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!

	Date	Topic	Material
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).	[Slides] 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).	[Slides] Chapter 4 of [GR2014]
Lecture 5	Sep 19	Comparative modeling of RNAs Application: Infernal & the Rfam database.	[Slides] Chapter 3 of [GR2014]
Lecture 6	Sep 21	Alignment of structured RNAs Application: RNAalifold.	[Slides] 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 Application: LocARNA	[Slides] Chapter 13 of [GR2014]
Lecture 8	Sep 28	Variations on RNA secondary structure prediction Application: The Vienna RNA package (kinefold).	[Slides] 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.	[Slides] Chapter 16 of [GR2014]
Lecture 10	Oct 5	RNA 3D Modeling Application: RNA-MoIP and MC-Sym	[Slides] Chapter 13 of [GR2014]
Lecture 11	Oct 10	Pseudo-knots and RNA-RNA interaction predictions Application: The Vienna RNA package (RNAup).	[Slides] Chapter 19 of [GR2014]
	Oct 12	Class cancelled
Lecture 12	Oct 17	RNA inverse folding Application: The Vienna RNA package (RNAinverse) and IncaRNAtion.	[Slides] Chapter 16 of [GR2014]
Lecture 13	Oct 19	Introduction to Protein structure. Timeline of protein structure prediction. Application: The protein data bank (PDB)	[Slides]
Lecture 14	Oct 24	Protein secondary structure prediction using Neural Networks (Part I) Application: PSIPRED	[Slides]
	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 Application: EVcoupling	[Slides]
Lecture 17	Nov 7	Protein Threading Application: RaptorX	[Slides]
Lecture 18	Nov 9	Minimalist models: The HP lattice model Application: The CPSP software suite	[Slides]
Lecture 19	Nov 14	Molecular dynamics simulation Application: GROMACS	[Slides] [Tutorial] [Tutorial 2] [Data]
Lecture 20	Nov 16	Protein-Protein Interaction networks Application: Struct2net, IsoRank	[Slides]
Lecture 22	Nov 21	Jesse Islam: "The Phyre2 web portal for protein modeling, prediction and analysis" by L.A. Kelley et al. Etienne Guillot-Marquet: "Protein 3D Structure Computed from Evolutionary Sequence Variation" By D. Marks et al. Eric Kissel: "Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach" by I. Chauvot de Beauchene et al. Theodore Morley: "sequence-based identification of 3D structural modules in RNA with RMDetect" by J. A. Cruz & E. Westhof
Lecture 22	Nov 23	Anurag Roy: "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction" by M. Boniecki et al. Eric Zhang: "An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization" bu P. Szalaj et al. Samy Coulombe: "Classifying leukemia types with chromatin conformation data" by M. Rousseau et al.
Lecture 21	Nov 28	3D Genomics Application: 3DGB
Lecture 22	Nov 30	Crowdsourcing molecular biology research Application: Phylo
Lecture 23	Dec 5	TBD

Note: This schedule is subject to modification.

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 policies
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.