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= LSM2241 Introductory Bioinformatics =
= LSM2241 Introductory Bioinformatics =
== MCQ Revision Questions ==
* [[L1P1]]
== LSM2241 CA1 ==


This Wiki page serves as a platform for students to present their perspective of the practical assessment (CA1) assigned to them.
This Wiki page serves as a platform for students to present their perspective of the practical assessment (CA1) assigned to them.
Line 5: Line 11:


== Presentation Guidelines ==
== Presentation Guidelines ==
For LSM2241 CA1, each group is required to present on the <b>real-life research applications of a given bioinformatics method/technique/tool</b> taught in the practical assigned to you. Each group is also required to create a <b>wiki page</b> on the presentation topic. The presentation and wiki page is worth 10% of the LSM2241 module grade <br>
For LSM2241 CA1, each group is required to present on the <b>real-life research applications of a given bioinformatics method/technique/tool</b> taught in the practical assigned to you. The presentation should be no longer than <b>30 minutes</b> including Q&A.
<br>
 
Each group is also required to create a <b>wiki page</b> on the presentation topic. The presentation and wiki page is worth 10% of the LSM2241 module grade <br>


=== Presentation scope ===
=== Presentation scope ===
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* Illustrate with examples from journal articles
* Illustrate with examples from journal articles
* Conclusion
* Conclusion
<br>


=== Checklist before CA1 presentation ===  
=== Checklist before CA1 presentation ===  
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* Uploaded your presentation slides and materials to the IVLE CA1 submission workbin
* Uploaded your presentation slides and materials to the IVLE CA1 submission workbin
* Completed your wiki page
* Completed your wiki page
<br>


=== Grading Criteria (class presentation) ===
=== Grading Criteria (class presentation) ===
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To learn more about the Wiki syntax, click on the link below
To learn more about the Wiki syntax, click on the link below
*[http://code.google.com/p/support/wiki/WikiSyntax Wiki Syntax]
*[http://code.google.com/p/support/wiki/WikiSyntax Wiki Syntax]
<br>


=== Marking Criteria (wiki page) ===
=== Grading Criteria (wiki page) ===


Students are to take note of the following criteria when preparing for the Wiki page:
Students are to take note of the following criteria when preparing for the Wiki page:
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* Critical assessment of the literature (include you own point of view of others work)
* Critical assessment of the literature (include you own point of view of others work)
* Reference adequately
* Reference adequately
<br>


== Peer Review Guidelines ==
== Peer Review Guidelines ==


After your group presentation, please complete the <b>peer review</p> for your groupmates. To do so, login to IVLE and go to "Project". Select your CA1 project group (by clicking on the goggles icon beside your group name) and click on "Project Evaluation".
After your group presentation, please complete the <b>peer review</b> for your groupmates. To do so, login to IVLE and go to "Project". Select your CA1 project group (by clicking on the goggles icon beside your group name) and click on "Project Evaluation".


The peer review is worth 5% of the LSM2241 module grade. Please complete the peer review within the <b>same week</b> of your group presentation
The peer review is worth 5% of the LSM2241 module grade. Please complete the peer review within the <b>same week</b> of your group presentation
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=== Group - Topic Title - Status ===
=== Group - Topic Title - Status ===


To be assigned
* [[LSM2241/AY1011S2A7 | A7]] - Exploring basic bioinformatics resources 
* [[LSM2241/AY1011S2B7 | B7]] - Exploring basic bioinformatics resources
* [[LSM2241/AY1011S2A3 | A3]] - Exploring bioinformatics software, tools and techniques
<br>
 
