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  • BI211 Protein-Protein Interactions

    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

    Session 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

    Session 2

    • 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

    Session 3

    • Exercises using Osprey: A short project
    • Exercises using iHOP, String, Bind, Genecards, MINT, HPRD
    • Summary, take home messages and evaluation

    This course is taught by Prashanth Suravajhala, Ph.D.

    This course was previously co-taught by Gary Bader and contains material developed by him.


    Registration for courses at takes two steps:

    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 this course by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

    On-demand course held on-line

    This course might be taught on-demand, on-line. Please check the list of on-demand courses to see if this course can be taken as such.

    An on-demand version provides pre-recorded video lectures. Once registered, you may begin by viewing the first lecture video, and if you have any questions, you may then email the instructor.

    Slides are available with both on-demand and live of courses, and many also have examples (such as data and scripts). Assignments are also provided for your edification but are not graded. And, when finished, you may request a certificate of attendance.

    On-demand course tuition:

    • For-profit & government: $600 USD
    • Non-profit & self-pay: $400 USD
    • See below for additional discounts.

    Students who've taken the on-demand version of this course can access the course page here.

    Live course held online

    This course might also be taught live, on-line. Please check the calendar to see if it will be held in the near future.

    Live, online course tuition:
    • For-profit & government: $1,000 USD
    • Non-profit & self-pay: $600 USD
    • See below for additional discounts.

    Registration deadline: When full

    Students who've taken the live course can continue to access their course pages here. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

    Live course held on-site

    We can come to your facility to teach this course. Please contact us for additional information.


    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).


    This course is certified by, one of the oldest and largest international affiliations in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within Students completing the course will receive a certificate attesting to that.

    Refund policy

    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.

    Additional information

    Please contact us for questions or additional information.

    See also


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