Difference between revisions of "ABC-INT-Genome annotation"

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=== Evaluation ===
 
=== Evaluation ===
 
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<!-- included from "../components/ABC-INT-Genome_annotation.components.wtxt", section: "evaluation" -->
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<!-- included from "ABC-unit_components.wtxt", section: "eval-INT-TBD" -->
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This "Integrator Unit" should be submitted for evaluation for a maximum of 8 marks if one of the written deliverables is chosen, resp. 16 marks for the oral exam<ref>Note: the oral exam will focus on the unit content but will also cover other material that leads up to it.</ref>.
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<b>Evaluation: Integrated Unit</b><br />
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:Please note the evaluation types that are available as options for this unit. Choose one evaluation type that you have not chosen for another Integrator Unit. (Each submitted Integrator Unit must be evaluated in a different way and one of your evaluations - but not your first one - must be an oral exam).
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:This unit should be submitted for evaluation for a maximum of 10 marks. Details TBD.
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{{Smallvspace}}
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<!--
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;Report option
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* Work through the tasks described in the scenario.
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* Document your results in a short report on a subpage of your User page on the Student Wiki. Describe your methods (R-code!) in an appendix;
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* When you are done with everything, add the following category tag to the page:
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::<code><nowiki>[[Category:EVAL-INT-Phylogeny]]</nowiki></code>
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:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
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{{Smallvspace}}
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-->
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;Interview option
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: Identify a laboratory whose work includes genome annotation, or re-annotation. Get in touch with the PI, a postdoc or senior graduate student in the laboratory and interview them in person or by eMail. Find out
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:* why this work is important;
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:* how they approach it methodologically;
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:* in particular, what features they are looking for, and what discoveries can be made by looking for these features (get very specific on that point, we are most interested in strategies for '''interpretation''' of data);
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:* what they have recently learned;
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:* what the major challenges, current discussions, or controversies are.
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:* write up your interview on a subpage of your User page of the Student Wiki;
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:* add information that may be required to understand the methodology;
 +
:* make sure that you have included important literature references.
 +
:* When you are done with everything, add the following category tag to the page:
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::<code><nowiki>[[Category:EVAL-INT-Genome_annotation]]</nowiki></code>
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:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
 +
{{Smallvspace}}
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<!--
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;Literature research option
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:Navigate to the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/ABC-INT-Phylogeny_topics '''Phylogeny Literature Research Topics] page on the Student Wiki.
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:* Pick a topic and enter your name in the table to claim it.
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:* Write a report on your research. Note: this is not a review, but a report. Think of a "whitepaper", not a publication. Write to a specialist technical audience and be specific to provide actionable information.
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:* write your report on a subpage of your User page of the Student Wiki;
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:* make sure that you have included all references and citations.
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:* When you are done with everything, add the following category tag to the page:
 +
::<code><nowiki>[[Category:EVAL-INT-Phylogeny]]</nowiki></code>
 +
:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
 +
{{Smallvspace}}
 +
-->
 +
<!--
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;Oral exam option
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* Work through the tasks described in the scenario. Remember to document your work in your journal.
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* Part of your task will involve writing an R script, place that code in a subpage of your User page on the Student Wiki and link to it from your Journal. (Do not add an evaluation category tag to that code).
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* Your work must be complete before 21:00 on the day of your exam.
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* Schedule an oral exam by editing the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/Signup-Oral_exams_2017 '''signup page on the Student Wiki''']. Enter the unit that you are signing up for, and your name. You must have signed-up for an exam slot before 21:00 on the day before your exam.
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{{Smallvspace}}
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-->
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<!--
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;R code option
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* Work through the tasks described in the scenario and develop code as required.
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* Put your code on a subpage of your User page on the Student Wiki;
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* When you are done with everything, add the following category tag to the page:
 +
::<code><nowiki>[[Category:EVAL-INT-Phylogeny]]</nowiki></code>
 +
:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
 +
-->
  
 
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Revision as of 21:49, 19 November 2017

Integration Unit: Genome annotation


 

Keywords:  Integrator unit: annotate sequences in a genome


 



 


Sorry!

This page is only a stub; it is here as a placeholder to establish the logical framework of the site but there is no significant content as yet. Do not work with this material until it is updated to "live" status.


 


Abstract

This page assesses the learning units for data management and sequence analysis of genomic sequence data.

  • choose a fungal genome
  • create a datamodel for domain annotations
  • implement as a dataframe
  • annotate signal sequence (or disordered stretches)
  • plot and analyze results


 


This unit ...

Prerequisites

You need to complete the following units before beginning this one:


 


Objectives

...


 


Outcomes

...


 


Deliverables

  • No separate deliverables: This unit collects other units and has no deliverables on its own.


 


Evaluation

This "Integrator Unit" should be submitted for evaluation for a maximum of 8 marks if one of the written deliverables is chosen, resp. 16 marks for the oral exam[1].

Please note the evaluation types that are available as options for this unit. Choose one evaluation type that you have not chosen for another Integrator Unit. (Each submitted Integrator Unit must be evaluated in a different way and one of your evaluations - but not your first one - must be an oral exam).
 
Interview option
Identify a laboratory whose work includes genome annotation, or re-annotation. Get in touch with the PI, a postdoc or senior graduate student in the laboratory and interview them in person or by eMail. Find out
  • why this work is important;
  • how they approach it methodologically;
  • in particular, what features they are looking for, and what discoveries can be made by looking for these features (get very specific on that point, we are most interested in strategies for interpretation of data);
  • what they have recently learned;
  • what the major challenges, current discussions, or controversies are.
  • write up your interview on a subpage of your User page of the Student Wiki;
  • add information that may be required to understand the methodology;
  • make sure that you have included important literature references.
  • When you are done with everything, add the following category tag to the page:
[[Category:EVAL-INT-Genome_annotation]]
Do not change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
 


 


Contents

This is a "milestone unit". Its purpose is merely to collect a number of preparatory units into a single, common prerequisite. It has no contents of its own; you are expected to be familiar and competent with all preparatory material at this point.


 


Further reading, links and resources

 


Notes

  1. ↑ Note: the oral exam will focus on the unit content but will also cover other material that leads up to it.


 


Self-evaluation

 



 



 

If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.


 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-09

Version:

0.1

Version history:

  • 0.1 First stub

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