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Computational Systems Biology

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Course Wiki for BCB420 (Computational Systems Biology) and JTB2020 (Applied Bioinformatics).
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<small>'''This is our main tool to coordinate information, activities and projects in University of Toronto's computational systems biology course BCB420'''. If you are not one of our students, you can still browse this site, however only users with a login  account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the [http://en.wikipedia.org/wiki/Bioinformatics Wikipedia article on bioinformatics], or visit [http://www.openwetware.org/wiki/Wikiomics Wikiomics]. Contact boris.steipe(at)utoronto.ca with any questions you may have.</small>


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== BCB420 / JTB2020 ==

These are the course pages for '''BCB420H (Computational Systems Biology)'''. Welcome, you'll feel right at home here.


These are also the course pages for '''JTB2020H (Applied Bioinformatics)'''. How come? Why is JTB2020 not the graduate equivalent of [[Applied Bioinformatics Main Page|BCB410 (<u>Applied Bioinformatics</u>)]]? Let me explain. When this course was conceived as a required part of the (then so called) ''Collaborative PhD Program in Proteomics and Bioinformatics'' in 2003, there was an urgent need to bring graduate students to a minimal level of computer skills and programming; prior experience was virtually nonexistent. Fortunately, the field has changed and the Program has changed, and now our graduate students are usually quite competent at least in some practical aspects of computational biology. Not uniformly however, and the wide disparity of previous experience has made it increasingly difficult to provide course offerings that address students' needs. JTB2020 therefore shares its lecture components with '''BCB420''' course, and there is a large range of topics in  [[Applied Bioinformatics Main Page|Applied Bioinformatics]] that are covered by students in self-study and discussion with the lecturer, customized to their actual needs.


<section begin=CSB_main_organization />
===Organization===
<div class="alert">

[[CSB Assignment Week 2|'''Assignment 2''']] is active.<br />
Second quiz in class: Wednesday, January 22., 14:00. Bring a red pen for marking!!!

</div>


;Dates
:BCB420/JTB2020 is a Winter Term course.
:Lectures: Wednesdays, 14:00 to 16:00.
:Exam: None for this course.


;Location
:MS4279 (Medical Sciences Building).


;General
:For BCB420 see the [http://biochemistry.utoronto.ca/undergraduates/courses/BCB420H/index.html BCB420 Course Web page] for general information.
:For JTB2020 see the [http://biochemistry.utoronto.ca/graduate_studies/courses/JTB2020H/index.html JTB2020 Course Web page] for general information.


;Submissions
:This is an '''electronic submission only''' course; but if you must print material, you might consider printing double-sided. Learn how, at the [http://printdoublesided.sa.utoronto.ca/ Print-Double-Sided Student Initiative].


====Recommended textbooks ====

: Depending on your background, various levels of textbooks may be suitable. I will bring my evaluation copies to class so you can decide what may work for you.

: [http://www.garlandscience.com/product/isbn/9780815340249 '''Understanding Bioinformatics''' (Zvelebil & Baum)] is a decent general introduction to many aspects of bioinformatics. It was published in 2007, an updated version is urgently needed. Still, some of the basics (like the algorithm for optimal sequence alignment) don't change. <small>[http://www.amazon.ca/Understanding-Bioinformatics-Marketa-J-Zvelebil/dp/0815340249 (Amazon)] [http://www.chapters.indigo.ca/books/Understanding-Bioinformatics-Marketa-J-Zvelebil-Jeremy-O-Baum/9780815340249-item.html (Indigo)] [http://www.abebooks.com/servlet/SearchResults?isbn=9780815340249 (ABE books)]</small>  

