Computational Systems Biology Main Page

Computational Systems Biology

Course Wiki for BCB420 (Computational Systems Biology) and JTB2020 (Applied Bioinformatics).

 

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, this site is unlikely to be useful. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.

 

Warning – this page and all associated course pages are currently under intense revision to prepare for the 2018 Winter session. I will contact students soon to enrol everyone in the course mailing list.

Note that this course starts Tuesday, January 9. 2018 and you will be notified by email of the first set of tasks. Our first class meeting is on Tuesday, January 16.

If you have not received an email from me by Tuesday, January 9 at noon, contact me - I may not be aware that you are enrolled in this course

 

 

 

BCB420 / JTB2020

These are the course pages for BCB420H (Computational Systems Biology). Welcome, you're in the right place.

These are also the course pages for JTB2020H (Applied Bioinformatics). How come? Why is JTB2020 not the graduate equivalent of BCB410 (Applied Bioinformatics)? 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 our current graduate students are usually quite competent at least in some practical aspects of computational biology. In this course we profit from the rich and diverse knowledge of the problem-domain our graduate students have, while bringing everyone up to a level of competence in the practical, computational aspects.

The 2018 course...

In this course we pursue a task in computational systems biology of human genes in project oriented format. This will proceed in three phases:

• First, we will review basic computational skills and bioinformatics knowledge to bring everyone to the same level. In all likelihood you will need to start with these tasks well in advance of the actual lectures. This phase will end with a comprehensive quiz in week 3;
• Next we'll focus on data integration and definition of features. As an example, we will integrate gene expression data from different experiments into a common set of features. Each student will contribute data from one experiment. The results of this phase will be the topic of our first Oral Exam;
• Finally, we will each adopt a biological "system" in human cells and use machine learning methods to attempt to refine its gene membership and assign roles to its member genes. The results will form the basis of our final Oral Exam;
• There are several meta-skills that you will pick up "on the side" these include time management, working according to best practice of reproducible research in a collaborative environment on GitHub; report writing, and keeping a scientific lab journal.

Organization

Dates

BCB420/JTB2020 is a Winter Term course.

Lectures: Tuesdays, 16:00 to 18:00. (Classes start at 10 minutes past the hour.)

Final Exam: None for this course.

Location

MS 4171 (Medical Sciences Building).

Departmental information

For BCB420 see the BCB420 Biochemistry Department Course Web page.

For JTB2020 see the JTB2020 Course Web page for general information.

Prerequisites and Preparation

This course has formal prerequisites of BCH441H1 (Bioinformatics) or CSB472H1 (Computational Genomics and Bioinformatics). I have no way of knowing what is being taught in CSB472, and no way of confirming how much you remember from any of your previous courses, like BCH441 or BCB410. Moreover there are many alternative ways to become familiar with important course contents. Thus I generally enforce prerequisites only very weakly and you should not assume at all that having taken any particular combination of courses will have prepared you sufficiently. What I try to do instead is make the contents of the course very explicit. If your preparation is lacking, you will have to expend a very significant amount of effort. This is certainly possible, but whether you will succeed will depend on your motivation and aptitude.

The course requires (i) a solid understanding of molecular biology, (ii) introductory level knowledge of bioinformatics, (iii) a working knowledge of the R programming language.

The preparation material detailed below will be the subject of our first Quiz in the third week of class.

1 – A working knowledge of R ...

• Work through the R tutorial on this site and complete the tasks and exercises in the tutorial and the associated scripts.

2 – A basic knowledge of Bioinformatics ...

Here is a list of detailed, introductory bioinformatics tutorials. If you have taken BCH441, the material will serve as a review. If you have not taken BCH441, this will help you get up to speed with basic concepts and R code.

• Data
• Sequence

---

• Structure
• Phylogeny
• Function

3 – Project specific prereading ...

