Free software to lab/sample management
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6.5 years ago
tiagoantao ▴ 690

Preamble: I am not a lab person, but I help quite a lot of laboratory technicians.

I was asked to help with sample management and submission issues (i.e. our lab manager wants to keep track of submitted sequences by allowing users to submit them via e.g. a web interface). Give the nature of the problem, I was inclined to code something up myself. But I was wondering if there was something out there that the community would recommend? I am not mature enough to make a decision myself - in a sense it would be easier to code along. But would be quite happy not to reinvent the wheel...

Thanks

laboratory lims • 4.2k views
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See also: Is there a Lims that doesn't suck? (Conclusion, possibly not ;)

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Not a stand alone software, but our lab uses this Quartzy

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6.5 years ago
GenoMax 121k

This is a thorny subject and in my experience a solution designed by someone else for their local use is rarely accepted elsewhere since the processes/business logic used at your location is going to be different (and people loath to change, in some cases that may be justifiable for specific reasons).

I assume you are asking for a solution to manage samples being submitted for sequencing (and not sequences themselves).
Sierra is a LIMS used by Babraham Bioinformatics Group and available as open source. I am sure you will get lots of other suggestions.

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6.5 years ago

Nowadays, you might be better off using a general Content Management System or Framework, eg. Drupal. Using Drupals Fields and View you can make flexible data types, forms, and reports without (mostly) programming. We have built a full RNAi-LIMS like that. CMS handle a lot of stuff for free, like authentication, file management, etc. and you will be much more agile in adapting the system to the needs of users (add a field = three clicks). Use autocompletion for field content? A module, it's already there.

Also, if you just do it for good-will, I wouldn't recommend to do it yourself from scratch. Think about these points:

  • You will be administrator for the system for life, nobody might be able to take over
  • People will want to project their frustrations about the system to something, it is better this is not only you, but so you can share the blame ("that's a bug in Drupal, nothing I can do" )
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