Graphical Bioinformatics applications to demo on HPC

[amjadcsu]

Hello,
The medical research organization i am working is looking for open source Bioinformatics/medical application with graphical user interface that can be used to demo the benefits of High performance computer . The idea is to show the speedup achieved using the parallel version of application on HPC .

[dpryan]

The only bioinfo applications that typically take advantage of multiple nodes simultaneously are assemblers, and those don't have a graphical interface. You might just install Galaxy (you can do this via docker to make your life simpler) and have it use the cluster. You'll want to do this anyway if you're trying to get wet-lab folks to use the cluster.

[amjadcsu]

Thanks Ryan for the answer. In that case, are there any bioinfo GUI applications that run on single node but uses multiple cores, in short multi-core Bioinfo GUI applications.?

[dpryan]

Multithreaded applications are pretty common, so you could just use RStudio or something like that. Note that GUIs are very uncommon in bioinformatics, more so on clusters.

[GenoMax]

If you wish to demonstrate acceleration in terms of execution speed achieved by using multiple cores you may have to do so via graphs/tables/charts (e.g. run an alignment with one, two, multiple cores etc).

I don't think there is any application that can visually demonstrate a "speedup" .. unless you write one (with animations etc, not that I am suggesting that you do).