POSTED 2/18/05 10:00 AM
The Contest is temporarily unavailable due to hardware maintenance.
CTC BioChallenge is a scientific application that uses Internet-connected computers to solve a real problem in science—calculating protein structure alignment. You don’t have to be a biology major to participate! This cycle-scavenging contest is open to all Cornell undergrads. First place prize is $500; second and third place prizes are $300 and $100, respectively.
The Application in Brief
One of the computational challenges in the post-genomic age is determining the shape of proteins, which are the products of genes. In recent years, a vast body of genomic data has been accumulated, yet understanding its function is mostly still unknown. The three-dimensional structure of a protein, how it “folds” into its biologically active form, is one of the clues that enables scientists to decipher its function. Recent discoveries indicate that a number of apparently unrelated diseases result from incorrectly folded proteins: Alzheimer’s disease, Cystic Fibrosis, and Mad Cow disease are three examples.
Unfortunately, predicting protein structure from the genomic sequence is not an easy task. One of the common techniques used—structural alignment—is the comparison of a proposed shape to a database of known shapes.
Take the Challenge
In this contest, you will be computing the structural comparison for all possible pairs of proteins in the Protein Data Bank (as of 9/04 PDB contained 27,000 protein structures). The scope of the whole problem would take four months to complete on 1,000 computers. Using Web Services, however, CTC has broken the problem into a cycle-scavenging application that can use idle desktops and laptops to generate the comparisons.
All you need is a computer running Windows XP (pro or Home), at least 512 MB of RAM and 10 MB of available hard disk space. You also need Microsoft .NET framework
1.1 and DirectX 9.0c Runtime. Download these for free at http://www.microsoft.com/downloads/details.aspx?FamilyID=262d25e3-f589-4842-8157-034d1e7cf3a3&displaylang=en and
http://www.microsoft.com/downloads/details.aspx?FamilyID=9226a611-62fe-4f61-aba1-914185249413&displaylang=en.
Download the CTC Computational Biology Challenge installer from http://www.tc.cornell.edu/biocontest/. Save the CTC_Contest.MSI file on your computer and double click to install the application. The application allows two modes of operation. The user can run the application one job at a time (click Run Once box). This will download two proteins, run the comparer and then store the results. Users may also run in continuous mode (click Run Continuous box), automatically running jobs until the user tells the application to stop (click Stop Job box).
Contest rules
The challenge starts February 15 and ends April 11 or when all of the protein structure comparisons have been completed. Winners will be identified by email address and will have submitted the highest total number of completed, validated jobs. The email address submitting the highest total number of completed, validated jobs will win. Invalid results will be disqualified and will result in disqualification of the individual.
All participating members must be 18 years of age or older. Employees of the Cornell Theory Center, Microsoft, Intel, and Unisys are not eligible to win prizes. The Cornell Theory Center, Microsoft, Intel, and Unisys and their employees, affiliates, subsidiaries, parent organizations, related companies, or advertising and promotional agencies are not responsible for technical, hardware, or software malfunctions, loss of or unavailable network connections, or failed, incorrect, or delayed electronic communications, whether caused by the sender or by any of the equipment or programming associated with or used by the contest; or for any damage caused to entrant’s computer systems as a result of entry in the contest or downloading of any information necessary to participate in the contest. All federal, state, and local taxes, and all other costs associated with acceptance or use of the prize are the sole responsibility of winners. The
Cornell Theory Center has the right to use names and likenesses of winners for publicity purposes.
Frequently Asked Questions (FAQ)
What privileges do I need to install this?
A regular user can install this program. It should be installed in a directory other than the C:\Program Files directory, because the program files folder is inherently secure; as such intermediary files cannot be written.
My computer seems to take a long time getting a result.
The calculation speed of this program is dependent on the speed of your processor. Also, since the size of the protein chains are different in each comparison it may take anywhere from 30 seconds to 30 minutes to achieve a result.
Why do I need the .NET Framework to participate in the contest?
The application is written using the Microsoft .NET Framework. You’ll need the Microsoft .NET Framework version 1.1 to run the application. Here is the link for downloading the .NET framework 1.1: http://www.microsoft.com/downloads/details.aspx?FamilyId=262D25E3-F589-4842-8157-034D1E7CF3A3&displaylang=en
The Microsoft .NET Framework 1.1 Service Pack 1 is found: http://www.microsoft.com/downloads/details.aspx?familyid=a8f5654f-088e-40b2-bbdb-a83353618b38&displaylang=en
Why do I need DirectX 9 loaded on my system to run the application?
The application renders images of the proteins that are being compared using DirectX 9. To download from the Web, go to http://www.microsoft.com/windows/directx/default.aspx
and use the Quick Links on the right hand side to get the DirectX 9.0c Runtime. Be sure to look at the instructions and Additional Information on the bottom of the page.
How is the contest being scored?
The contest is being scored by the number of calculation results that are returned. The results will be verified before a winner is announced.
How can I tell who is winning?
Check out our status Web page: http://www.tc.cornell.edu/biocontest/topten/
What is installed on my system when I run CTC_Contest?
The install program will create a shortcut on your desktop and add a menu item CTC to your All Programs start menu. The install program will create a main folder, which you can name; the default is CTC_Contest. All application files, including temporary files, are in this folder. There is a file that is created in the main directory that holds the contest user’s email address. This file is created the first time the user runs the application and the user is prompted for an email address. Email addresses will be used to notify winners.
How do I uninstall the application?
There are two ways to uninstall the application. You can double click on the .MSI file and when prompted choose Remove the Application. You can also go into Add/Remove Programs in the user’s Control Panel folder. Note: The email file mentioned above is not removed by the uninstaller. At the end of the contest the user will have to delete this file and its folder by hand.
Do I need to be on the Internet to run the application?
Yes. The application calls Web services on servers at CTC. There is no off-line mode for the application.
I cannot seem to get the application to run properly. Why?
Problem when running continuous mode:
The underlying connection was closed: Unable to connect to remote server. A new version of the client is now available and resolves this issue. The new version has V1.01 in the title bar. The previous version does not. Only the latest version is available for download. If you have a previous version installed, you will need to uninstall and re-install the latest version.
Please email your questions to biocontest@tc.cornell.edu. A CTC staff member will work with you on an individual basis.