: [http://www.garlandscience.com/product/isbn/9780815344568 '''Practical Bioinformatics''' (Agostino)] covers some of the material of the BCH441 exercises. Expect a no-nonsense introduction to the very most basic stuff. I have my pet peeves about this book (as I have for many others, eg. why in the world do they still teach CLUSTAL when all available studies demonstrate it to be the least accurate MSA algorithm '''by a margin'''???), but if you haven't taken BCH441, this may serve you well. And if you did take BCH441, it may consolidate some ideas that I wasn't clear about. <small>[http://www.amazon.ca/Practical-Bioinformatics-Michael-Agostino/dp/0815344562 (Amazon)] [http://www.chapters.indigo.ca/books/Practical-Bioinformatics-Michael-Agostino/9780815344568-item.html (Indigo)] [http://www.abebooks.com/servlet/SearchResults?isbn=9780815344568 (ABE books)]</small>  

: If you are aware of recent good textbooks, or have your own opinions about these or other books, let me know.



<section end=CSB_main_organization />


<section begin=CSB_main_grading />

===Grading and Activities===

Exercises for the course  will be linked from Assignment Pages. I expect everyone to complete them, however there will be no required submissions for exercises. Exercise-related questions as well as pre-reading related questions will be part of the weekly quizzes. Don't expect to do well on the quizzes unless you have done the exercises and completed the pre-reading carefully. This course demands a lot of your discipline and time-management. A large portion of your grade will be contributed by the [[CSB_Open_project|'''Open Project''']]. JTB2020 students will also complete a number of [[APB_Exercises|'''Applied Bioinformatics Exercises''']]. Deliverables for the course will be completed well before end-of-term crunch time and there will be no final exam. 


<table>

<tr class="sh">
<td><b>Activity</b></td>
<td><b>Weight</b><br><small>BCB410 - (Undergraduates)</small></td>
<td><b>Weight</b><br><small>JTB2020 - (Graduates)</small></td>
</tr>

<tr><td colspan="3" class="sp"></td></tr>

<tr class="s2">
<td>[[CSB_Quizzes|'''9 In-class quizzes''']]</td>
<td>54 marks <small>(9 x 6)</small></td>
<td>36 marks <small>(9 x 4)</small></td>
</tr>

<tr class="s1">
<td>[[CSB_Open project|'''Open project''']]</td>
<td>30 marks</td>
<td>30 marks</td>
</tr>

<tr class="s2">
<td>[[CSB_Participation|'''"Classroom" participation''']]</td>
<td>16 marks</td>
<td>16 marks</td>
</tr>

<tr class="s1">
<td>[[APB_Exercises|'''Applied Bioinformatics Exercises''']]</td>
<td>&nbsp;</td>
<td>18 marks</td>
</tr>

<tr><td colspan="3" class="sp"></td></tr>

<tr class="s1">
<td>'''Total'''</td>
<td>100 marks</td>
<td>100 marks</td>
</tr>

</table>


;A note on marking
It is not my policy to adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades). I feel strongly that such "normalization" detracts from a collaborative and mutually supportive learning environment. If your classmate gets a great mark because you helped him with a difficult concept, this should never have the effect that it brings down your mark through class average adjustments. Collaborate as much as possible, it is a great way to learn. <small>I may however adjust marks is if I phrase questions ambiguously on quizzes.</small>
<section end=CSB_main_grading />

== Prerequisites ==

You must have taken an introductory bioinformatics course as a prerequisite, or otherwise acquired the necessary knowledge. Therefore I expect familiarity with the material of my [[Bioinformatics_Main_Page|BCH441 course]]. If you have not taken BCH441, please update your knowledge and skills '''before the course starts'''. I will not make accommodations for lack of prerequisites. Please check the syllabus for this course below to find whether you need to catch up on additional material, and peruse this site to find the information you may need. A (non-exhaustive) overview of topics and useful links is [[CSB prerequisites|linked '''here''']].

==Exercises and Pre-reading==

All course units will have associated exercises that are topics for the following week's quiz.

All course units will have assigned pre-readings that are topics for the current week's quiz.



== Timetable and syllabus ==


;Subject to change on short notice...

