Chinook

Description

Chinook is a peer-to-peer (P2P) bioinformatics service. The goal of the Chinook platform is to facilitate exchange of analysis techniques within a local community and/or worldwide. Chinook operates by turning command-line applications into web services (or RMI services) which are broadcast over a virtual network. Currently, there are over 25 analysis services that have been made "Chinook-ready". These range from alignment to regulation prediction algorithms. Furthermore, Chinook is designed to make it extremely easy to add new services. This is facilitated using XML and/or a GUI.

Chinook is funded by Genome Canada as part of the Bioinformatics of Mammalian Gene Regulation grant. Stephen Montgomery is a Ph.D. graduate student in Genetics at the University of British Columbia. He is funded by the Michael Smith Foundation for Health Research. His work is performed primarily at Canada's Michael Smith Genome Sciences Centre as part of the Gene Regulation Informatics team. Steven Jones is the Head of Bioinformatics for the CMSGSC. He is a Scholar of the Michael Smith Foundation for Health Research.

Chinook is the winner of the Best Overall Application in the BCNET Coolest Applications Contest 2004

Citing Chinook

Montgomery SB, Guan J, Fu T, Lin K, Jones SJM "An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs" Nature Methods, 2005

Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application instead of the Java client or Perl Engine. The web application dynamically discovers new bioinformatics services across a heterogeneous network and presents them to users of the Chinook Online webpage. The Chinook Online page was designed and implemented using Java Struts, a flexible open-source framework for building web applications. Use Chinook Online now!

The ORC web application is powered by Chinook to provide competing assessments of tools involved in transcription factor binding site discovery. As new motif discovery tools become available through Chinook, users have the ability to run analyses using their own custom datasets against these tools to determine specificity, sensitivity, positive predictive value and which combination of tools has the best correlation cooefficient. ORC is a demonstration of how Chinook can be used to create assessment infrastructure in bioinformatics. Run the Open Regulatory Competition now!

About Peer-to-peer computing and Chinook

The recent explosion of growth in peer-to-peer (P2P) systems is largely fueled by consumer demand for multimedia files (music, video, software). Estimates report 60-80% of the global ISP traffic is utilized for this activity. However, what is legitimate, successful technology often gets bogged down in the quagmire of important issues related to copyright infringement and Internet security.... To read more click here

The Chinook Java Client offers a flexible way of discovering distributed utilities, managing submitted jobs, and linking to toolmakers websites. Try it out and e-mail chinook@bcgsc.bc.ca with your comments. Use the Java Chinook Client now!

The folks at Java.NET have been kind enough to host Chinook in the Global Education and Learning: Academic Research Community. All the Chinook code is available for download either through one of the installers at our download page below, or through the CVS at Java.NET under the LGPL license. Feel free to communicate to the Chinook community either through our mailing list here or through a membership on Java.NET. Visit the Chinook CVS server at Java.NET now!

Chinook enables researchers to discover and run bioinformatics programs programatically using the Chinook Perl engine. Using the Chinook perl modules allows for writing scripts that access multiple, distributed, and disparate bioinformatics applications with relative ease. For more information on Grid computing for Bioinformatics using Chinook check out the Grid Computing for Chinook page.

Quick help and FAQs for various Chinook-related experiences is available here

Chinook as an API within the Sockeye 3D Comparative Genomics Application

Chinook allows advanced applications like Sockeye to access a diverse network of bioinformatics functionality when used as an API. Within Sockeye, a user can run alignments, look for transcription factors, or predict primers all over the Chinook network. Click here for more information on Chinook's usage within Sockeye.

Chinook / Biomoby Integration

The BioMoby project is aimed at creating a semantic web for biology using web services. Ben Good (BioMoby) has been collaborating with Chinook to coadvertise Chinook services over the BioMoby system. Currently, we are ~75% done this implementation and will be releasing the code as soon as it is finished. Click here to read more about Chinook/Biomoby integration.

Chinook License

This work is licensed under the LGPL (Lesser GNU Public License). It is therefore OSI-certified. Disregard all mention to the Creative Common's license; however it would be nice if you still attributed us. Please contact Stephen Montgomery, at smontgom |SUBSTITUTE_AN_ @ _SYMBOL_HERE| bcgsc.bc.ca if you have any concerns regarding this license or would like to contribute to the Chinook project.

Chinook allows users to specify complex data and send it to servers using a wide-variety of objects. All objects are dynamically loaded into the Chinook system. Special objects can even have dynamically loaded database support. For instance, these objects can be obtained from many different locations by the Chinook server for you. We have currently integrated ENSEMBL, a genome annotation database, and JASPAR, an open access transcription factor database. This means that users of Chinook can automatically fetch data from these sources without having to acquire it beforehand. Chinook can easily be extended to support any type of database for any type of information, using Java's dynamic classloading.

Chinook mentioned in Genome Technology

Check out the mention of Chinook development in the May 2004, Genome Technology Magazine here (membership required)

Chinook Service Status (Real-time)

This is now OFFLINE use Chinook Online web application instead
Click here to find out what services are being offered by Chinook right now!
(Uses the Chinook Perl Interface)

• Two Chinook Servers are at the BC Genome Sciences Centre in Vancouver, see these servers here
• One Chinook Server is at Wyeth Wasserman's lab at the Centre for Molecular Medicine and Therapeutics in Vancouver, see the server here
• One Chinook Server is at CANARIE in Ottawa, see the server here
• One Chinook Server is at Zhipeng Weng's lab (hosted by Ulaz Karaoz) at Boston University, see this server here
• Your Chinook server here...?