Bridges User Guide

Gateways

Bridges hosts a number of gateways - web-based, domain-specific user interfaces to applications, functionality and resources that allow users to focus on their research rather than programming and submitting jobs.  Gateways  provide intuitive, easy-to-use interfaces to complex functionality and data-intensive workflows.

Gateways can manage large numbers of jobs and provide collaborative features, security constraints and provenance tracking, so that you can concentrate on your analyses instead of on the mechanics of accomplishing them.

 

Among the gateways implemented on Bridges are:

Galaxy, an open source, web-based platform for data intensive biomedical research.  

Researchers preparing de novo transcriptome assemblies via the popular Galaxy platform for data-intensive analysis have transparent access to Bridges, without the need to obtain their own XSEDE allocation. Bridges is ideal for rapid assembly of massive RNA sequence data.

A high-performance Trinity tool has been installed on the public Galaxy Main instance at usegalaxy.org. All Trinity jobs in workflows run from usegalaxy.org will execute transparently on large memory nodes on Bridges. These tools are free to use for open scientific research.

Trinity jobs can be run on Bridges by going to https://usegalaxy.org.

For more general information on Galaxy, see https://galaxyproject.org/.

 

SEAGrid,  the Science and Engineering Applications Grid, provides access for researchers to scientific applications across a wide variety of computing resources.  SEAGrid also helps with creating input data, producing visualizations and archiving simulation data.  

For more information on SEAGrid, see https://seagrid.org/home.

 

The Causal Web Portal, from the Center for Causal Discovery, offers easy to use software for causal discovery from large and complex biomedical datasets, applying Bayesan and constraint based algorithms. It includes a web application as well as API’s and a command line version.

For more information about the Causal Web Portal, see http://www.ccd.pitt.edu/tools/

To access the Causal Web Portal on Bridges, see https://ccd2.vm.bridges.psc.edu/ccd/login

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