<table>

<tr class="st">
<td colspan="5">'''I n t r o d u c t i o n'''</td>
</tr>

<tr class="sh">
<td class="sc">'''Week'''</td>
<td class="sc">'''Date'''</td>
<td class="sc">'''Topics'''</td>
<td class="sc">'''Activities'''</td>
<td class="sc">'''Assignment'''</td>
</tr>

<tr class="s1">
<td class="sc">1</td>
<td class="sc">Jan.&nbsp;6&nbsp;&ndash;&nbsp;12</td>
<td class="sc">
<div class="table-intro-text">Computational Biology aims to bring biology from its descriptive beginnings to a truly predictive science, based on consistent and well understood principles. In the systems biology field of computational biology, we deal primarily with large-scale, cross-sectional data, its relationships and hierarchies.</div>
* Course Organisation
* [[CSB_Introduction|Introduction to Computational Systems Biology]]
</td>
<td class="sc">&mdash;</td>
<td class="sc">[[CSB_Assignment_Week_1|Assignment&nbsp;1]]</td>
</tr>

<!-- ===================    THEME    ===================   -->
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
<tr class="st">
<td colspan="5">'''D a t a'''</td>
</tr>
<tr class="sh">
<td class="sc">'''Week'''</td>
<td class="sc">'''Date'''</td>
<td class="sc">'''Topics'''</td>
<td class="sc">'''Activities'''</td>
<td class="sc">'''Assignment'''</td>
</tr>
<!-- ===================    /THEME   ===================   -->

<tr class="s1">
<td class="sc">2</td>
<td class="sc">Jan. 13 - 19</td>
<td class="sc">
<div class="table-intro-text">In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is the question of how to define ''function'' and make this concept computable; from this arises the central role that ontologies play in the field.</div>
* [[CSB_Web_tools|CSB on the Web: Databases and services]]
* [[Data_integration|Data integration]]
* [[CSB_Ontologies|Ontologies and phenotypes]]
* [[Function_prediction|Prediction of function]]
</td>
<td class="sc">Quiz 1</td>
<td class="sc">[[CSB_Assignment_Week_2|Assignment&nbsp;2]]</td>
</tr>

<tr class="s1">
<td class="sc">3</td>
<td class="sc">Jan. 20 - 26</td>
<td class="sc">
<div class="table-intro-text">The large volume of data in any given systems biology experiment basically precludes the manual, gene-by-gene analysis of results. Questions arise regarding computational strategies for ''gene lists'', especially the statistical tools and strategies we have at our disposal, and a minimum set of programming and automation skills.</div> 
* Lists of genes - a common outcome of high-throughput experiments
** [[CSB Gene lists|Gene lists]]
** [[Enrichment|Enrichment analysis]]
* Statistics
** [[Statistics|Principles of Statistics in molecular biology]]
** [[R]]
** [[Bioconductor]]
** [[Clustering|Clustering and Classification]]
** [[EDA|Exploratory Data Analysis]]
** [[Data_mining|Data mining]]
* Programming
** [[Informal_programming|Informal programming]]
** [[IDE|Using an IDE (Integrated Development Environments)]]
</td>
<td class="sc">Quiz 2</td>
<td class="sc">[[CSB_Assignment_Week_3|Assignment&nbsp;3]]</td>
</tr>


<!-- ===================    THEME    ===================   -->
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
<tr class="st">
<td colspan="5">'''''"-omics"'''''</td>
</tr>

<tr class="sh">
<td class="sc">'''Week'''</td>
<td class="sc">'''Date'''</td>
<td class="sc">'''Topics'''</td>
<td class="sc">'''Activities'''</td>
<td class="sc">'''Assignment'''</td>
</tr>
<!-- ===================    /THEME   ===================   -->

<tr class="s2">
<td class="sc">4</td>
<td class="sc">Jan. 27 - Feb. 2</td>
<td class="sc">
<div class="table-intro-text">Genome sequencing brought the first complete overview of the information underlying life; the associated concept of the ''transcriptome'' - a description of which portion of the genome is expressed at what time - is the most basic ''functional'' description of this information.</div>
* [[-omics]]
* [[Genome|Genome]]
* [[Transcriptome|Transcriptome]]
</td>
<td class="sc">Quiz 3, [[BIO_Open_project#First_Stage:_Vision|Open Project vision]] due in class</td>
<td class="sc">[[CSB_Assignment_Week_4|Assignment&nbsp;4]]</td>
</tr>

