Difference between revisions of "Group project"

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You will be assigned to groups of four students. Each student will take on one workflow to annotate.
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<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
 +
The Group Mini-Project
 +
</div>
  
As a group, you will jointly define and structure the workflow.
+
&nbsp;
 +
&nbsp;
  
Individually, you will annotate some of the data items or procedures of the workflow.
+
You have been assigned to groups of three or four students.  
  
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.  
  
  
 +
<!-- For a limited time-period ...
  
;Details to be posted here.
+
* 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.
 +
 
 +
Please be fair to your group members and alert me immediately in case you plan to drop the course.-->
 +
 
 +
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>
  
  
 
==Groups==
 
==Groups==
  
;Note this is a preliminary assignment into groups and still subject to change.
 
  
 
<table>
 
<table>
Line 24: Line 63:
 
<td>'''Name'''</td>
 
<td>'''Name'''</td>
 
<td>'''Name'''</td>
 
<td>'''Name'''</td>
 +
<td>'''Name'''</td>
 +
<td>'''Topic'''</td>
 +
<td>'''TA'''</td>
 +
<td>'''Species'''</td>
 
</tr>
 
</tr>
  
Line 30: Line 73:
 
<tr class="s0">
 
<tr class="s0">
 
<td>'''Alanine'''</td>
 
<td>'''Alanine'''</td>
 +
<td>Maria Soloveychik</td>
 +
<td>Alison Muir</td>
 +
<td>Zarnaben Shah</td>
 +
<td>Herman Badwal</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>&nbsp;</td>
+
<td>Identify whether a human gene of interest may be involved in a disease</td>
<td>&nbsp;</td>
+
<td>Yaqi</td>
<td>&nbsp;</td>
+
<td>''Aspergillus fumigatus'' (Af293)</td>
 
</tr>
 
</tr>
  
 
<tr class="s1">
 
<tr class="s1">
 
<td>'''Cysteine'''</td>
 
<td>'''Cysteine'''</td>
<td>&nbsp;</td>
+
<td>Yuan Yao</td>
<td>&nbsp;</td>
+
<td>Adam Santoro</td>
<td>&nbsp;</td>
+
<td>Yuanfan Yang</td>
<td>&nbsp;</td>
+
<td>Marco Fiume</td>
 +
<td>Edwin Yip</td>
 +
<td>Use protein structural alignments for phylogenetic analysis</td>
 +
<td>Boris</td>
 +
<td>''Aspergillus nidulans'' (FGSC A4)</td>
 
</tr>
 
</tr>
  
Line 50: Line 101:
 
<td>Marja Cemma</td>
 
<td>Marja Cemma</td>
 
<td>Isuru Wijesoma</td>
 
<td>Isuru Wijesoma</td>
 +
<td>&nbsp;</td>
 +
<td>Protein structure prediction</td>
 +
<td>Philip</td>
 +
<td>''Candida albicans'' (SC5314)</td>
 
</tr>
 
</tr>
  
Line 57: Line 112:
 
<td>Leo Wan</td>
 
<td>Leo Wan</td>
 
<td>Ying Zhu</td>
 
<td>Ying Zhu</td>
 +
<td>Alice Thach</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Identify whether a human gene of interest may be involved in a disease</td>
 +
<td>Yaqi</td>
 +
<td>''Candida glabrata'' (CBS138)</td>
 
</tr>
 
</tr>
  
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<td>'''Phenylalanine'''</td>
 
<td>'''Phenylalanine'''</td>
 
<td>Bell Ho</td>
 
<td>Bell Ho</td>
<td>Theodore Pham</td>
+
<td>Kris Hon</td>
 
<td>Jason Yau</td>
 
<td>Jason Yau</td>
 
<td>Vincent Leung</td>
 
<td>Vincent Leung</td>
 +
<td>&nbsp;</td>
 +
<td>Distinguish between structural and functional conservation</td>
 +
<td>Philip</td>
 +
<td>''Coprinopsis cinerea'' (okayama 7#130)</td>
 
