Commercial Software vs. Freeware

[gsgs]

I never learned UNIX/Linux, but I do feel that command-line programs
(cmd.exe) are just better than mouse-clicking stuff.
More flexible, can run from batch, easier to adapt to new tasks,
easier to correct/repair/expand. Easier to describe to others,
how to use - just print the command in email -
no list of instructions what windows may open, where to click.
And I do remember, that I felt sad )and still do) when Windows appeared
to replace DOS-command-line utilities

[dnart]

As a biologist, I'm not really interested in learning Unix. As far as buying a bunch of infrastructure and learning to use terminal, I think a more attractive alternative for me might be to go with a commercial solution where I stream my data to their hosted solution or buy my own resources on a cloud such as Amazon. Does anyone have any experience with this route?

[FractalExpression]

This is an issue my clients and I have dealt with in both academic & industrial settings. The "cost of free" software is high in-terms of usability, while the current commercial packages lack flexibility (not to mention the learning curves associated). What you want & need is become comfortable with terminal, as a modern researcher this is fast becoming a necessity.

With this in mind some friends and I have been putting together what you could call "Unix training wheels"...essentially like an old video game like zelda that can walk you through performing complex bioinformatics tasks by simple Q&A dialogue.

Check out the screenshot,

If this looks like something you'd be interested in, just say so and I can send you the .app and help you get started.

And if anyone else wants to give us some feedback, I'm all ears

[GenoMax]

My local environment is that we all have either PC's or Macs and none of us are familiar with Linux or scripting - we are medical researchers not bioinformaticists. To get substantial IT resources would require paying for someone to provide that. So, yes, by "hiring a bioinformaticist" I am referring to a long term gig, which I guess is pretty clearly much more expensive than buying a commercial software package that comes with technical support. To the previous poster, yes, we are concerned about the *real cost* of "free" software.

dnart: If you are planning to do a substantial number of samples (and their analysis) then you should look at investing time/effort into setting up centralized infrastructure. Using standalone PC's/Mac will work to some extent but you will soon find yourself looking for storage/compute cycles. It may seem attractive to buy a bunch of externals disks and use them as your long/short term storage but the downsides may bite you at the worst possible time (e.g. having to recover some irreplaceable data and finding problems with the disks).

Hiring a bioinformatics person is just one part of the equation and may be the first thing you will do. But please budget for/plan to put some reasonable IT infrastructure in place if you expect the informatics person to deliver results.

By "environment" I was mainly referring to administrative/accounting chain of command at your place of work and their tolerance for a substantial amount of expense that is bound to be incurred as you move forward. Think of it (or sell it) as a part of the total package (buying/paying for the actual sequencers or a sequence provider if you get your sequencing done elsewhere).

[dnart]

My local environment is that we all have either PC's or Macs and none of us are familiar with Linux or scripting - we are medical researchers not bioinformaticists. To get substantial IT resources would require paying for someone to provide that. So, yes, by "hiring a bioinformaticist" I am referring to a long term gig, which I guess is pretty clearly much more expensive than buying a commercial software package that comes with technical support. To the previous poster, yes, we are concerned about the *real cost* of "free" software.

[GenoMax]

You may have already looked at a previous thread with discussion on this topic: http://seqanswers.com/forums/showthread.php?t=23905

A lot may depend on your local "environment". It would be hard to enumerate that setup in a discussion forum so ultimately you will need to decide what makes sense in your case. I would definitely suggest talking with local IT resources to gauge their support, specially with respect to infrastructure (networking, storage, clusters).

Are you referring to "hiring a bioinformaticist" as a one time consulting gig or will there be enough work to keep the person employed/interested long term. Something to think about.

[turnersd]

Sounds like you've discovered the true cost of "free" software. I'd say I use free software for 90% of my work, but there are advantages to paying for something, namely, the support. I wrote a blog post discussing free vs paid software after I evaluated Golden Helix SVS (I don't use the software any more, as I rarely do genetic epidemiology / GWAS any more).

http://gettinggeneticsdone.blogspot.com/2012/05/stepping-outside-my-open-source-comfort.html

[dnart]

Our lab is trying to decide whether to go with commercial software, freeware, or a combination for our NGS data analysis.
I am not a programmer or bioinformaticist, and I'm a bit overwhelmed by the number of tools out there and the whole command line / Linux environment. I've tried Galaxy online as I thought I don't need to know command line or Linux to use it, but again I am a bit overwhelmed by all the tools and options included in it that I have no idea how to configure.

So my question to the community, is which is more cost effective? Hire a bioinformaticist to help me install, configure, and run these tools, or go with a commercial software package? Why do you feel this way? Note: I am not looking for recommendations on a particular package, just a general discussion.