• Vogelstein et al. (2013) Cancer genome landscapes. Science 339:1546-58. (pmid: 23539594)

  [ PubMed ] [ DOI ] Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of "mountains" (genes altered in a high percentage of tumors) and a much larger number of "hills" (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or "drive" tumorigenesis. A typical tumor contains two to eight of these "driver gene" mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.

  • Leiserson et al. (2015) Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nat Genet 47:106-14. (pmid: 25501392)

    [ PubMed ] [ DOI ] Cancers exhibit extensive mutational heterogeneity, and the resulting long-tail phenomenon complicates the discovery of genes and pathways that are significantly mutated in cancer. We perform a pan-cancer analysis of mutated networks in 3,281 samples from 12 cancer types from The Cancer Genome Atlas (TCGA) using HotNet2, a new algorithm to find mutated subnetworks that overcomes the limitations of existing single-gene, pathway and network approaches. We identify 16 significantly mutated subnetworks that comprise well-known cancer signaling pathways as well as subnetworks with less characterized roles in cancer, including cohesin, condensin and others. Many of these subnetworks exhibit co-occurring mutations across samples. These subnetworks contain dozens of genes with rare somatic mutations across multiple cancers; many of these genes have additional evidence supporting a role in cancer. By illuminating these rare combinations of mutations, pan-cancer network analyses provide a roadmap to investigate new diagnostic and therapeutic opportunities across cancer types.

    • Leiserson et al. (2016) A weighted exact test for mutually exclusive mutations in cancer. Bioinformatics 32:i736-i745. (pmid: 27587696)

      [ PubMed ] [ DOI ] MOTIVATION: The somatic mutations in the pathways that drive cancer development tend to be mutually exclusive across tumors, providing a signal for distinguishing driver mutations from a larger number of random passenger mutations. This mutual exclusivity signal can be confounded by high and highly variable mutation rates across a cohort of samples. Current statistical tests for exclusivity that incorporate both per-gene and per-sample mutational frequencies are computationally expensive and have limited precision. RESULTS: We formulate a weighted exact test for assessing the significance of mutual exclusivity in an arbitrary number of mutational events. Our test conditions on the number of samples with a mutation as well as per-event, per-sample mutation probabilities. We provide a recursive formula to compute P-values for the weighted test exactly as well as a highly accurate and efficient saddlepoint approximation of the test. We use our test to approximate a commonly used permutation test for exclusivity that conditions on per-event, per-sample mutation frequencies. However, our test is more efficient and it recovers more significant results than the permutation test. We use our Weighted Exclusivity Test (WExT) software to analyze hundreds of colorectal and endometrial samples from The Cancer Genome Atlas, which are two cancer types that often have extremely high mutation rates. On both cancer types, the weighted test identifies sets of mutually exclusive mutations in cancer genes with fewer false positives than earlier approaches. AVAILABILITY AND IMPLEMENTATION: See http://compbio.cs.brown.edu/projects/wext for software. CONTACT: braphael@cs.brown.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The "Knowledge Network"

Supporting learning units for this course are organized in a "Knowledge Network" of self-contained units that can be worked on according to students' individual needs and timing. Here is the detailed map. It contains links to all of the units.

• <command>-Click to open the Learning Units Map in a new tab, scale for detail.

A map of the BCB420 learning units.

• Hover over a learning unit to see its keywords.
• Click on a learning unit to open the associated page.
• The nodes of the learning unit network are colour-coded:
  •   Live units   are green
  •   Units under development   are light green. These are still in progress.
  •   Stubs   (placeholders) are pale. These still need basic contents.
  •   Milestone units   are blue. These collect a number of prerequisites to simplify the network.
  •   Integrator units   are red. These embody the main goals of the course.
  •   Units that require revision  are pale orange.
• Units that have a   black border   have deliverables that can be submitted for credit. Visit the node for details.
• Arrows point from a prerequisite unit to a unit that builds on its contents.

(Many new units will be added to the map as the course progresses, reload the map frequently.)

