An introduction to computational structural and systems biology. Theory and practice of Protein and RNA structure prediction, RNA-RNA, Protein-RNA, protein-protein interaction prediction, biological network analysis.
This class extends the material covered in COMP462/561 (i.e. Computational Biology Methods and Research). We introduce fundamental concepts and techniques in computational structural biology
This course covers the theory and practice of computational techniques used in these research areas, such as dynamic programming algorithms for RNA structure analysis, molecular dynamics and machine learning techniques for protein structure prediction, and graphical models for biological networks analysis. We also feature practical sessions introducing how to use state-of-the-art software.
|Prof. Jérôme Waldispühl||Tuesday 14:00-15:00||ENGTR 3106|
Course Webpage: http://www.cs.mcgill.ca/~jeromew/comp598.html
All the material needed for this class will be available on the public course web page. There is no required textbook. Although, we recommend the following textbooks to deepen the material presented in class:
Your final grade will be calculated as follows:
|Release Date||Due Date||Announce|
|Dec 10||Dec 19||The final exam is scheduled on December 19th at 18h30.|
|Dec 10||A practice final exam is now available.|
|Nov 20||Formatting guidelines for paper presentation: (i) Slides should be in PDF or PPT; (ii) include a title slides, introduction/background section, results, discussion ; (iii) max 30 slides. Be clear and do not make busy slides. Minimum font: 20pt. Each presentation will be approx. 20min + 5min questions.|
|Nov 5||Dec 7||The second assignment is now available. Return your answers by email to the instructor.|
|Nov 4||Please, return your answers to Assignment 1 by email to the instructor.|
|Oct 31||Extra Office Hours at 2pm.|
|Oct 26||The class is cancelled.|
|Oct 12||The class is cancelled.|
|Oct 5||Nov 1||The first assignment is now available. You must return your answers electronically on MyCourse.|
|Oct 5||Oct 13||The list of papers available for review is now available. Fill the form to give your preferences (at least 5).|
|Sep 5||Welcome to COMP598!|
|Lecture 1||Sep 5||Syllabus. Introduction to RNA structure and function. Timeline of RNA bioinformatics.||[Slides]|
|Lecture 2||Sep 7||RNA minimum free energy secondary structure prediction.|
Application: The Vienna RNA package (RNAfold).
Chapter 2 of [GR2014]
|Lecture 3||Sep 12||Boltzmann ensemble of RNA secondary structures.||[Slides]|
Chapter 4 of [GR2014]
|Lecture 4||Sep 14||Rational sampling of RNA secondary structures.|
Application: The Vienna RNA package (RNAsubopt).
Chapter 4 of [GR2014]
|Lecture 5||Sep 19||Comparative modeling of RNAs|
Application: Infernal & the Rfam database.
Chapter 3 of [GR2014]
|Lecture 6||Sep 21||Alignment of structured RNAs|
Chapter 5, 8, and 9 of [GR2014]. Chapter 6, 9, and 10 of [DEKM1998].
|Lecture 7||Sep 26||Simultaneous folding and alignment of structured RNAs|
Chapter 13 of [GR2014]
|Lecture 8||Sep 28||Variations on RNA secondary structure prediction|
Application: The Vienna RNA package (kinefold).
Chapter 19 of [GR2014]
|Lecture 9||Oct 3||Evolution of RNAs and sequence-structure maps|
Application: Jupyter notebook for simulation of the evolution of RNA populations.
Chapter 16 of [GR2014]
|Lecture 10||Oct 5||RNA 3D Modeling|
Application: RNA-MoIP and MC-Sym
Chapter 13 of [GR2014]
|Lecture 11||Oct 10||Pseudo-knots and RNA-RNA interaction predictions|
Application: The Vienna RNA package (RNAup).
Chapter 19 of [GR2014]
|Oct 12||Class cancelled|
|Lecture 12||Oct 17||RNA inverse folding|
Application: The Vienna RNA package (RNAinverse) and IncaRNAtion.
