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BioHPC
Computational Biology Application Suite for High Performance Computing
 
What's new Using BioHPC BioHPC NextGen Support Architecture Applications Web Services Access Future Directions BioHPC @ CBSU Using BioHPC Administration of BioHPC Installing on cluster Installing on server Real-time scheduler Download from CBSU

Welcome to BioHPC Home Page

One of the challenges of High Performance Computing (HPC) for biology is resource accessibility. Most biologists are focused on experimental aspects of their research and are not familiar with HPC environment. They often know the algorithms and programs required for analysis of their data, but they have no expertise to use them efficiently in HPC environment. Very often the analysis is computationally intensive and cannot be carried out locally or using free web-based Internet tools. This forces biological research groups to acquire their own computer resources. Even then, using these resources often proves to be a challenge, since there are few user-friendly interfaces available for HPC bioinformatics, and the existing ones are expensive. These problems become even more important now with the increasing flow of next generation sequencing data requiring specialized computational infrastructure integration.

At the Cornell University Computational Biology Service Unit we have developed a suit of computational biology applications for HPC (BioHPC) that allows researchers from biological laboratories to submit their jobs to a parallel cluster through an easy-to-use web interface, as well as manage their jobs and data. Users don't need to deal with parallel job submission, queues, clusters: knowing the application, parameters and input is all that is required.

The newest additions to BioHPC are the support for next generation sequencing and web service layer. BioHPC is now able to interact with a sequencing centers and has components for data distribution and management. Sequencing data managed at BioHPC can be used for further analysis with a need of data transfers. Web service layer allows job submission and control through other clients, such as MS Excel or Perl scripts. Through web services, BioHPC can be integrated with various software platforms.

BioHPC is a suite of applications modified and adapted for efficient use in an HPC environment with ASP.NET interface allowing both easy access and use, as well as easy administration of users, applications, data and other features. For more information about the interface, administration and usage please see our info pages or documentation.

BioHPC interacts with Microsoft Windows HPC Server 2008 or Microsoft Windows Compute Cluster Server 2003   as a cluster scheduler, it also works with remote clusters via HPC Profile/JSDL.

The suite  is freely available for download and use. We only request that each installation be registered with us. Any new modules, applications and improvements that you wish to share should be submitted to us, so they can be incorporated into BioHPC release and made available to all. See the license for more details.

BioHPC is quite complex, but installation is not that difficult and you can always contact us with any questions. Examples of working BioHPC installations that were made available for guests are listed in the implementations section. You may want to register with BioHPC in order to receive notifications about new releases and bug fixes.

Development of BioHPC is currently supported in part by Microsoft Research.

An example of BioHPC installation used for local and remote access is BioHPC installation at Cornell University.

For more information please consult other parts of this website, or some recent posters and presentations about BioHPC: BioHPC general poster, BioHPC next generation support poster, BioHPC overview on MSR external research symposium (April 2010).


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