <!-- | ||
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. | 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. | ||
| − | |||
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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| | ||
| − | ===Second stage: | + | ===Second stage: Compiling a list of genes (12 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. | + | Details to be announced ... |
| + | |||
| + | <!-- 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. | Develop this on the same page of the Student Wiki as your concept. | ||
| + | --> | ||
| + | | ||
| − | + | ===Final stage: Documentation (9 marks max.)=== | |
| + | |||
| + | Details to be announced... | ||
| − | + | <!-- 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? | |
| − | 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? | ||
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# Time management is up to you. However there are three stages of the project and three deadlines. | # Time management is up to you. However there are three stages of the project and three deadlines. | ||
| + | --> | ||
===Due dates=== | ===Due dates=== | ||
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| | ||
<div class="alert"> | <div class="alert"> | ||
| − | The ''' | + | The '''function choice''' is due by the end of '''week 6'''.<br /> |
| − | The ''' | + | The '''compilation of the list of genes''' is due by the end of '''week 10'''.<br /> |
| − | The ''' | + | The '''documentation''' are due by the end of '''week 12'''.<br /> |
</div> | </div> | ||
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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. | 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. | + | 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 | + | 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 ... | Received on the ... | ||
Revision as of 21:24, 15 September 2015
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 your term project I would like you to identify a defined biological "function". Then you should collect all genes that collaborate towards that function. This would correspond to a "system". The problem 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. This means you should
- define the function 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 list;
- 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 function would be defined at a level where it is realized with some 20, 30 genes or so, not much more.
Contents
Open topic
The function you choose is open. I'll probably provide a list of suggestions. However, you should ensure you don't choose the same function as someone else in class.
First stage: Choosing a suitable function (5 marks max.)
Details to be anounced ...
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 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. 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
