Computational Systems Biology Main Page
BCB420 - Computational Systems Biology
Welcome to the BCB420 Course Wiki.
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 Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.
Contents
The Course
Organization
- Dates
- Lectures: Monday, 10:00 to 11:00 and Wednesday, 10:00 to 11:00 (... according to the Calendar. However we will decide on more suitable times at the first meeting and most likely we will meet in one two-hour slot rather than in two slots.)
- First lecture: Monday, January 9. 2012 at 10:00 - Organization. Whatever you do, don't miss this lecture or you will immediately fall behind.
- Location
- TBD (Medical Sciences Building) - watch this space or e-mail the coordinator at (boris.steipe(at)utoronto.ca)
- General
- See the Course Web page for general information.
- Textbook
- ???
- Submissions
- This is an electronic submission only course; but if you must print material, you might consider printing double-sided. Learn how, at the Print-Double-Sided Student Initiative.
Grading and Activities
| Activity | Weight (Undergraduates) |
Weight (Graduates) |
| 5 Assignments | 15 marks (5 x 3) | 10 marks (5 x 2) |
| 5 In-class quizzes | 35 marks (5 x 7) | 25 marks (5 x 5) |
| Open project | 7 marks | 5 marks |
| "Classroom" participation | 3 marks | 3 marks |
| Graduate project | 17 marks | |
| Final exam | 40 marks | 40 marks |
| Total | 100 marks | 100 marks |
- 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. However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.
Assignments
Timetable and syllabus
| I n t r o d u c t i o n | ||||||
| Week | Date | Lecturer | Contents | |||
| 1 | Jan. 9 - 14 | Steipe | Organisation and Orientation | |||
| A r e a | ||||||
| Week | Date | Lecturer | Contents | |||
| 2 | Jan. 16 - 21 | Steipe | Text | |||
| 3 | Jan. 23 - 28 | Steipe | Text | |||
| 4 | Jan. 30 - Feb. 3 | Steipe | Text | |||
| 5 | Feb. 6 - 10 | Steipe | Text | |||
| 6 | Feb. 13 - 17 | Steipe | Text | |||
| Feb. 20 - 24 | Reading Week - School closed | |||||
| 7 | Feb. 27 - Mar. 2 | Steipe | Text | |||
| 8 | Mar. 5 - 9 | Steipe | Text | |||
| 9 | Mar. 12 - 16 | Steipe | Text | |||
| 10 | Mar. 19 - 23 | Steipe | Text | |||
| 11 | Mar. 26 - 30 | Steipe | Text | |||
| 12 | Apr. 2 - 6 | Steipe | Text | |||
- Topics collection
- Bioinformatics (databases, services, tools and where to find information)
- Systems-biology data sources: genomics and proteomics and their associated databases
- graph theory, graph types and metrics; small-world or random-geometric, date-hubs and party-hubs
- Interactions: physical vs. genetic interactions
- Gene expression data (and extracting regulatory networks therefrom)
- Structural network analysis http://www.csb.ethz.ch/research/structural
- Systems dynamics http://www.csb.ethz.ch/research/dynamic
- Computational Synthetic Biology http://www.csb.ethz.ch/research/synthetic
- Clustering
- Cytoscape
- R and Bioconductor
- informal programming with perl/php/MySQL/
- Gene regulatory networks
- Signal transduction networks
- Metabolic networks
- KEGG, BioCYC
- GO
- Quantitative evolution: signals of recent change and selective pressure
- Prediction of function
- genomics
- transcriptome
- proteome, interactome
- metabolome, glycome, lipidome
- network
- Data integration: Loose coupling, combining datasets to improve annotation quality, evidence combination
- Systems and module discovery: mutual information, clustering, network metrics
- Computable models: representation (SBML, CellML)
- Computable models: methods (ODEs, PDEs and their stochastic counterparts, Petri Nets, Cellular Automata)
- Computable models: methods process calculi (pi-calculus, )
- Computable models: examples (E-Cell, M-Cell, Virtual Cell)
- Computable models: constraint based modeling, Flux balance analysis
- Synthetic biology
- Introducing Computational Systems Biology
- Enabling Information and Integration Technologies for Systems Biology:
- Databases for Systems Biology.
- Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology
- Integrated Imaging Informatics
- Simpathica: A Computational Systems Biology Tool within the Valis Bioinformatics Environment
- Standards, Platforms and Applications
- Foundations of Biochemical Network Analysis and Modeling
- Introduction to Computational Models of Biochemical Reaction Networks
- Biological Foundations of Signal Transduction and the Systems Biology Perspective
- Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis
- Integrated Regulatory and Metabolic Models
- Computer Simulations of Dynamic Networks
- A Discrete Approach to Network Modeling
- Gene Networks: Estimation, Modeling and Simulation
- Computational models for circadian rhythms: Deterministic versus stochastic approaches
- Multi-Scale Representations of Cells and Emerging Phenotypes
- Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks
- Spatio-Temporal Systems Biology
- Cytomics—from cell states to predictive medicine
- The IUPS Physiome Project: Progress and Plans.
In depth...
Resources
- Course related
- The Course Web site.
- The Course Google Group.
- Netiquette for the Group mailing list
- Previous Exam_questions
- 2007 course feedback
- 2008 course feedback
- Contents related
- The VMD tutorial
- A Stereo Vision tutorial
- MetaDatabase
- NAR January-2008 Database issue
- NAR July-2008 Web server issue