Chapter 16 of [GR2014]
|Lecture 13||Oct 19||Introduction to Protein structure. Timeline of protein structure prediction.|
Application: The protein data bank (PDB)
|Lecture 14||Oct 24||Protein secondary structure prediction using Neural Networks (Part I)|
|Oct 26||Class cancelled|
|Lecture 15||Oct 31||Protein secondary structure prediction using Neural Networks (Part II)|
|Lecture 16||Nov 2||Protein residue contact prediction|
|Lecture 17||Nov 7||Protein Threading|
|Lecture 18||Nov 9||Minimalist models: The HP lattice model|
Application: The CPSP software suite
|Lecture 19||Nov 14||Molecular dynamics simulation|
[Tutorial] [Tutorial 2] [Data]
|Lecture 20||Nov 16||Protein-Protein Interaction networks|
Application: Struct2net, IsoRank
|Lecture 22||Nov 21||
|Lecture 22||Nov 23||
|Lecture 21||Nov 28||3D Genomics|
|Lecture 22||Nov 30||Crowdsourcing molecular biology research|
|Lecture 23||Dec 5||TBD|
Background & Pre-requisites
Good understanding of basic algorithms (equivalent to COMP251), and core molecular biology concepts (i.e. DNA, RNA, Proteins structure and function). A basic progamming in Python.
Undergraduate students: You can register to this class with the permission of the instructor. If you have not taken it yet, it is possible (and even recommended) to register at the same time to COMP462/561. We will synchronize the material taught in COMP598 with the one of COMP462/561.
Policy on discussion Board
Please follow common sense rules and etiquette for discussion board postings: be polite, avoid texting shorthand ("ur" instead of "you are", ...), choose a suitable subject line for your posting and use multiple postings for multiple subjects, keep your postings brief, etc.
Policy on collaborations
We greatly encourage you to discuss the assignment problems with each other. However, these discussions should not go so far that you are sharing code or giving away the answer. A rule of thumb is that your discussions should considered public in the sense that anything you share with a friend should be sharable with any student in the class. We ask you to indicate on your assignments the names of the persons with who you collaborated or discussed your assignments (including TA’s and instructors).
Policy on re-grading
If you wish us to re-grade a question on an exam (or assignment), we will do so. However, to avoid grade ratcheting, we reserve us the right to re-grade other questions on your exam as well.
Policy on final grades
I will use the same rules and formula for calculating the final grade for everyone. We understand that your performances may be influenced by many factors, possibly out of your control. However, that is the only way we can be fair. The only exceptions will be medical exceptions. In that case, I will require a medical note, which has to be also reported to McGill, and to be informed as early as possible. Failure to comply to these rules, may results in the impossibility to invoke a medical exception.
Policy on Assignments
Due date/time, location/mode for returning your solutions, and accepted formats will be announced in class and indicated on the course web page.
Failure to return your assignment in time will results in penalties or even absence of grading. Late submission of 24h or less will receive a penalty of 20%. In all other cases, your assignment will be refused and not graded.
Importantly, solutions that do not follow the requested format will receive a penalty. By default, we only accept PDF or TEXT files. Images (if any) must be embedded in a PDF. Do not compress your files. All files must open on LINUX SOCS workstations.
The quality of the presentation of your solution is very important. Unreadable material, cryptic notations, or bad organization of the material will results in penalties, and potentialy even an absence of grading. If you scan your hand-written solutions, it is your responsability to ensure that you submit a high-quality image (i.e. excellent luminosity, contrast, focus and resolution). The clarity of your explanations will also be an integral part of your final grade.
Policy on programming code
Questions in assignments may require you to write a Python program. We will provide, as much as possible, input and output data to test your programs. However, it will be your duty to ensure that your Java files compile on LINUX SOCS workstations. We will not grade programs that do not compile on these machines.
Submission of class files (instead of Java source files) will be considered as an absence of submission. Do not compress your files.
Use of French in assignments and exams
In accordance with McGill University’s Charter of Students’ Rights, students in this course have the right to submit in English or in French any written work that is to be graded.
McGill University values academic integrity. Therefore, all students must understand the meaning and consequences of cheating, plagiarism and other academic offenses under the Code of Student Conduct and Disciplinary Procedures. See this link for more information.
If you have any additional question, you can contact the instructor:
3630 University Street, Room 3106, Montreal QC H3A 0C6
(Phone) +1 514 398 5018