<tr class="s1">
<td class="sc">5</td>
<td class="sc">Feb. 3 - 9</td>
<td class="sc">
<div class="table-intro-text">Many more holistic, or cross-sectional descriptions of the molecular composition and assembly of the cell are being worked on.</div>
*  [[Proteome|Proteome]]
*  [[Metabolome|Metabolome]]
*  [[Glycome|Glycome]]
*  [[Lipidome|Lipidome]]
</td>
<td class="sc">Quiz 4</td>
<td class="sc">[[CSB_Assignment_Week_5|Assignment&nbsp;5]]</td>
</tr>

<!-- ===================    THEME    ===================   -->
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
<tr class="st">
<td colspan="5">'''I n t e r a c t i o n s , &nbsp;  P a t h w a y s &nbsp;  a n d &nbsp;  N e t w o r k s'''</td>
</tr>

<tr class="sh">
<td class="sc">'''Week'''</td>
<td class="sc">'''Date'''</td>
<td class="sc">'''Theme'''</td>
<td class="sc">'''Activities'''</td>
<td class="sc">'''Assignment'''</td>
</tr>
<!-- ===================    /THEME   ===================   -->

<tr class="s1">
<td class="sc">6</td>
<td class="sc">Feb. 10 - 16</td>
<td class="sc">
<div class="table-intro-text">Fundamentally, ''-omics'' descriptions provide us with lists of components. However, to understand how things work, we need to address the ''relationships'' of the components - how things are put together: the molecular blueprints. At its most basic level, this is the question of molecular interactions in the cell.  A quantitative description of molecular interactions relies heavily on the mathematical discipline of ''graph theory''. ''Cytoscape'' is a visualization and analysis platform for molecular interactions. </div>
* [[Graph_theory|Graph theory]]
* [[Cytoscape|Cytoscape]]
</td>
<td class="sc">Quiz 5</td>
<td class="sc">[[CSB_Assignment_Week_6|Assignment&nbsp;6]]</td>
</tr>

<tr class="s2">
<td class="sc">&nbsp;</td>
<td class="sc">Feb. 17 - 23</td>
<td class="sc">''Reading Week - School closed''</td>
<td class="sc">&nbsp;</td>
<td class="sc">&nbsp;</td>
</tr>

<tr class="s1">
<td class="sc">7</td>
<td class="sc">Feb. 24 - Mar. 2</td>
<td class="sc">
<div class="table-intro-text">Here we focus on the biological objects of "Interaction Science".</div>
* [[Interactome|The Interactome]]
* [[Interaction_databases|Interaction databases]]
* [[Pathways_and_Networks|Pathways and Networks]]
* [[Interaction_prediction|Interaction prediction]]
</td>
<td class="sc">Quiz 6, [[BIO_Open_project#Second_Stage:_Outline|Open Project outline]] due in class</td>
<td class="sc">[[CSB_Assignment_Week_7|Assignment&nbsp;7]]</td>
</tr>

<!-- ===================    THEME    ===================   -->
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
<tr class="st">
<td colspan="5">'''S y s t e m s'''</td>
</tr>

<tr class="sh">
<td class="sc">'''Week'''</td>
<td class="sc">'''Date'''</td>
<td class="sc">'''Topics'''</td>
<td class="sc">'''Activities'''</td>
<td class="sc">'''Assignment'''</td>
</tr>
<!-- ===================    /THEME   ===================   -->

