Difference between revisions of "BCB410"

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#REDIRECT [[BCB410 2015]]
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<div id="APB">
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<div class="b1">
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BCB410H1F - 2017
 +
</div>
 +
 
 +
 
 +
 
 +
 
 +
__TOC__
 +
 
 +
==Objectives and Participants==
 +
 
 +
 
 +
The "Applied Bioinformatics" course is offered as a part of the BCB Program curriculum to ensure that our students know enough about application issues in the field to be able to put their knowledge into practice in a research lab setting. This is to support the Specialist Program goal: to prepare students for graduate studies in the discipline.
 +
 
 +
As a required course in the BCB curriculum, BCB410 assumes the prerequisites and goals of fourth-year students in the BCB Specialist Program. Other students may be permitted to enrol on a case by case basis, but they may need to catch up on prerequisites in computer science or life-science courses that BCB students have taken at this point. Generally speaking, this is an advanced course that presupposes familiarity with programming principles, algorithm analysis, and methods of modern systems biology, as well as introductory knowledge of linear algebra, graph theory, information theory, statistics, as well as molecular&ndash;, structural&ndash; and cellular biology. The varying topics will be discussed at a '''highly technical level''' that is likely only useful for students who plan to integrate much of this material into their actual practice.
 +
 
 +
{{Vspace}}
 +
 
 +
==Organization==
 +
 
 +
<div class="alert">
 +
Details for the 2017 course are not yet available and will be discussed in our first class session, Wednesday, September 13, at 10:00 in Bahen BA025.
 +
 
 +
It is imperative that you attend the first class session in person. Do not enrol in this course if you can't attend the first class session.
 +
</div>
 +
 
 +
{{Vspace}}
 +
 
 +
=== Dates and Location ===
 +
 
 +
Classes meet Wednesdays between 10:00 and 12:00 in [http://map.utoronto.ca/utsg/building/080 BA025 (Bahen Centre)] throughout the Fall Term. Classes start at 10 minutes past the hour.
 +
 
 +
{{Vspace}}
 +
 
 +
{{#lst:User:Boris|Coordinator}}
 +
{{#lst:User:Boris|Office_hours}}
 +
 
 +
=== Contact ===
 +
 
 +
Contact within the class is easiest via the [https://groups.google.com/forum/#!forum/bcb410_2017 '''Google Group'''] that you will subscribe to at the beginning of class.
 +
 
 +
{{Vspace}}
 +
 
 +
 
 +
<!--
 +
=== Marking ===
 +
 
 +
&nbsp;
 +
 
 +
<table>
 +
 
 +
<tr class="sh">
 +
<td><b>Activity</b></td>
 +
<td><b>Weight</b></td>
 +
</tr>
 +
 
 +
<tr><td colspan="3" class="sp"></td></tr>
 +
 
 +
<tr class="s1">
 +
<td>Design and coordination of your unit</td>
 +
<td>20 marks</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td>Delivery and contents of presentation</td>
 +
<td>15 marks</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td>Quality of exercises/assignments</td>
 +
<td>30 marks</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td>Participation<ref>Regular attendance; active and constructive contribution to discussions that shows you have done the pre-reading; contributions to the course mailing-list; helpful feedback on the exercises.</ref></td>
 +
<td>15 marks</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td>Final exam</td>
 +
<td>20 marks</td>
 +
</tr>
 +
 
 +
<tr><td colspan="3" class="sp"></td></tr>
 +
 
 +
<tr class="s2">
 +
<td>'''Total'''</td>
 +
<td>100 marks</td>
 +
</tr>
 +
</table>
 +
 
 +
{{Vspace}}
 +
 
 +
What makes an ''excellent'' grade? [[Grading|'''See here.''']]
 +
 
 +
{{Vspace}}
 +
-->
 +
 
 +
<!--
 +
== Contents ==
 +
 
 +
{{Vspace}}
 +
 
 +
-->
 +
 
 +
<!--
 +
===A syllabus of learning units===
 +
 
 +
Working from a general collection of topics in the field, we identify learning units that are of the greatest interest and greatest relevance for the students in the class. We jointly select the most suitable topics. '''Every student in class will take responsibility for development and delivery of one of the learning units.'''
 +
 
 +
{{Vspace}}
 +
 
 +
-->
 +
 
 +
<!--
 +
===Unit contents and delivery===
 +
 
 +
The detailed contents for each unit is to be be discussed with the coordinator. Each student will to lead a one-hour session on their topic.
 +
 
