Difference between revisions of "Group project"
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Each group will take on one workflow to annotate. As a group, you will jointly define and structure the workflow. Individually, you will annotate some of the data items or procedures of the workflow. Your mark will be based on both components. | Each group will take on one workflow to annotate. As a group, you will jointly define and structure the workflow. Individually, you will annotate some of the data items or procedures of the workflow. Your mark will be based on both components. | ||
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<!-- For a limited time-period ... | <!-- For a limited time-period ... | ||
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* You may change into open spots of other groups, if you request this by e-mail. | * You may change into open spots of other groups, if you request this by e-mail. | ||
| − | * You may swap groups, if both of you request this after class. --> | + | * You may swap groups, if both of you request this after class. |
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| + | Please be fair to your group members and alert me immediately in case you plan to drop the course.--> | ||
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| + | The project will proceed as follows: | ||
| + | |||
| + | #A number of topics from the general area of functional annotation are listed in the table below. | ||
| + | #Jointly, as a group, choose one of the topics and one alternative (in case too many groups choose the same topic). If you would like to propose a different topic you are interested in, you may do so. | ||
| + | #Discuss within your group your understanding of the topic, what databases and tools could be relevant and a proposed process - a sequence of steps - to address the topic. You may involve your TA into the discussion at any time. | ||
| + | #Plan your time to be able to communicate about the project within the group, go through some improvements, and finish by the due date. | ||
| + | #Summarize the results of the discussion (your plan how to go about this) in a paragraph of text, and e-mail it to your TA for feedback and iterated improvements. | ||
| + | #Once the improvements are done, the following milestones should be achieved: | ||
| + | ##Task is broken down into a number of procedures | ||
| + | ##Each procedure has clearly defined input data, an algorithm operating on that data, and output data | ||
| + | ##There is a designated group member for each procedure | ||
| + | ##The entire process has been summarized in approximately one page, jointly written. | ||
| + | #Individually, describe your designated procedure(s) in approximately one page. Define input data, algorithm, parameters, alternatives, output data etc. Give references. You may request feedback from TAs and from your group members and classmates. However you will take author's responsibility for the result. | ||
| + | #Submit a collated hardcopy of the process summary and your individual procedure descriptions by the due date. Make sure your individual contributions are clearly identified with your name. | ||
| + | |||
| + | ;The due date is Thursday, December 4. (last day of class) at 6 p.m. | ||
| + | <hr> | ||
| + | ;Topics: | ||
| + | *Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein | ||
| + | *Distinguish between structural and functional conservation ([http://www.ncbi.nlm.nih.gov/pubmed/12547207 1], [http://www.ncbi.nlm.nih.gov/pubmed/16644792 2], [http://www.ncbi.nlm.nih.gov/pubmed/16809388 3]) | ||
| + | *Predict domain boundaries ([http://www.ncbi.nlm.nih.gov/pubmed/17430200 1], [http://www.ncbi.nlm.nih.gov/pubmed/17430199 2]) | ||
| + | *Identify whether a gene of interest has been under recent positive selection ([http://www.ncbi.nlm.nih.gov/pubmed/18627454 1], [http://www.ncbi.nlm.nih.gov/pubmed/17473869 2]) | ||
| + | *Obtain a profile/profile alignment of distant homologues ([http://www.ncbi.nlm.nih.gov/pubmed/18247410 1], [http://www.ncbi.nlm.nih.gov/pubmed/16713709 2]) | ||
| + | *Identify whether a human gene of interest may be involved in a disease ([http://www.ncbi.nlm.nih.gov/pubmed/17638813 1] [http://www.ncbi.nlm.nih.gov/pubmed/17493278 2]) | ||
| + | *Calculate a column-wise conservation score ([http://www.ncbi.nlm.nih.gov/pubmed/12112692 1], [http://www.ncbi.nlm.nih.gov/pubmed/17710364 2]) | ||
| + | *Predict membrane topology ([http://www.ncbi.nlm.nih.gov/pubmed/18075166 1]) | ||
| + | *Predict protein/protein interactions for a gene of interest ([http://www.ncbi.nlm.nih.gov/pubmed/18095187 1] [http://www.ncbi.nlm.nih.gov/pubmed/18314580 2]) | ||
| + | *Identify and evaluate linear sequence motifs ([http://www.ncbi.nlm.nih.gov/pubmed/18508681 1], [http://www.ncbi.nlm.nih.gov/pubmed/18460207 2]) | ||
| − | + | (Some PubMed links are provided to get you started. Make use of the "Related Articles" feature in PubMed.) | |
| + | <hr> | ||
Revision as of 15:43, 13 November 2008
The Group Mini-Project
You have been assigned to groups of three or four students.