* [[LSM2241/AY1011S2A6 | A6]] - Visualizing sequence comparisons
* [[LSM2241/AY1011S2B2 | B2]] - Visualizing sequence comparisons
<br>
* [[LSM2241/AY1011S2A5 | A5]] - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences
* [[LSM2241/AY1011S2B3 | B3]] - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences
<br>
* [[LSM2241/AY1011S2A2 | A2]] - Hunting for biological patterns and profiles
* [[LSM2241/AY1011S2B8 | B8]] - Hunting for biological patterns and profiles
<br>
* [[LSM2241/AY1011S2A1 | A1]] - Viewing and annotating 3D structures from PDB
* [[LSM2241/AY1011S2B4 | B4]] - Viewing and annotating 3D structures from PDB
<br>
* [[LSM2241/AY1011S2A4 | A4]] - Homology modelling
<br>


<font color="red">Note: students should aim to achieve the standard set by previous LSM2241 students (see hyperlink below for examples)</font>
<font color="red">Note: students should aim to achieve the standard set by previous LSM2241 students (see hyperlink below for examples)</font>


<br>
<br>


=AY1011 Sem I=
=AY1011 Sem I=
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* [[LSM3241 | LSM3241]] - Bioinformatics and Biocomputing
* [[LSM3241 | LSM3241]] - Bioinformatics and Biocomputing
* [[LSM2104 | LSM2104]] - Essential Bioinformatics and Biocomputing (AY06-AY08; AY09 onwards replaced by LSM2241)
* [[LSM2104 | LSM2104]] - Essential Bioinformatics and Biocomputing (AY06-AY08; AY09 onwards replaced by LSM2241)
[[Category:Modules]]

Latest revision as of 18:52, 17 August 2012

LSM2241 Introductory Bioinformatics

MCQ Revision Questions

LSM2241 CA1

This Wiki page serves as a platform for students to present their perspective of the practical assessment (CA1) assigned to them. The weightage of CA1 is 15% (10% class presentation & Wiki page + 5% peer review).

Presentation Guidelines

For LSM2241 CA1, each group is required to present on the real-life research applications of a given bioinformatics method/technique/tool taught in the practical assigned to you. The presentation should be no longer than 30 minutes including Q&A.

Each group is also required to create a wiki page on the presentation topic. The presentation and wiki page is worth 10% of the LSM2241 module grade

Presentation scope

  • (Brief) introduction to the bioinformatics method/technique/tool
  • Describe how can the bioinformatics method/technique/tool be applied to life science research
  • Illustrate with examples from journal articles
  • Conclusion

Checklist before CA1 presentation

Before your presentation, please make sure that you have:

  • Uploaded your presentation slides and materials to the IVLE CA1 submission workbin
  • Completed your wiki page

Grading Criteria (class presentation)

For class presentations, the grading criteria include:

  • Content of the material presented
  • Presentation skills
  • Flow of the presentation
  • Clarity
  • Is there a focus
  • Does the presenter include her own point of view
  • Adequate Referencing
  • Engagement of the audience
  • Handling of questions by the audience
  • Time management

Wiki Guidelines

A wiki account is needed for each group to create and author their wiki page. Prior to their presentation slot, each group is to approach the TA in charge to obtain their group wiki username and password. Links to the wiki page for each group are displayed below.

To edit your group's wiki page, please login to the wiki site. Go to your group's page, and click on the "edit" tab at the top of the page.

Wiki How To

To learn more about the Wiki syntax, click on the link below

Grading Criteria (wiki page)

Students are to take note of the following criteria when preparing for the Wiki page:

  • Focus on the topic/theme
  • Flow of the presentation
  • Clarity
  • Critical assessment of the literature (include you own point of view of others work)
  • Reference adequately

Peer Review Guidelines

After your group presentation, please complete the peer review for your groupmates. To do so, login to IVLE and go to "Project". Select your CA1 project group (by clicking on the goggles icon beside your group name) and click on "Project Evaluation".