<tr class="s1">
<td class="sc">8</td>
<td class="sc">Mar. 3 - 9</td>
<td class="sc">
<div class="table-intro-text">Several key networked systems exist in the cell. Here we discuss their paradigms, how they are constructed from experimental data and examples of how they can be organized in databases.</div>
* [[Gene_regulatory_networks|Gene regulatory networks]]
* [[Metabolic_networks|Metabolic networks]]
* [[Signaling_networks|Signaling networks]]
* [[Developmental_networks|Developmental networks]]
* [[Pathway databases|Pathway and network databases]]
** [[KEGG]]
** [[BioCyc]]
</td>
<td class="sc">Quiz 7</td>
<td class="sc">[[CSB_Assignment_Week_8|Assignment&nbsp;8]]</td>
</tr>

<tr class="s2">
<td class="sc">9</td>
<td class="sc">Mar. 10 - 16</td>
<td class="sc">
<div class="table-intro-text">Obviously, one of the key challenges of computational systems biology is to define ''systems'' from ''-omics'' scale data. This task is sometimes referred to as "reverse engineering", it employs a multitude of methods; among them information theory has proven to be one of the cornerstones through the quantification of ''mutual information''.</div>
* [[CSB_Systems extraction|Extracting systems from ''-omics'' data]]
</td>
<td class="sc">Quiz 8</td>
<td class="sc">[[CSB_Assignment_Week_9|Assignment&nbsp;9]]</td>
</tr>

<tr class="s1">
<td class="sc">10</td>
<td class="sc">Mar. 17 - 23</td>
<td class="sc">
<div class="table-intro-text">Life is not static, only death is. Yet, the dynamic nature of biological systems is often overlooked.</div>
* [[Systems dynamics|Systems dynamics]]
</td>
<td class="sc">Quiz 9</td>
<td class="sc">[[CSB_Assignment_Week_10|Assignment&nbsp;10]]</td>
</tr>

<!-- ===================    THEME    ===================   -->
<tr><td colspan="5" class="sp">&nbsp;</td></tr>
<tr class="st">
<td colspan="5">'''M o d e l s'''</td>
</tr>

<tr class="sh">
<td class="sc">'''Week'''</td>
<td class="sc">'''Date'''</td>
<td class="sc">'''Theme'''</td>
<td class="sc">'''Activities'''</td>
<td class="sc">'''Assignment'''</td>
</tr>
<!-- ===================    /THEME   ===================   -->

<tr class="s1">
<td class="sc">11</td>
<td class="sc">Mar. 24 - 30</td>
<td class="sc">
<div class="table-intro-text">The notion that computational biology will at some time become predictive is tied to the idea that we will be able to model the cell's systems. Many approaches exist, each with its own strengths and weaknesses; how to integrate such models - preferrably across multiple scales -  is a question of its own.</div> 
* [[CSB_modelling_principles|Modelling principles]]
* [[CSB_model_representations|Model representations]] 
* [[CSB_modelling_methods|Modelling methods]]
* [[CSB_modelling_examples|Modelling examples]]
</td>
<td class="sc">[[BIO_Open_project#Third_Stage:_Implementation|Open Project implementation]] due in class</td>
<td class="sc">[[CSB_Assignment_Week_11|Assignment&nbsp;11]]</td>
</tr>

<tr class="s2">
<td class="sc">12</td>
<td class="sc">Mar. 31 - Apr. 6</td>
<td class="sc">
<div class="table-intro-text">Do we really ''understand'' systems biology? Computational Synthetic Biology is the ultimate test.</div>
* [[Computational Synthetic Biology]]
</td>
<td class="sc">&mdash;</td>
<td class="sc">[[CSB_Assignment_Week_12|Assignment&nbsp;12]]</td>
</tr>

</table>

==In depth...==
* [[Glossary]]
* [[Mutation Data Matrices]]
* {{WP|List_of_standard_amino_acids|Amino acids}}
<!-- * [[Database Identifiers]] -->


== Resources ==

;Course related
*[[CSB prerequisites|Prerequisites for the course]]
*The [http://groups.google.com/group/bcb420_2013 Course Google Group].
*[[Netiquette]] for the Group mailing list


;Contents related
*The '''[[VMD]]''' tutorial
*A '''[[Stereo Vision]]''' tutorial


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[[Category:Computational Systems Biology]]
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