 +
'''Presenter's responsibilities''' include<ref>Details may vary as required, by mutual agreement.</ref>:
 +
* Write an outline of your unit contents, and e-mail it to me at least '''two weeks in advance'''; This needs to include:
 +
** a detailed lecture outline that includes an introduction, discussion of algorithms, presentation of examples, exposition of practical- and implementation issues and an outlook on future developments in the field;
 +
** suitable pre-reading material;
 +
** an outline of practical and relevant class-exercises;
 +
* Iterate this contents with me, to be completed at least '''ten days in advance'''.
 +
* Develop a set of exercises at least '''one week in advance'''. The exercises must be posted on the Student Wiki, [https://creativecommons.org/licenses/by/4.0/ '''CC-By'''] licensed for future classes, and work for Mac OS X, Windows and Linux platforms. Include a section for feedback as the last item of your page;
 +
* Communicate pre-reading materials to your classmates, at least '''on the Friday before your presentation''';
 +
* Deliver your lecture at a sufficiently technical level to be appropriate for an advanced fourth-year course and engaging the class in discussion. Don't go over time. You must make sure '''ahead of your presentation''' that you can connect your computer to the projector, that your wireless network connection works, and that you have all required assets and resources installed on your computer;
 +
* Post your exercise materials to the Student Wiki and announce this to the class on the same day as the lecture;
 +
* Draft a final-exam question that tests the successful completion of the exercises, at the latest '''one week after the lecture''' and send it to me.
 +
 
 +
 
 +
Note that your marks will suffer if your items are late.
 +
 
 +
 
 +
'''Audience responsibilities''' include:
 +
* Pre-reading before class;
 +
* Active participation in the discussion;
 +
* Brief, written feedback on the exercises in the Student Wiki within two weeks of the lecture.
 +
 
 +
{{Vspace}}
 +
 
 +
-->
 +
 
 +
<!--
 +
===First Class===
 +
{{Vspace}}
 +
 
 +
# Overview of how this course will work.
 +
# Overview of presenter and audience responsibilities and marking scheme.
 +
# Define a first list of topics.
 +
# Assign topics and dates.
 +
# Subscribe everyone to [https://groups.google.com/forum/#!forum/bcb410_2016 the mailing list].
 +
# Create a [http://steipe.biochemistry.utoronto.ca/abc/students Student Wiki] account for everyone.
 +
 
 +
{{Vspace}}
 +
 
 +
-->
 +
 
 +
<!--
 +
===A selection of topics for consideration===
 +
 
 +
{{Vspace}}
 +
 
 +
;Confirmed
 +
 
 +
* Naina: ''de novo'' assembly from HTS data
 +
* Fupan: Bioinformatics in the '''Cloud''': use cases, platforms (AWS?, Azure?), code deployment (Docker?), example, practice - with an emphasis on CUDA
 +
* Lindsay: Comparison of Variant Callers with an emphasis on detecting antibiotic resistance
 +
* Won June: Adam
 +
* James: Deep learning with CUDA architectures
 +
* Charles: [https://www.rosettacommons.org/ '''Rosetta'''] protein structure prediction and/or design
 +
* Moeen: TF binding site discovery: [http://opossum.cisreg.ca/oPOSSUM3/ '''oPOSSUM-3''']
 +
* Allana: Current Cheminformatics: [http://www.eyesopen.com/ '''OpenEye'''] and other tools. Use cases. Workflows...
 +
* Tom: [http://robpatro.com/blog/?p=260 RapMap] from reads to transcriptome mapping
 +
* Chloe: ''Big Data'' in bioinformatics: sources, challenges, strategies, practice
 +
* Hari: Function prediction with the [http://rast.nmpdr.org/ '''RAST server''']
 +
* Pruthvi: Differential expression analysis with RNAseq (vs. microarrays): what are the statistics issues? How does this relate to GEO2R?
 +
* Bhawan: ''Deep Learning'' how and why does it work? Bioinformatics use cases. '''R''' packages <code>darch</code>, <code>H<sub>2</sub>O</code> and <code>deepnet</code> (or newer ?). Practical example.
 +
* Bro: Bioconductor - Navigator workflow
 +
* Sabrina: [http://www.genemania.org/ '''GeneMANIA''']
 +
* Ish: [http://www.yandell-lab.org/software/maker.html '''MAKER 2'''] genome annotation pipeline or more recent alternatives
 +
 
