Question: which language to use for such a bioinformatics web services infrastructure?
1
gravatar for lait
2.5 years ago by
lait70
Germany
lait70 wrote:

This is the scenario:

  • I have multiple command-line bioinformatics applications written in different languages such as java, Python, Ruby, C, perl ... etc. These applications should be integrated in an online web services infrastructure.

  • The results from running those tools should be visualized to the user in a user friendly interface.

  • NoSQL should be used

  • This whole infrastructure should handle NGS Data upload/download.

What is the best programming language/ framework to use ?

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by lait70
3

have you tried galaxy?

ADD REPLYlink written 2.5 years ago by Giovanni M Dall'Olio25k

Yes, but we are trying to make something that is very personalized to our needs.

ADD REPLYlink written 2.5 years ago by lait70
3

So take Galaxy and personalize it to your needs. That can be done on a time-scale of days, rather than the months involved in your original proposal.

ADD REPLYlink written 2.5 years ago by Devon Ryan73k

As long as I can do the mentioned four points, this would be super perfect! I will check it now. Thanks a lot for the info.

ADD REPLYlink written 2.5 years ago by lait70
3

Do you really want to reinvent the wheel? As Giovanni said, Galaxy already does all of this (heck, you can even run it in a Docker container so that setup is trivial).

ADD REPLYlink written 2.5 years ago by Devon Ryan73k
You might also want to look at http://arvados.org
ADD REPLYlink written 2.5 years ago by peter.amstutz250
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