Lab Samples Database "JuliaBase" Published As Open Source

First time accepted submitter bronger writes After six years of closed-source development, the Research Centre Jülich published its database solution for laboratory samples and processes as open source, while continuing maintaining it. JuliaBase is a framework written in Python/Django that enables research institution or research group to set up browser-based samples tracking and measurement management easily. Next to Bika and LabLey, this is one of the very few open source LIMS systems, and in contrast to the others, not specialized in biomedicine or service labs.

LIS, LMS

[CurryCamel]

http://en.wikipedia.org/wiki/L... [wikipedia.org]

So much stuff one has never heard about.

Re:

[Marillion]

The problem is that lab systems need to be specific to the academic domain being studied. Even in similar studies, the results can vary greatly.

Re:LIS, LMS

[plopez]

No I do not think so. I have used LIMS and database applications to track samples extensively. If you understand database normalization and Object Orientation you will find that most LIMS can follow a pattern very much the same regardless of the domain. You have samples, which then have tests, which mostly look for constituents, results of the tests, test methods (often ANSI or ISO), blanks, dupes, spikes, counts, densities or concentrations, some decay rates (chemical or radiological), and some other rates such as death rates of test subjects.

That's a huge chuck of chemistry and biology. I have used LIMS for hydrology; which included chemical and boilogical tests; geology; chemical and lithographic; and remediation; which included chemical and biological tests, and materials science which includes chemical and physical properties of materials.

I have seen and spoken with people in medicine and biology and the overlap is quite large with what I have written above. If it does not work either the standard is garbage or you do not understand how LIMS works.

Re:LIS, LMS, LIMS

[lemoene]

Big, no huge, LIMS LIS market out there. Many products, 500+ and growing, A fist full of FOSS, say 20. Many from academic background, and in even faster growing Bioinformatics and Biobanking. Because of those odds, forgive me the punt: please read http://www.bikalims.org/ [bikalims.org], and lend us your weight among the suits at the LIMS Circus, http://goo.gl/nK6xqv [goo.gl]. Appreciated

Everything seems like a hammer to me

[operator_error]

Full disclosure: I am a Drupal CMS web developer, and I know nothing about Python/Django.

I explored the demo and what I saw, to me, looked like in 2015 it would be most efficient to re-write the system using the Drupal CMS going forward, using the current system as a Functional Requirements specification to meet or better. The development bang-for-buck goes with Drupal for managing the content required, while gaining much from using Drupal, while lowering development costs. Since the system was closed-sourc

Re:

[Anonymous Coward]

I just left Drupal forever. I had spent about 18 months beating on it. The documentation is 90/10: 90% wrong, 10% right. The API is abysmal. Unless you are doing something that everyone else is doing, you get nowhere very fast, and stay nowhere. Drupal is 'in the box'. If your project is 'out of the box' then Drupal is not your box. "Never Hack Core" but then you steal from core and hack that. I switched to another CMS. I won't mention it because you will only bash it. But it works immensely bette

Re:

[operator_error]

But isn't the OP actually looking for a CMS, with roles-management? That's how I assessed it, but like I wrote in my original message, as a Drupal developer, ...everything looks like a hammer to me. My own lengthy experience with Drupal has been positive, and I don't share the complaints others here have written.

For one thing, Best Practices call for Continuous Integration and Unit Testing. When starting with solid Drupal code, building on top of that using a well-managed GIT workflow, well, that's how most

LIMS and CMS Re: Everything hammers to me

[lemoene]

Bika LIMS uses the Plone Framework, Python. Can be a bit top heavy, but the gains of having a strong community assisting with, and providing most of, the heavy lifting in areas such as authorisation and security, workflow engines, content management and versioning, i18n, etc. is a tremendous bonus. [Disclosure: Bika Open Source LIMS collective founder]

Re:

[lexluther]

LIMS is an acronym (Laboratory Information Management System) not a buzzword like web 2.0 or turnkey or full-stack ...

Comes Pre-Broken

[FlyingGuy]

So Yet Another Web Based Thingy ( YAWBT ) written by academics who don't understand how to write software. There I was in a sample and I clicked on the owner, was taken to the owners page, and yes, no obvious way to get back, except to hit the back button, which as we all know is perfection.

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[MikeBabcock]

Does everything seriously need a breadcrumb these days? The back button works just fine; every browser has one.

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[FlyingGuy]

Frankly, no; however, this is not just text as it wants to be taken seriously as a data portal and should therefor be written with just a little more polish and not have to rely simply on the back button.

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[lexluther]

It's great that GNU has a LIMS candidate, but it would be nice if one could "try it out" or at least see some some screen shots. I feel GNU has such a deep marketing/branding issue -- case and point, the tryton framework which seemingly should be a Drupal/Django competitor doesn't ever seem to come into the conversation. I'm not trolling, I'm a big fan, just pointing out that by not concentrating on the "people use the software" problem they might be accelerating their path to obsolescence in areas where th

Published but not released yet.

[Fnord666]

According to their info page, juliabase has not had a 1.0 release yet.

JuliaBase is organized in a public Git repository on GitHub. So far, there is no public release of JuliaBase 1.0. However, the master branch in the repository is a release candidate, ...

I'm not sure I would solely trust my lab results to a LIMS system that is pre-release.

Re: Published but not released yet.

[smaddox]

Neither would I. Then again, I would trust my data to any single point of failure. That's why I have copies scattered around.

Re: Published but not released yet.

[smaddox]

...wouldn't trust...

Re:

[account_deleted]

Comment removed based on user account deletion

Julia Re:Juliabase?

[lemoene]

Any relation to the Julia language? http://julialang.org/ [julialang.org] All Python to me