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.

Comments

LIS, LMS

[CurryCamel]

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

So much stuff one has never heard about.

Re:LIS, LMS

[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.

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-source to begin-with, in doing as I have suggested, I see many other Drupal developers being able to join and contribute towards on-going and future development. The barrier to entry for those developers to be able to contribute seems lower than at present, so far as I can tell from these cheap seats in the Slashdots.

Drupal offers what is known as Drupal Distributions, which are different installed flavors of Drupal that have been pre-configured. For example OpenAtrium is an intranet-in-a-box, doing calendaring and task management and tracking. You might release the next version as a Distribution of Drupal, while joining the Drupal development community?

But that's just me and I might be wrong. Everything looks like a hammer to me, because what I see looks like totally normal stuff do-able and more efficient with the Drupal CMS/API, but development is inefficient as it stands now, from what I can tell.

Re:Everything seems like a hammer to me

[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 better. Where I had to write modules to get things done in Drupal, I can just write very small amounts of code. I don't have to keep re-writing the wheel over and over. One of my bigger complains about Drupal was that instead of just writing what I needed for content, I needed to add lots and lots of other code. Adding in 3rd party libraries was a non-starter: you do it all in Drupal or you don't do it. I found most Drupal developers only create very simple websites and have nasty pissy attitudes "you need to learn to code drupal k?", yet when given a reasonable question about the stupid behaviour of Drupal, would scramble around looking for answers and then come back and ask "why do you want to do that? No one else wants to do that!" At best they could offer partial or incomplete or non-answers (like dropping the request 'too hard, can't be done'). For the horrid nightmare that is Drupal, quit trying to turn *anything* into Drupal. Use better CMS's (they are out there). They are professional, they work, and this is the one thing that really caught me: they are very much faster and better. Needless to say, my site now has better social media content, better graphics, is more responsive, has a smaller database footprint, is more extensible, and is wildly easier to maintain because I dropped Drupal. And that's one of the bigger reasons why I dropped Drupal. Even minor changes would whitescreen and you had to be extremely careful. There were craploads of bugs when I first installed it, and I would have to patch libraries, modules, everything for months. Things wouldn't work well and there was no explanation, and then suddenly an updated module or a patch and things are working ok, but the whole thing seemed so fragile: one tiny problem and everything collapses. Its like the developers tried to make it a PITA to write/service/maintain. I still use PHP and JavaScript (and C and Bash behind it). And that still all works well. Drupal? Crap software. Don't walk, RUN!

Re:Everything seems like a hammer to me

[madak3]

Django is fantastic framework for these kind of systems. Great ORM and "apps" management. Drupal is terrible to trying to be anything more than a CMS, also the code and PHP is horribe and unmaintable. The even more horrible solution I can think about would be Sharepoint och something

Re:Everything seems like a hammer to me

[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 businesses I know run Drupal. For a well-written explanation of Continuous Integration and how this relates to Drupal hosting, read this document (written by Acquia Corporation, who I have no ties to whatsoever. I don't use any of their stuff): http://www.linuxjournal.com/co....

CNN, Reuters, NYSE, ABC, CBS, NBC/Sports, FOX, WarnerBros also share my positive experience with Drupal as they obviously have invested heavily for their own Drupal-managed content infrastructures.

Not a database.

[Anonymous Coward]

Three words into the Headline and the submitter already gets it wrong.

And of course, the Slashdot "Editors" aren't going to help him.

Everything seems like a hammer to me

[Anonymous Coward]

Ironically having a extensive knowledge of PHP and Python/Django, I would say it would be a far better to rewrite Drupal with Python/Django.

It's become clear that PHP is burning platform, with ever more ambiguous roadmap.

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.

Re:Comes Pre-Broken

[Anonymous Coward]

After all, we all know that Slashdot is written perfectly.

Re:Comes Pre-Broken

[MikeBabcock]

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

Re:Comes Pre-Broken

[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.

Occhiolino - the GNU LIMS

[Anonymous Coward]

You can add to the short list of LIMS, Occhiolino, the GNU LIMS - http://lims.gnu.org/

Re:Occhiolino - the GNU LIMS

[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 there's not a huge community that is essentially captive, e.g., GCC.

Re:Oh jesus fuck.

[lexluther]

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

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:Published but not released yet.

[Anonymous Coward]

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

Neither has Inkscape.

I wonder what Bennet Haselton would think about this...

Comment removed

[account_deleted]

Comment removed based on user account deletion

PIN number

[Anonymous Coward]

LIMS the 's' is for 'system'. like the 'n' in PIN is for number. so LIMS system is as dumb and PIN number. and ATM machine. regardless, Dango makes me cringe.

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/, and lend us your weight among the suits at the LIMS Circus, http://goo.gl/nK6xqv. Appreciated

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]

Julia Re:Juliabase?

[lemoene]

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