BCB410 2014

BCB410 2014

Objectives and Participants

The "Applied Bioinformatics" course is offered as a part of the BCB curriculum to ensure that our students know enough about application issues in the field to be able to put their knowledge into practice in a research lab setting. This is to support the Specialist Program goal: to prepare students for graduate studies in the discipline.

As a required course in the BCB curriculum, BCB410 assumes the prerequisites and goals of fourth-year students in the BCB Specialist Program. Other students may participate but they may need to catch up on prerequisites in computer science or life-science courses that BCB students have taken at this point. They may also need to consider whether their objectives match the course objectives well. Generally speaking, this is an advanced course that presupposes familiarity with programming principles, algorithm analysis, and methods of modern systems biology, as well as introductory knowledge of linear algebra, graph theory, information theory, statistics as well as molecular–, structural– and cellular biology.

Organization

The 2014 course will begin on Wednesday, September 10. 2014 with a class meeting at 10:00 in room HA 316 (Haultain Building).

We will discuss course organization at this time, coordinate presentation schedules, and you will be provided crucial information about how to sign up for mailing list and a topic of your choice that you will prepare and present for the class. If you miss this lecture, I may not be able to accommodate your preferences but will simply assign a topic and time slot.

Dates and Location

 

Classes meet Wednesdays between 10:00 and 12:00 in HA 316 (Haultain Building) throughout the Fall Term.

 

Contact

 

Contact within the class is easiest via the Google Group that you will subscribe to at the beginning of class.

 

Marking

 

Activity	Weight
Design and coordination of your unit	20 marks
Delivery and contents of presentation	20 marks
Quality of exercises/assignments	30 marks
Participation	10 marks
Final exam	20 marks
Total	100 marks

 

Contents

 

A syllabus of learning units

 

Working from a general collection of topics in the field, we identify learning units that are of the greatest interest and greatest relevance for the students in the class. We jointly select the most suitable topics. Every student in class will take responsibility for development and delivery of one of the learning units.

 

Unit contents and delivery

The detailed contents for each unit is to be be discussed with the coordinator. Each student will to lead a two hour session on their topic.

Presenter's responsibilities include:

• Outline of the unit contents, to be completed at least three weeks in advance; This is to include:
  • a detailed lecture outline that includes an introduction, discussion of algorithms, presentation of examples, exposition of practical- and implementation issues and an outlook on future developments in the field;
  • suitable pre-reading material;
  • an outline of exercises for the class;
• Iteration of the unit contents with the coordinator, to be completed at least two weeks in advance.
• Developing a set of exercises (iterated with the coordinator) around the implementation of the topics , at least one week in advance;
• Communication of pre-reading materials to your classmates, at least one week in advance;
• Delivery of your lecture at a sufficiently technical level to be appropriate for an advanced fourth-year course and engaging the class in discussion;
• Communication of exercise materials to the class, at or directly after the lecture;
• Drafting a final-exam question that tests the successful completion of the exercises, at the latest one week after the lecture.

Audience responsibilities include:

• Pre-reading before class;
• Active participation in the discussion;
• Feedback on the exercises and completion in due time.

A selection of topics for consideration

• Rosetta protein structure prediction
• Rosetta protein structure design
• Calculating volumetric data and displaying it with Chimera
• Phyre2
• GeneMANIA
• Function prediction with the RAST server
• Modeller
• Any of the Bioconductor workflows
• Screenscraping
• Advanced clustering and cluster-quality metrics with R
• Maximal Information Content (MIC): The R Minerva package
• TF binding sites: oPOSSUM-3
• Broad Institute GATK (Genome Analysis ToolKit)
• Survival Analysis in R
• Differential expression analysis with RNAseq
• OpenEye cheminformatics tools
• MAKER 2 genome annotation pipeline
• other topics on the Applied Bioinformatics Page of this Wiki ...
• ... or other topics for which you have particular expertise or in which you are especially interested.

 

Schedule

TBD

Students may swap their presentation dates among themselves but the coordinator must be informed of swaps.

 

Week	Date	Presenter	Topic	Contents
1	Sept. 17	Boris Steipe	Regular expressions	Link
2	Sept. 24	None
3	Oct. 1	Boris	Screenscraping
4	Oct. 8
5	Oct. 15	Victor	SBML
6	Oct. 22	Vaishali	Dijkstra's algorithm (et al.)
7	Oct. 29	Xiao	RNA seq.
8	Nov. 5	Boris	Dynamic Programming
9	Nov. 12	Boris	Python Scripting for Chimera
10	Nov. 19	Hareem	Cluster Quality Metrtics
11	Nov. 26	Hareem	Knot theory

^* Older material and/or previous lectures on these topics are available. Coordinate with me ...

 

Notes