Each group will take on one workflow to annotate. As a group, you will jointly define and structure the workflow. Individually, you will annotate some of the data items or procedures of the workflow. Your mark will be based on both components.
The project will proceed as follows:
- A number of topics from the general area of functional annotation are listed in the table below.
- Jointly, as a group, choose one of the topics and one alternative (in case too many groups choose the same topic). If you would like to propose a different topic you are interested in, you may do so.
- Discuss within your group your understanding of the topic, what databases and tools could be relevant and a proposed process - a sequence of steps - to address the topic. You may involve your TA into the discussion at any time.
- Plan your time to be able to communicate about the project within the group, go through some improvements, and finish by the due date.
- Summarize the results of the discussion (your plan how to go about this) in a paragraph of text, and e-mail it to your TA for feedback and iterated improvements.
- Once the improvements are done, the following milestones should be achieved:
- Task is broken down into a number of procedures
- Each procedure has clearly defined input data, an algorithm operating on that data, and output data
- There is a designated group member for each procedure
- The entire process has been summarized in approximately one page, jointly written.
- Individually, describe your designated procedure(s) in approximately one page. Define input data, algorithm, parameters, alternatives, output data etc. Give references. You may request feedback from TAs and from your group members and classmates. However you will take author's responsibility for the result.
- Submit a collated hardcopy of the process summary and your individual procedure descriptions by the due date. Make sure your individual contributions are clearly identified with your name.
- The due date is Thursday, December 4. (last day of class) at 6 p.m.
- Topics
- Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein
- Distinguish between structural and functional conservation (1, 2, 3)
- Predict domain boundaries (1, 2)
- Identify whether a gene of interest has been under recent positive selection (1, 2)
- Obtain a profile/profile alignment of distant homologues (1, 2)
- Identify whether a human gene of interest may be involved in a disease (1 2)
- Calculate a column-wise conservation score (1, 2)
- Predict membrane topology (1)
- Predict protein/protein interactions for a gene of interest (1 2)
- Identify and evaluate linear sequence motifs (1, 2)
(Some PubMed links are provided to get you started. Make use of the "Related Articles" feature in PubMed.)
Groups
| Group | Name | Name | Name | Name | Name | TA | Species |
| Alanine | Maria Soloveychik | Alison Muir | Zarnaben Shah | Herman Badwal | Philip | Aspergillus fumigatus (Af293) | |
| Cysteine | Yuan Yao | Adam Santoro | Yuanfan Yang | Marco Fiume | Boris | Aspergillus nidulans (FGSC A4) | |
| Aspartate | Nikko Torres | Natalia Thawe | Marja Cemma | Isuru Wijesoma | Philip | Candida albicans (SC5314) | |
| Glutamate | Joyce Lam | Leo Wan | Ying Zhu | Alice Thach | Philip | Candida glabrata (CBS138) | |
| Phenylalanine | Bell Ho | Kris Hon | Jason Yau | Vincent Leung | Philip | Coprinopsis cinerea (okayama 7#130) | |
| Glycine | Fan Zhang | Fang Cai | Greg Clark | Alexandr Bezginov | Ryder | Cryptococcus neoformans (var. neoformans JEC21) | |
| Histidine | Yi-an Chen | Rachel Ford | Kiera Clayton | Hang Shi | Ryder | Debaryomyces hansenii (CBS 767) | |
| Isoleucine | Eric Wong | Louis Barbier | Youssef Youssef | Da Yu | Ryder | Giberella zeae (PH-1) | |
| Lysine | Wasan Abada | Madhavi Patel | Jing Huang | Shafa Chaudry | Ryder | Kluyveromyces lactis (NRRL Y-1140) | |
| Leucine | Wei Tang | Rui Chen | YinYing Zhang | Miao Yu | Yaqi | Magnaporthe grisea (70-15) | |
| Methionine | Neurospora crassa (OR74-A) | ||||||
| Asparagine | Devin Trudeau | Julia Li | Jiayi Hu | Alex Ling | Yaqi | Pichia stipitis (CBS 6054) | |
| Proline | Jestyn Liew | Curtis Foong | Maryam Foumani | Jennifer D'Cruz | Yaqi | Schizosaccharomyces pombe (972h-) | |
| Glutamine | Anand Iyer | Kevin Lau | Cecilia Chan | Dilpreet Dhesi | Yaqi | Ustilago maydis (521) | |
| Arginine | Cheng Yu | Risa Yuk Low | Lakshmi Sugavaneswaran | Linda Zhao | Zhongyuan Zhang | Boris | Yarrowia lipolytica (CLIB122) |
| Serine | |||||||
| Threonine | |||||||
| Valine | |||||||
| Tryptophan | |||||||
| Tyrosine | |||||||
