BI211 Protein-Protein Interactions
From Bioinformatics.Org Wiki
This course will dig into some of the fundamental issues concerning protein-protein interactions (PPIs), including their need and use in research. It will introduce various tools and provide examples for finding true, positive interactors from Web searches and interfaces. The exercises and take-home messages will encourage participants to give the topics some thought and then hopefully build some excitement about the top-down approach of systems biology involving protein-protein interactions.
After completing the course, students should be able to understand and find answers to the following questions:
- Why 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?
Target audience: The course requirement is that you be a graduate or pursuing graduation from biology and have a basic knowledge of computer science and molecular biology. You should be able to download Osprey from http://www.biodata.mshri.on.ca/osprey/
- Prashanth Suravajhala, Ph.D. is a postdoctoral fellow in Denmark with interests in protein-protein interactions and the systems biology of hypothetical proteins in humans, with a focus on mitochondrial proteins. He is also on the Board of Directors of Bioinformatics.Org and mentors students online through MentorNet and Bioclues.org.
This course was previously co-taught by Gary Bader and contains material developed by him.
The taught program includes a maximum of eight hours, covering the following topics in three sessions. Ample time is set aside for the participants to digest the sessions. Participants who miss the live lectures can view the recorded talks some other time.
- 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
- Types of interactions and networks
- Data validation and integration
- Networkology: Data representations, capabilities of networks
- A look at sample PPI data
- Introduction to Cytoscape, Osprey and Ingenuity
- Recent developments in interactomics and future challenges
- Exercises using Osprey: A short project
- Exercises using iHOP, String, Bind, Genecards, MINT, HPRD
- Summary, take home messages and evaluation
If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)
- Step 1
- If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
- Step 2
- Register for the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).
Please also check the course tuition rates and discounts.
Registration deadline: When full
Tuition & discounts
- Live instruction held on-line
- For-profit & government: $1,000 USD
- Non-profit & self-pay: $600 USD
- Live instruction held on-site
- For-profit & government: $1,200 USD
- Non-profit & self-pay: $800 USD
- On-demand instruction held on-line
- For-profit & government: $600 USD
- Non-profit & self-pay: $400 USD
Additional discounts are available as follows:
- Professional members: 20% discount
- Limited scholarships may also be available for those residing in low-income economies (please inquire).
The necessary software, lecture notes and exercises will be provided.
Live instruction held on-line
On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about two hours, 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 AVI video files 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 Java. A microphone and webcam are not required but may be used.
This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.
Please contact us for questions or additional information.