 

Navigating the course

Everything starts with the following three units:

• Introduction to editing Wiki pages

This should be the first learning unit you work with, since your Course Journal will be kept on a Wiki, as well as all other deliverables. This unit includes an introduction to authoring Wikitext and the structure of Wikis, in particular how different pages live in separate "Namespaces". The unit also covers the standard markup conventions - "Wikitext markup" - the same conventions that are used on Wikipedia - as well as some extensions that are specific to our Course- and Student Wiki. We also discuss page categories that help keep a Wiki organized, licensing under a Creative Commons Attribution license, and how to add licenses and other page components through template codes.

• Your Course Journal

Keeping a journal is an essential task in a laboratory. To practice keeping a technical journal, you will document your activities as you are working through the material of the course. A significant part of your term grade will be given for this Course Journal. This unit introduces components and best practice for lab- and course journals and includes a wiki-source template to begin your own journal on the Student Wiki.

• The "insights!" page

In paralell with your other work, you will maintain an insights! page on which you collect valuable insights and learning experiences of the course. Through this you ask yourself: what does this material mean - for the field, and for myself.

• Once you have completed these three units, get started immediately on the Introduction-to-R units. You need time and practice, practice, practice to acquire the programming skills you will need for the course.

• Whenever you want to take a break from studying R, get done with the other preparatory units.

At the end of our preparatory phase (after week 2) we will hold a comprehensive, non-trivial quiz on the preparatory units and on R basics.

 

Grading and Activities

 

Activity	Weight BCB410 - (Undergraduates)	Weight JTB2020 - (Graduates)
Self-evaluation and Feedback session on preparatory material("Quiz")	20 marks	20 marks
First Oral Exam	20 marks	15 marks
Second Oral Exam	30 marks	25 marks
Journal	25 marks	25 marks
Insights	5 marks	5 marks
Manuscript Draft		10 marks
Total	100 marks	100 marks

 

Oral Exams

Contents and reflection of participation ...

 

Journals

Start forming a habit and even get marks for it too ...

 

Marks adjustments

I do not 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 them 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. But do keep it honest and carefully consider our rules on Plagiarism and Academic Misconduct.

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 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 linked here.

Timetable and syllabus

Syllabus and activities in progress for the 2018 Winter Term ...

 

Week	In class: Tuesday, January 9	This week
1	No class meeting this day!	Preparations I Syllabus Projects Important dates Grading Organization Signup to mailing list and Student Wiki.

 

Week	In class: Tuesday, January 16	This week
2	First class meeting Review of preparatory materials (you should have worked through all of the materials in preparation for class). Practice quiz on preparations (not for credit)	Preparations II Defining the class projects

 

Week	In class: Tuesday, January 23	This week
3	First Quiz	Data Integration I Data sources and workflows Development principles Writing R packages Collaboration tools

 

Week	In class: Tuesday, January 30	This week
4	...	Data Integration II

 

Week	In class: Tuesday, February 6	This week
5	...	Data Integration III

 

Week	In class: Tuesday, February 13	This week
6	Finish Data Integration tasks Discuss and adopt Systems tasks	First Oral Exams

 

Week	In class: Tuesday, February 20	This week
–	No class meeting - Reading Week	Systems readings

 

Week	In class: Tuesday, February 27	This week
7	...	Systems I

 

Week	In class: Tuesday, March 6	This week
8	...	Systems II

 

Week	In class: Tuesday, March 13	This week
9	...	Wednesday March 14: BCB420S drop date Systems III

 

Week	In class: Tuesday, March 20	This week
10	...	Systems IV

 

Week	In class: Tuesday, March 27	This week
11	...	Systems V

 

Week	In class: Tuesday, April 3	This week
12	Finish up and review Systems tasks	Final Oral Exams

 

In depth...

• Glossary
• Mutation Data Matrices
• Amino acids

Resources

Course related

• Student Wiki
• The Course Google Group.
• Netiquette for the Group mailing list

325C78

7097B8

9BACCF

A8A5CC

D7C0F0

 

Notes