The peer review is worth 5% of the LSM2241 module grade. Please complete the peer review within the same week of your group presentation

AY1011 Sem 2

Group - Topic Title - Status

  • A7 - Exploring basic bioinformatics resources
  • B7 - Exploring basic bioinformatics resources
  • A3 - Exploring bioinformatics software, tools and techniques


  • A6 - Visualizing sequence comparisons
  • B2 - Visualizing sequence comparisons


  • A5 - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences
  • B3 - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences


  • A2 - Hunting for biological patterns and profiles
  • B8 - Hunting for biological patterns and profiles


  • A1 - Viewing and annotating 3D structures from PDB
  • B4 - Viewing and annotating 3D structures from PDB


  • A4 - Homology modelling


Note: students should aim to achieve the standard set by previous LSM2241 students (see hyperlink below for examples)


AY1011 Sem I

Group - Topic Title - Status

  • A3 - Exploring basic bioinformatics resources


  • A? - Visualizing sequence comparisons
  • B2 - Visualizing sequence comparisons


  • A1 - Hunting for biological patterns and profiles
  • B3 - Hunting for biological patterns and profiles


  • A5 - Exploring bioinformatics databases, tools and techniques
  • B1 - Exploring bioinformatics databases, tools and techniques


  • A6 - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences
  • B6 - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences


  • A4 - Analysing mass spectrometry data
  • B5 - Analysing mass spectrometry data
  • B9 - Analysing mass spectrometry data


  • A8 - MSA and phylogenetic analysis
  • B7 - MSA and phylogenetic analysis


  • A7 - Viewing and annotating 3D structures from PDB
  • B4 - Viewing and annotating 3D structures from PDB


  • A2 - Homology modelling
  • B8 - Homology modelling


AY0910 Sem II

Group - Topic Title - Status

  • A8 - Exploring basic bioinformatics resources - DONE
  • B8 - Exploring basic bioinformatics resources - DONE


  • A1 - Exploring bioinformatics tools and techniques - DONE
  • B9 - Exploring bioinformatics tools and techniques - DONE


  • A7 - Visualizing sequence comparisons - DONE
  • B1 - Visualizing sequence comparisons - DONE
  • B10 - Visualizing sequence comparisons - DONE


  • A3 - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences - DONE
  • B2 - BLAST: Searching for unknown sequences using known ones; Building a BLAST-searchable database from sequences - DONE


  • A9 - Hunting for biological patterns and profiles - DONE
  • B3 - Hunting for biological patterns and profiles - DONE


  • A5 - Viewing and annotating 3D structures from PDB & Homology modelling) - DONE
  • B4 - Viewing and annotating 3D structures from PDB & Homology modelling) - DONE
  • B6 - Viewing and annotating 3D structures from PDB & Homology modelling) - DONE


  • B5 - MSA and phylogenetic analysis I & II - DONE
  • B7 - MSA and phylogenetic analysis I & II - DONE


  • B11 - Analysing mass spectrometry data I & II - DONE


AY0910 Sem I

Group - Topic Title - Status

  • A3 - Exploring basic bioinformatics resources - DONE
  • B1 - Exploring basic bioinformatics resources - DONE


  • A7 - Exploring bioinformatics tools and techniques - DONE
  • B3 - Exploring bioinformatics tools and techniques - DONE


  • A6 - Visualizing sequence comparisons - DONE
  • B8 - Visualizing sequence comparisons - DONE


  • A4 - BLAST: Searching for unknown sequences using known ones - DONE
  • B5 - BLAST: Searching for unknown sequences using known ones - DONE
  • A9 - BLAST: Searching for unknown sequences using known ones - DONE


  • A8 - Hunting for biological patterns - DONE
  • B4 - Hunting for biological patterns - DONE


  • B2 - MSA and phylogenetic analysis - DONE
  • A2 - MSA and phylogenetic analysis - DONE


  • A1 - Analysing mass spectrometry data - DONE
  • B6 - Analysing mass spectrometry data - DONE


  • A5 - Viewing and annotating 3D structures - DONE
  • B7 - Viewing and annotating 3D structures - DONE


Note: students should aim to achieve the standard set by previous LSM2104 students (see hyperlink below for examples)

Related Links

  • LSM3241 - Bioinformatics and Biocomputing
  • LSM2104 - Essential Bioinformatics and Biocomputing (AY06-AY08; AY09 onwards replaced by LSM2241)
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