BI211A Protein-Protein Interactions
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Contents |
Objective
With systems biology budding as a discipline, there is a colossal need for biologists to understand the interactions within biological networks. There has been much talk about systems biology and protein-protein interactions (PPI), and this course will dig into some of the fundamental issues concerning PPIs, their need and usage.
This course is a starter with introduction to various tools and some examples to find true positive interactors from web searches and web interfaces. The exercises and take-home messages should probably encourage participants to give some thought to the topics covered and hopefully build some excitement about the top-down approach of systems biology involving protein-protein interactions. Nevertheless, this course shouldn't be considered too difficult for beginners. After completing the course, students should be able to understand and find answers to the following questions:
- Whither systems biology?
- Why PPIs? What else does systems biology involve?
- What has made systems biology distinct from bioinformatics?
- Would PPIs bring out a function for umpteen orphan genes?
- What are the types of interaction data and their layouts?
- What are the online tools for analyzing networks?
- How good are the high-throughput methods employed to measure interactions?
- How are interactions validated?
- Exercises covering all web interfaces, tools and Osprey as a visualization tool.
Target Audience: The course requirement is that you be a graduate or pursuing graduation from Biology and a basic knowledge of Computer science and Molecular Biology. You should be able to download Osprey from www.biodata.mshri.on.ca/osprey/
Course outline
Day 1:
- Bioinformatics to Systems Biology: An essential ascent
- Introduction to Protein-Protein interactions: A Computational Biologist's perspective
- Why Systems Biology?
- Computational Systems Biology vs. Molecular Systems Biology
- Assays, tools and techniques in PPIs: Pros and Cons
- A short exercise
Day 2:
- Types of interactions and networks
- Data validation and integration
- Capabilities of networks
Day 3:
- A look at a sample PPI data
- Future challenges
- Introduction to Cytoscape, Osprey and Ingenuity
- Networkology: Data representations
Day 4:
- Exercises using Osprey: A short project
- Exercises with iHOP, String, Bind, PreBind, Genecards, MINT, HPRD
Day 5:
- Summary, take home messages and evaluation
Instructor
- Prashanth Suravajhala is a PhD fellow at Nature, Systems and Models, Roskilde University, Denmark. His home page is at http://ruc.dk/~prash.
Course schedule
This course has been offered once. Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues. If you are interested in an upcoming course, register using instructions below.
Note
This course was earlier taught at Bioinformatics.Org during May 5-9, 2007. The present version is the improvised version of the course titled Systems Biology in present day Bioinformatics: Tools, Tricks, Ticks and Traps taught through bioclues.org and Bioinformatics.Org on a couple of occasions.
Registration
Registration comprises of two steps. First, create an online account to access the educational section of our website. Second, register for this course by making a payment using either the online registration form (click on the scheduled course above; use this form only for credit card payments via secured PayPal), or by sending in the mail-in registration form (~150 kB PDF, use this form if paying by US checks, credit card or corporate purchase order). Please check the tuition rates and discounts below.
Registration deadline: When full
Tuition & discounts
The fee for this course is $595 USD (commercial and government)
Discounted rates are available, as follows:
- Academic and non-profit research organizations, $397
- Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), please inquire
- Professional members get an additional 20% discount
- Limited scholarships may also be available for those in low-income economies.
Logistics
Online courses are offered via online meeting system. Access information will be provided prior to the start of the course. Each lecture will last 45 to 90 minutes, depending on the topics covered. For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as Flash videos (resolution reduced by 30%) each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.
Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and the Adobe Flash plugin. A microphone and webcam is not required for this course. The necessary software, lecture notes and exercises will be provided.
Certification
This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 5 "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
Additional information
If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 978 562 4800.
