An introduction to computational structural and system 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 will introduce fundamental concepts and techniques in computational structural biology and computational system biology.
Computational structural biology aims to model and predict the structure of bio-molecules (e.g., proteins, DNA, RNA), and computational system biology provides methods to model and study biological systems. These fields of study has a broad impact on the understanding of gene regulation processes and biological system mechanisms. It also open new research directions in synthetic biology such as the design of new bio-molecular devices and the re-engineering of biological functions.
This class will cover the theory and practice of computational techniques in these research areas. Each session will feature a description of the methods and algorithms, and will be completed by a pratical session in which we will describe how to use state-of-the-art software.
|Prof. Jérôme Waldispühl||Tuesday 14:30-16:00||ENGTR 3106|
|Alexander Butyaev||Thursday 11:30-13:00||ENGTR 3110|
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 9||Dec 12||An incomplete draft of a practice final exam is now available. The structure of the final exam will be the following: (1) 15-20 short questions (1-2 sentences, 40 points total); (2) 2 problems (30 point each).|
You will be allowed to use a 2 pages of notes. However, books and electronic devices will not be allowed.
|Dec 9||Dec 12||The final exam is scheduled on Dec 12 at 9am in Building SH688 Room 295.|
|Dec 1||GROMACS 5 is now installed on SOCS servers. Please, read this documents with updated commands if you are using it.|
|Nov 13||Dec 8 at 11:59pm||The second assignment is now available.|
|Nov 6||Nov 8||You can now select your project online.|
|Nov 2||Nov 8||The descriptions of research projects are now available.|
|Oct 27||Oct 31||Assignment 1 has been updated (One question went to bonus and threshold used in Q3 has been updated).|
|Oct 19||Oct 20||The class of Oct 20 has been cancelled.|
|Oct 16||Nov 15||Paper review assignment is now available.|
|Oct 6||The office hours of Alexander Butyaev are cancelled today.|
|Oct 1||Oct 14||A selection of paper to review is now available. Please enter your preferences by October 14 in the online form.|
|Sep 29||Dec 12 at 9:00am||The final exam has been scheduled on December 12 at 9am. The location has not been confirmed yet|
|Sep 27||Oct 31 at 11:59pm||The first assignment is now available.|
|Sep 13||Sep 14 at 1:30pm||Bioinformatics lab project presentation in Trottier 3120|
|Sep 6||Welcome to COMP598!|
|Lecture 1||Sep 6||Syllabus. Introduction to RNA structure and function. Timeline of RNA bioinformatics.||[Slides]|
|Lecture 2||Sep 8||RNA minimum free energy secondary structure prediction.|
Application: The Vienna RNA package (RNAfold).
Chapter 2 of [GR2014]
|Lecture 3||Sep 13||Boltzmann ensemble of RNA secondary structures.||[Slides]|
Chapter 4 of [GR2014]
|Lecture 4||Sep 15||Rational sampling of RNA secondary structures.|
Application: The Vienna RNA package (RNAsubopt).
Chapter 4 of [GR2014]
|Lecture 5||Sep 20||Beyond thermodynamic models|
Application: The Rfam database.
Chapter 3 of [GR2014]
|Lecture 6||Sep 22||Alignment of structured RNAs|
Chapter 5, 8, and 9 of [GR2014]. Chapter 6, 9, and 10 of [DEKM1998].
|Lecture 7||Sep 27||Simultaneous folding and alignment of structured RNAs|
Chapter 13 of [GR2014]
|Lecture 8||Sep 29||Pseudo-knots and RNA-RNA interaction predictions.|
Application: The Vienna RNA package (RNAup).
Chapter 19 of [GR2014]
|Lecture 9||Oct 4||RNA 3D Modeling. RNA 3D modules and 3D motifs databases.|
Application: MC-Sym and the RNA 3D Hub
Chapter 13 of [GR2014]
|Lecture 10||Oct 6||Evolution of RNAs. RNA sequence/structure maps. RNA neutral network.|
Application: Jupyter notebook for simulation of the evolution of RNA populations.
Chapter 16 of [GR2014]
|Lecture 11||Oct 11||RNA inverse folding|
Application: The Vienna RNA package (RNAinverse) and IncaRNAtion.
Chapter 16 of [GR2014]
|Lecture 12||Oct 13||Introduction to Protein structure. Timeline of protein structure prediction.|
Application: The protein data bank (PDB)
|Lecture 13||Oct 18||Protein secondary structure prediction using Neural Networks|
|Lecture 14||Oct 25||Protein residue contact prediction|
|Lecture 15||Oct 27||Protein Threading|
|Lecture 16||Nov 1||Minimalist models: The HP lattice model|
Application: The CPSP software suite
|Lecture 17||Nov 3||Molecular dynamics simulation|
|Lecture 18||Nov 8||Guest lecture by M. Smaoui ``Development Platform for Artificial Pancreas Algorithms''|
|Lecture 19||Nov 10||Protein-Protein Interaction networks|
Application: Struct2net, IsoRank
|Lecture 20||Nov 15||
|Lecture 21||Nov 17||
|Lecture 22||Nov 22||
|Lecture 22||Nov 24||
|Lecture 24||Nov 29||3D Genomics|
|Lecture 25||Dec 1||Crowdsourcing molecular biology research|
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