</tr>
 
</tr>
  
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<td>Fan Zhang</td>
 
<td>Fan Zhang</td>
 
<td>Fang Cai</td>
 
<td>Fang Cai</td>
<td>Alison Mair</td>
+
<td>Greg Clark</td>
<td>Tim Tang</td>
+
<td>Alexandr Bezginov</td>
 +
<td>&nbsp;</td>
 +
<td>Predict protein/protein interactions for a gene of interest</td>
 +
<td>Ryder</td>
 +
<td>''Cryptococcus neoformans'' (var. neoformans JEC21)</td>
 
</tr>
 
</tr>
  
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<td>Rachel Ford</td>
 
<td>Rachel Ford</td>
 
<td>Kiera Clayton</td>
 
<td>Kiera Clayton</td>
 +
<td>Hang Shi</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Predict protein/protein interactions for a gene of interest</td>
 +
<td>Philip</td>
 +
<td>''Debaryomyces hansenii'' (CBS 767)</td>
 
</tr>
 
</tr>
  
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<td>Louis Barbier</td>
 
<td>Louis Barbier</td>
 
<td>Youssef Youssef</td>
 
<td>Youssef Youssef</td>
 +
<td>Da Yu</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Distinguish between structural and functional conservation</td>
 +
<td>Yaqi</td>
 +
<td>''Giberella zeae'' (PH-1)</td>
 
</tr>
 
</tr>
  
Line 95: Line 170:
 
<td>'''Lysine'''</td>
 
<td>'''Lysine'''</td>
 
<td>Wasan Abada</td>
 
<td>Wasan Abada</td>
<td>Senjuti Saha</td>
 
 
<td>Madhavi Patel</td>
 
<td>Madhavi Patel</td>
 
<td>Jing Huang</td>
 
<td>Jing Huang</td>
 +
<td>Shafa Chaudry</td>
 +
<td>&nbsp;</td>
 +
<td>Predict membrane topology</td>
 +
<td>Ryder</td>
 +
<td>''Kluyveromyces lactis'' (NRRL Y-1140)</td>
 
</tr>
 
</tr>
  
Line 105: Line 184:
 
<td>Rui Chen</td>
 
<td>Rui Chen</td>
 
<td>YinYing Zhang</td>
 
<td>YinYing Zhang</td>
 +
<td>Miao Yu</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Predict membrane topology</td>
 +
<td>Ryder</td>
 +
<td>''Magnaporthe grisea'' (70-15)</td>
 
</tr>
 
</tr>
  
 
<tr class="s0">
 
<tr class="s0">
 
<td>'''Methionine'''</td>
 
<td>'''Methionine'''</td>
<td>Zhungyuan Zhang</td>
+
<td>&nbsp;</td>
<td>Edwin Yip</td>
+
<td>&nbsp;</td>
<td></td>
+
<td>&nbsp;</td>
<td></td>
+
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>''Neurospora crassa'' (OR74-A)</td>
 
</tr>
 
</tr>
  
Line 122: Line 209:
 
<td>Jiayi Hu</td>
 
<td>Jiayi Hu</td>
 
<td>Alex Ling</td>
 
<td>Alex Ling</td>
 +
<td>&nbsp;</td>
 +
<td>Identify whether a gene of interest has been under recent positive selection</td>
 +
<td>Yaqi</td>
 +
<td>''Pichia stipitis'' (CBS 6054)</td>
 
</tr>
 
</tr>
  
Line 128: Line 219:
 
<td>Jestyn Liew</td>
 
<td>Jestyn Liew</td>
 
<td>Curtis Foong</td>
 
<td>Curtis Foong</td>
 +
<td>Maryam Foumani</td>
 +
<td>Jennifer D'Cruz</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>&nbsp;</td>
+
<td>Distinguish between structural and functional conservation</td>
 +
<td>Philip</td>
 +
<td>''Schizosaccharomyces pombe'' (972h-)</td>
 
</tr>
 
</tr>
  
Line 138: Line 233:
 
<td>Cecilia Chan</td>
 
<td>Cecilia Chan</td>
 
<td>Dilpreet Dhesi</td>
 
<td>Dilpreet Dhesi</td>
 +
<td>&nbsp;</td>
 +
<td>Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein</td>
 +
<td>Ryder</td>
 +
<td>''Ustilago maydis'' (521)</td>
 