 +
 
 +
 
 +
;Proposed
 +
* The github workflow for open source collaborative development: Commits? Master and branches? Pull? Merge? Issues? Blame?
 +
* Test driven Development: principles, and practice with the <code>RUnit</code> package.
 +
* The BioConductor data model: ranges, annotations etc. and how they relate to the architecture of bioconducter S4 objects...
 +
* Any of the [http://www.bioconductor.org/help/workflows/ '''Bioconductor workflows''']
 +
* Maximal Information Content (MIC): The '''R''' Minerva package: Pearson vs. MIC for co-Expression analysis.
 +
* [http://www.broadinstitute.org/gatk/guide/best-practices Broad Institute '''GATK'''] (Genome Analysis ToolKit)
 +
* Calculating volumetric data and displaying it with [https://www.cgl.ucsf.edu/chimera/ '''Chimera''']
 +
* Structural genomics: [http://genome3d.eu/ Genome 3D] and [http://www.sbg.bio.ic.ac.uk/phyre2 '''Phyre2''']
 +
* [https://salilab.org/modeller/ '''Modeller''']
 +
* ... or other topics that you have encountered in a BCB330 or BCB430 project, for which you have particular expertise, or in which you are especially interested.
 +
 
 +
 
 +
Boris: screenscraping, regular expressions, Chimera python programming, dynamic programming ...
 +
* Advanced clustering and cluster-quality metrics with '''R'''
 +
* [http://qiime.org/ Qiime] - demultiplexing community sequencing data
 +
* other topics on the [[Applied Bioinformatics Main Page|Applied Bioinformatics Page]] of this Wiki ...
 +
 
 +
 
 +
{{Vspace}}
 +
 
 +
-->
 +
 
 +
<!--
 +
===Schedule===
 +
 
 +
;TBD
 +
 
 +
Students may swap their presentation dates among themselves but the coordinator '''must''' be informed of swaps.
 +
 
 +
{{Vspace}}
 +
 
 +
<table>
 +
 
 +
<tr class="sh">
 +
<td class="wp"><b>Week</b></td>
 +
<td class="wp"><b>Date</b></td>
 +
<td class="wp"><b>Presenter 1</b></td>
 +
<td class="wp"><b>Presenter 2</b></td>
 +
</tr>
 +
 
 +
 
 +
<tr><td colspan="3" class="sp"></td></tr>
 +
 
 +
<tr class="s1">
 +
<td class="wp">2</td>
 +
<td class="wp">Sept. 21</td>
 +
<td class="wp">Boris<br />Screenscraping – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Boris/BCB410_Screenscraping '''Link''']</span></td>
 +
<td class="wp">&nbsp;</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="wp">3</td>
 +
<td class="wp">Sept. 28</td>
 +
<td class="wp">Bro<br />Bioconductor - NAViGaTOR – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Bronnil.hawill/NAViGaTOR_Workflow '''Link''']</span></td>
 +
<td class="wp">&nbsp;</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td class="wp" >4</td>
 +
<td class="wp" >Oct. 5</td>
 +
<td class="wp">Won June<br />Adam – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Wonjunetai/ADAM '''Link''']</span></td>
 +
<td class="wp">&nbsp;</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="wp" >5</td>
 +
<td class="wp" >Oct. 12</td>
 +
<td class="wp" colspan="2" style="color:#777777;">No class meeting this week.</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td class="wp" >6</td>
 +
<td class="wp" >Oct. 19</td>
 +
<td class="wp">James<br />Deep Learning using CUDA – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:James.yuan/DeepLearningWithCUDA '''Link''']</span></td>
 +
<td class="wp">&nbsp;</td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="wp" >7</td>
 +
<td class="wp" >Oct. 26</td>
 +
<td class="wp">Pruthvi<br />RNAseq vs. microarrays – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Pruthvi.desai/Presentation '''Link''']</span></td>
 +
<td class="wp">&nbsp;</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td class="wp" >8</td>
 +
<td class="wp" >Nov. 2</td>
 +
<td class="wp">Lindsay<br />Variant callers – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Lindsay.liang/VarianceCallers '''Link''']</span></td>
 +
<td class="wp">Charles<br />Autodock – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Charles.Ding/Autodock_Vina '''Link''']</span></td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="wp" >9</td>
 +
<td class="wp" >Nov. 9</td>
 +
<td class="wp">Bhawan<br />Deep learning for computer vision – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Bhawan_Panesar/DeepLearning '''Link''']</span></td>
 +
<td class="wp">&nbsp;</td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td class="wp" >10</td>
 +
<td class="wp" >Nov. 16</td>
 +
<td class="wp">Sabrina<br />Horizontal Gene Transfer – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Sabrina.ge/BCB410-project '''Link''']</span></td>
 +
<td class="wp">Fupan<br />The Cloud (with emphasis on code reproducibility) – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Gosuzombie/BCB410 '''Link''']</span></td>
 +
</tr>
 +
 
