Biovia Next Gen Sequencing

Question

[reo1977]

Hi all,

I just started a job as the first bioinformatics scientist in a large pharmaceutical company. I am new to pharma and human genomics (previously did microbial bioinformatics), and I am trying to get a workstation and computing environment ordered, up and running. I requested a souped-up Linux desktop for scripting work and pipeline development, and plan to outsource bigger jobs to AWS or something similar. However, my request for a Linux-OS was denied because the company is Windows-exclusive. The IT department offered me Biovia Pipeline Pilot NGS as a Windows-based alternative to the many Linux-based open source tools.

http://accelrys.com/products/collaborative-science/biovia-pipeline-pilot/component-collections/next-generation-sequencing.html

Is anyone here familiar or have experience with this software? How customizable and adaptable is it to new NGS tools that are being developed? It's obviously very expensive and I'd prefer not to go there, but I'd like to better understand its capabilities and limitations, so that I can re-submit a stronger justification for the open source tools if it's not suitable. Any comments or suggestions would be appreciated.

Thanks!

Answer 1

[GenoMax]

You are not going to find many here who will support a commercial product over open source software, though in my book commercial software has its utility and place for specific applications.

That said if you need to work within the bounds set by your local IT then your choices are limited. Even if they are windows-only shop, would they allow you to run virtual OS's on the workstation? Would you have admin rights on your local machine (this may be a sticky issue, if you won't).

If your company has a license for Biovia in place you could test drive it and see what is feasible. Not every open source software is usable in a commercial environment and you may have to look into licensing, on a case by case basis.