Office computers on Windows

Question

[Ellen]

My company outsources much of their bioinformatics processing -- I am trying to learn more and bring more things in house. I have a lot of roadblocks due to security/IT limitations, and also all of our PCs are Windows operated. I have found a lot of answers on this site, but I can't use any of the command line scripts, etc. that are frequently posted. Is this just because I'm on Windows and not Unix/Linux? Is there a bridge program or software that can be installed in order to use? What can I do to learn or make a workable system on our Windows PCs? I have some programming experience, but never really outside of a class setting.

Thanks so much.

[cpad0112]

Set up a GNU-linux/unix server or shift to cloud. Windows is windows even if WSL is available.

Answer 1

[jared.andrews07]

You're looking for the Windows Subsystem for Linux. It provides a UNIX environment in Windows and generally works pretty well for most things.

Answer 2

[Mensur Dlakic]

There are several ways of doing Linux under or along Windows, most of which are listed here. Yet another way that is not listed there is running Linux from a separate partition from a dual-boot system.

I don't think there is much point in making deep recommendations, because no matter what we suggest or what you come up with on your own, the IT people will have to approve it. I am guessing you can't do their job and assess all the potential security problems, so they might as well research the whole thing and find out what works best within the security parameters of your company.

Answer 3

[M__]

I'd go straight to the cloud computing without hesitation, GCP (Google) or AWS (Amazon).

1. Dual function Windows /research machine rarely work out, not merely in terms of computer power (e.g. simulators are slower) there are always issues and its not worth rediscovering conflicts it causes not just with non-bioinformatics colleagues but also in-house tech support (they will worry about security issues).
2. NCBI is shifting wholesale to GCP and AWS and that is the entire direction of play.

For GCP you just need to admin permission to load Cloud SDK and its Google I don't see the problem.

This will give you each Windows machine all the command line tools you need to run GCP which runs Debian Linux. GCP runs its own version of ftp called gs://. FTP to GCP is not permitted and that should also reassure your computer admin people over security.

You'll need to learn GCP (AWS might be easier), but after just dial up your machine for that given job and your away and everything is there: process intensive - check; RAM intensive - check; ulta big dataset - check; GPU for machine/deep learning - check. They'll be courses.

You'd likely need to pay for GCP/AWS tech support and in a commercial environment I'm not certain whether GCP's turn around is slick enough, they are friendly enough however.