 +
<tr class="s2">
 +
<td class="wp" >11</td>
 +
<td class="wp" >Nov. 23</td>
 +
<td class="wp">Allana<br />Cheminformatics – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Allanapereira/Cheminformatics_Presentation '''Link''']</span></td>
 +
<td class="wp">Moeen<br />TF binding site discovery – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Bagherig/oPOSSUM_3.0_material '''Link''']</span></td>
 +
</tr>
 +
 
 +
<tr class="s1">
 +
<td class="wp" >12</td>
 +
<td class="wp" >Nov. 30</td>
 +
<td class="wp">Naina<br />''de novo'' assembly from HTS data – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Naina.Singh/Assembly '''Link''']</span></td>
 +
<td class="wp">Tom<br />GATK – <span style="font-size:80%;">[http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Yulong.piao/GATK '''Link''']</span></td>
 +
</tr>
 +
 
 +
 
 +
</table>
 +
 
 +
{{Vspace}}
 +
 
 +
<sup>*</sup> Older material and/or previous lectures on these topics are available. Coordinate with me ...
 +
-->
 +
 
 +
<!--
 +
==OLDER MATERIAL==
 +
 
 +
&nbsp;
 +
===Selection of topics for consideration===
 +
 
 +
 
 +
* '''Basics'''
 +
**UNIX
 +
***UNIX commands
 +
***The UNIX pipe ("|")
 +
***Installation of programs
 +
***shellscripts
 +
**IDE (Integrated Development Environment)
 +
**Screenscraping
 +
**wget
 +
**Regular expressions
 +
**HTML
 +
**CGI
 +
* '''Perl'''
 +
**CPAN
 +
**Perl programming
 +
**Perl one-liners
 +
* '''PHP'''
 +
* '''MySQL'''
 +
**MySQL installation
 +
 
 +
 
 +
 
 +
-->
 +
 
 +
==Notes==
 +
<references />
 +
 
 +
 
 +
{{Vspace}}
 +
 
 +
[[Category:Applied_Bioinformatics]]
 +
</div>

Revision as of 14:33, 7 September 2017

BCB410H1F - 2017



Objectives and Participants

The "Applied Bioinformatics" course is offered as a part of the BCB Program curriculum to ensure that our students know enough about application issues in the field to be able to put their knowledge into practice in a research lab setting. This is to support the Specialist Program goal: to prepare students for graduate studies in the discipline.

As a required course in the BCB curriculum, BCB410 assumes the prerequisites and goals of fourth-year students in the BCB Specialist Program. Other students may be permitted to enrol on a case by case basis, but they may need to catch up on prerequisites in computer science or life-science courses that BCB students have taken at this point. Generally speaking, this is an advanced course that presupposes familiarity with programming principles, algorithm analysis, and methods of modern systems biology, as well as introductory knowledge of linear algebra, graph theory, information theory, statistics, as well as molecular–, structural– and cellular biology. The varying topics will be discussed at a highly technical level that is likely only useful for students who plan to integrate much of this material into their actual practice.


 

Organization

Details for the 2017 course are not yet available and will be discussed in our first class session, Wednesday, September 13, at 10:00 in Bahen BA025.

It is imperative that you attend the first class session in person. Do not enrol in this course if you can't attend the first class session.


 

Dates and Location

Classes meet Wednesdays between 10:00 and 12:00 in BA025 (Bahen Centre) throughout the Fall Term. Classes start at 10 minutes past the hour.


 


Coordinator

Boris Steipe


 



Office hours

(Virtual) face to face meetings are by appointment, if required. However, we will be able to resolve almost all issues by e-mail. You will find that discussions by e-mail are both more efficient and effective than meetings. Moreover e-mail discussions leave you with a document trail of what was discussed, can contain links to information sources, and we can share points of general interest more easily with the class.


 


Contact

Contact within the class is easiest via the Google Group that you will subscribe to at the beginning of class.


 






Notes



 
Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BCB410&oldid=9792"