</tr>
 
</tr>
  
 
<tr class="s0">
 
<tr class="s0">
 
<td>'''Arginine'''</td>
 
<td>'''Arginine'''</td>
<td>&nbsp;</td>
+
<td>Cheng Yu</td>
<td>&nbsp;</td>
+
<td>Risa Yuk Low</td>
<td>&nbsp;</td>
+
<td>Lakshmi Sugavaneswaran</td>
<td>&nbsp;</td>
+
<td>Linda Zhao</td>
 +
<td>Zhongyuan Zhang</td>
 +
<td>Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein</td>
 +
<td>Boris</td>
 +
<td>''Yarrowia lipolytica'' (CLIB122)</td>
 
</tr>
 
</tr>
  
Line 154: Line 257:
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>''&nbsp;''</td>
 
</tr>
 
</tr>
  
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<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>''&nbsp;''</td>
 
</tr>
 
</tr>
  
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<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>''&nbsp;''</td>
 
</tr>
 
</tr>
  
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<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>''&nbsp;''</td>
 
</tr>
 
</tr>
  
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<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>&nbsp;</td>
 +
<td>''&nbsp;''</td>
 
</tr>
 
</tr>
  
 
</table>
 
</table>

Latest revision as of 19:32, 20 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:

  1. A number of topics from the general area of functional annotation are listed in the table below.
  2. 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.
  3. 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.
  4. Plan your time to be able to communicate about the project within the group, go through some improvements, and finish by the due date.
  5. 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.
  6. Once the improvements are done, the following milestones should be achieved:
    1. Task is broken down into a number of procedures
    2. Each procedure has clearly defined input data, an algorithm operating on that data, and output data
    3. There is a designated group member for each procedure
    4. The entire process has been summarized in approximately one page, jointly written.
  7. 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.
  8. 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 Topic TA Species
Alanine Maria Soloveychik Alison Muir Zarnaben Shah Herman Badwal   Identify whether a human gene of interest may be involved in a disease Yaqi Aspergillus fumigatus (Af293)
Cysteine Yuan Yao Adam Santoro Yuanfan Yang Marco Fiume Edwin Yip Use protein structural alignments for phylogenetic analysis Boris Aspergillus nidulans (FGSC A4)
Aspartate Nikko Torres Natalia Thawe Marja Cemma Isuru Wijesoma   Protein structure prediction Philip Candida albicans (SC5314)
Glutamate Joyce Lam Leo Wan Ying Zhu Alice Thach   Identify whether a human gene of interest may be involved in a disease Yaqi Candida glabrata (CBS138)
Phenylalanine Bell Ho Kris Hon Jason Yau Vincent Leung   Distinguish between structural and functional conservation Philip Coprinopsis cinerea (okayama 7#130)
Glycine Fan Zhang Fang Cai Greg Clark Alexandr Bezginov   Predict protein/protein interactions for a gene of interest Ryder Cryptococcus neoformans (var. neoformans JEC21)
Histidine Yi-an Chen Rachel Ford Kiera Clayton Hang Shi   Predict protein/protein interactions for a gene of interest Philip Debaryomyces hansenii (CBS 767)
Isoleucine Eric Wong Louis Barbier Youssef Youssef Da Yu   Distinguish between structural and functional conservation Yaqi Giberella zeae (PH-1)
Lysine Wasan Abada Madhavi Patel Jing Huang Shafa Chaudry   Predict membrane topology Ryder Kluyveromyces lactis (NRRL Y-1140)
Leucine Wei Tang Rui Chen YinYing Zhang Miao Yu   Predict membrane topology Ryder Magnaporthe grisea (70-15)
Methionine               Neurospora crassa (OR74-A)
Asparagine Devin Trudeau Julia Li Jiayi Hu Alex Ling   Identify whether a gene of interest has been under recent positive selection Yaqi Pichia stipitis (CBS 6054)
Proline Jestyn Liew Curtis Foong Maryam Foumani Jennifer D'Cruz   Distinguish between structural and functional conservation Philip Schizosaccharomyces pombe (972h-)
Glutamine Anand Iyer Kevin Lau Cecilia Chan Dilpreet Dhesi   Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein Ryder Ustilago maydis (521)
Arginine Cheng Yu Risa Yuk Low Lakshmi Sugavaneswaran Linda Zhao Zhongyuan Zhang Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein Boris Yarrowia lipolytica (CLIB122)
Serine                
Threonine                
Valine                
Tryptophan                
Tyrosine