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Old 08-07-2009, 01:46 AM   #1
steven
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Default NGS data analysis survey

Hi all,

I have been doing some bioinformatics analyzes of NGS data (from various RNA-Seq experiments) and I am considering wrapping/recoding my dirty scripts into some proper analysis package to make them easily available to -non computational- biologists. The goal is a kind of NGS-specialized Galaxy that could run on a lab regular PC, with an intuitive user interface and a "new generation" genome browser. The problem is that it would require substantial work from my colleagues and me and we would not like ending up with a heavy, invasive and expensive commercial software.

To make a long story short: I designed a short survey that could be useful to better define the needs of the community in terms of bioinformatics tools for NGS data analysis. I made it very concise yet hopefully relevant. If you could check it out it would be great, it takes only 2 or 3 minutes. I would be happy to share the results of course, as this is of general interest.

It's there:
http://bit.ly/16fz9F

Any feedback is greatly appreciated.
Thanks a lot for your participation!
s.
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Old 08-07-2009, 08:04 AM   #2
ECO
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This didn't belong at the end of the software packages thread, so it's here now.

And the unshortened URL is: http://www.surveymonkey.com/s.aspx?s...rILf1j4Q_3d_3d

Would you mind letting us know who you are, or at least what academic institute you're from? Thanks and welcome!
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Old 08-07-2009, 11:26 AM   #3
steven
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Hi ECO and Anthony,

Thanks for your interest

As for my precise situation, although most of my research activities have been done in the academic domain so far, I am now an employee of a private company. Does this make my questions "corporate"? I think this is an interesting (corporate?) question... Anyway, I did not specified any "disclaimer" simply because I am not advertising nor selling anything here. As I said in my introduction, this may indeed end up in proposing a software package at some point, yes (hence the location of my initial post in the "software package" thread BTW, sorry if it was not appropriate). If so, I would like these tools to be as useful as possible, and that is the main purpose of this survey. I honestly think it is of general interest.
Now, why not telling my name? Well, precisely because it can be linked to that of my company, which is not officially involved yet. Believe it or not, I mainly did the survey myself, and -thanks to the anonymity- I can speak on my behalf. Just look at the survey, you will realize it is obviously not done by a marketing department
Anyway, I hope you understand my situation and that there is nothing wrong here. Please let me know if you have any concern or suggestion, or if there is anything more I can do!
Thanks for your attention, sorry for the confusion, and enjoy the survey!
s.
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Old 08-07-2009, 02:01 PM   #4
apfejes
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Just for the record, If you are doing work outside of your employer's business hours on something related to what the employer does for a living, you may be in for a surprise as to the ownership of the software.

I would clear this with your employer as soon as possible - your contract (if you're in north america) is likely to have a clause in it that prevents you from doing freelance work on your own time if it conflicts with that of the company... or worse.

Anyhow, good luck with your packages. Maybe you'd consider merging your scripts with one of the many open source packages that are currently available for working with NGS. (=

Anthony
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Old 08-10-2009, 07:24 AM   #5
steven
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Quote:
Originally Posted by apfejes View Post
Maybe you'd consider merging your scripts with one of the many open source packages that are currently available for working with NGS. (=
If you saw them, you would maybe not say this

I bet any computational biologist could do most of the analyzes I did using available open source tools, but I fear this does not apply to other biologists (not used to Linux/Unix command lines for instance), and here is my point.
As my programming skills in Windows/Mac GUI (interface), database, code optimization, etc, are very limited, the best option I am given right now to make my ideas and my tools available to more biologists than I can collaborate with is to have computer pros coding the stuff into a stable and easy to use package. This work has a value, hence a price. This said, I would like to keep this price as low as possible in order to eventually have people use it. And above all, I don't want to end up with some pretty but empty box, if you see what I mean. Scientific accuracy is my concern, as you can see from the survey. I would like to know better what people need before developing anything in order to be sure to propose something useful! I hope I am honest enough. If I am missing something important, please let me know!
cheers,
s.

PS: thanks for your concerns regarding my professional situation, but don't worry, I know about Intellectual Property. And my employers know I am interested in NGS, and that I am posting in public forums -on my behalf. No conflict here either
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Old 08-10-2009, 08:16 AM   #6
steven
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Default NGS survey: preliminary results

Folks,
Here is the first batch of results (I'm splitting them in two sets of files to check if the upload is ok). 12 persons answered, which is not huge but not bad at all given the timing (the survey has been around for just a bit more than a week end of August). Thanks a lot to them, I think the results are already interesting!
As expected, most of the people who took the survey are familiar with NGS data, have an academic background and are more working in front of a computer than at a lab bench. As for the application, in the RNA-Seq field -which seems to be a general interest- the features that attract the highest interest so far are the ease of use, the compatibility with external data sources and the quality control of the reads. This should give an idea about the kind of results we can expect from this survey, and hopefully get more people involved...
If you haven't participated yet, please feel free to jump in!
cheers,
s.
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Old 08-10-2009, 08:32 AM   #7
steven
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Default NGS survey: preliminary results (2)

Here is the second part of the preliminary results, v1.0. Hope you'll like it.
Don't hesitate to forward this survey around!
keeping you in touch,
s.

PS: admins, please let me know if this is too much uploading/posting.
PPS: I used surveymonkey and screenhunter, but I am not in business with the corresponding companies (I just like these tools).
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Old 09-21-2009, 10:25 AM   #8
steven
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Default NGS survey: results v2

Hi all,
Here is an update of the NGS survey results, after 20 people replied to it. Thanks a lot to them, we are approaching the threshold of statistical significance!
Let's hope more people get in, it is very short and quickly done!
You can find the link to the survey at the beginning of the thread.
cheers,
s.
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