LIMS 101
October 31, 2011 8:49 AM   Subscribe

I need a very simple laboratory information management system.

For a small scale biobanking project I want to be able to simplify the process of scanning in and databasing new biological samples, and their associated phenotypic information.

I imagine this is best achieved using an off-the-shelf solution for printing barcodes on stickers, and scanning them to a simple database, but I don't know where to look.
posted by roofus to Science & Nature (8 answers total) 4 users marked this as a favorite
 
Somewhat out there suggestion: create a simple Ruby on Rails app and host it either internally on Heroku. I'm sure there's a barcode creator out there that will interface with Ruby, and you can use a barcode scanner to direct output to a text search or input field. You could either pay someone for a few hours to make this simple app, or spend a few days learning Ruby on Rails (or an equivalent language), depending on your technical proficiency.
posted by iamscott at 9:01 AM on October 31, 2011


This kinda sounds like something for GCStar. It supports barcode scanners but I don't know of any barcode printers integrated with GCStar.

Not that barcode printing is hard. I wonder if you can buy pre-printed barcode labels somewhere. Or you can probably just buy avery sheets and find a template you can populate.
posted by pwnguin at 9:37 AM on October 31, 2011


I wonder if you can buy pre-printed barcode labels somewhere

Lots of places do this (ask the goog), and will customize them with your org/project/whatever info. Cheap, too.
posted by bfranklin at 9:39 AM on October 31, 2011


a very simple laboratory information management system

Such a beast does not exist. From experience, this can quickly turn into a can of worms. LIMS are prone to featuritis and one-programmer syndrome (one programmer writes it, moves on, no one can fix it ever again).

We just finished a survey of public and private labs in the course of deciding what LIMS to buy ourselves. LabWare, LabVantage and StarLIMS were the top three responses. LIMS, in general tend to be more functional than well-liked. Interfaces are really, really tough to get right and feel natural for users. Training seems to be the biggest problem with commercial systems, in every aspect.

Because interfaces are so difficult to get right, and because of the one-programmer problem, I encourage you to look at off the shelf systems, rather than write it yourself. This will save you and your sucessors much pain, IME.

Even within that, you have a couple of choices. You can pick one of the big commercial packages (LabWare, LabVantage or StarLIMS) which will be able to handle what you need, guaranteed, but will likely cost a significant amount to install and require on-going licence fees. You can pick a less well known package, supported by a small company, but that can run into support issues and expansion is often limited and difficult. Finally, you can use a general purpose inventory system, like the recommendation for GCStar above. This is probably your cheapest option, but the least flexible.

As a note, bar codes and automatic sample labels generation and reading are typically add-on modules in the larger LIMS systems, but you will need to pay attention for the custom and smaller company solutions. You can either print them yourself or get preprinted ones. Printer technology for labels also needs consideration: solvent safe (thermal no!), LN2 safe (lots of standard glues aren't), abraison resistant (laser-printer ones, not), longevity.
posted by bonehead at 10:03 AM on October 31, 2011


I have had this problem before. If you are really doing this for yourself and not as part of a larger sponsored study you have avoided the first huge problem of being forced to use a LMS somebody else chose that may or may not fit your needs.

Assuming you're not dealing with more than a couple thousand samples, I think the simplest way to do this would be with a barcode scanner and a simple MS Access database. Plenty of scanners can be told to just scan and dump text/numbers into a field. I use this one but that's an accident of history, not an endorsement. If you're interested in seeing a simple mock-up memail me.

Also do not overlook what bonehead says above about making sure your labels can handle the conditions. Even at -80, let alone LN2, some labels will not work well. If you're not doing too many samples or if it's a short-term project you could probably just write with a fine point sharpie on some regular labels, but as your system gets more complex so do your labeling needs.
posted by Wretch729 at 10:32 AM on October 31, 2011


If you are not exposing your samples to extreme temperatures or chemicals (Xylene), then something like these direct thermal barcode printers printers should do the trick.

Orchard and Siemens are commonly used LIS software products.
posted by Andy's Gross Wart at 3:45 PM on October 31, 2011


I don't have a recommendation for you for an off-the-shelf solution, but if it helps inform your decision at all I'm a database and application developer for an FDA and ISO 9001 certified lab that specializes in a form of biobanking, and building and maintaining our LIMS is what I do for a living.

In our lab we use a custom LIMS solution that we built in-house, utilizing FileMaker Pro for the UI and MS SQL for the backend data storage. This is a very capable and flexible setup for us; FileMaker Pro is easy to use, with a WYSIWYG, click-and-drag interface. It is well suited for rapid development prototyping and building client UIs, both desktop and web-based. The latest version interfaces cleanly and easily with both MS SQL and MySQL for data storage, and also integrates reasonably well with MS Active Directory. This combination works very well for us and has proven very easy to maintain and update.

For label printing, we print code 128 barcode labels directly from FileMaker to several different models of Zebra label printers, using Zebra's EPL2 code (we store the code in FileMaker scripts and send it to the label printers serially). We use a mix of standard and cryo-capable labels, depending on the type of label we need for a particular task.

With LIMS, the perfect is often the enemy of the good. I'm sure there are other arrangements that would work as well or better, but unless you already have development chops they will likely have steeper learning curves. Our system is used continuously for 18 hours a day/365 days a year with very little downtime, and our users and management are very happy with the stability, ease of use, flexibility and relatively low overhead our system requires.
posted by mosk at 5:51 PM on October 31, 2011


these direct thermal barcode printers printers

Refrigeration degrades the printing on thermal paper, in my experience. I've lost a few dozen archive samples learning this lesson.
posted by bonehead at 9:32 PM on October 31, 2011


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