05 May, 2011

Bika, an OpenSource LIMS

I've fooled with many a LIMS _Laboratory Information Management Systemes_; as an enduser working within existing systems, as a customer looking for a LIMS solution, and as someone who is curious about the orchestration of data flow within a laboratory setting. One huge frustration common to proprietary solutions is rigidity.

Thankfully, after leaving the GLP game for my bfff Independent Research Institute I am no longer constrained by the shackles of working in a LIMS environment. However, just because my data are not fed into what have traditionally been ungainly and inflexible systems doesn't mean I can ignore them or that there is nothing to learn from developments in the LIMS world.

With EHR Meaningful Use almost upon us, developments and advancements in the LIMS world are about to become relevant to everyone; Medical Information Management Systems _MIMS_ draw much from and share a common ancestry with LIMS.

Bika is an OpenSource LIMS solution which has been in development since 2004. I've been following the development since 2005? via the listserve (Bika-Users@lists.sourceforge.net). When I first played with Bika I was using WATSON's predecessor Nautilus (ThermoFisher / Thermo). Daily, I would find myself frustrated by the system's inability to allow usergenerated queries and a total lack of access to what was going on under the hood.

So, I want you to know, there are choices out there when it comes to your LIMS. You don't have to settle for an expensive gargantuan that doesn't meet YOUR lab's data management needs. And, if you aren't shopping for a solution, like me, it's still fun to watch OpenSource. To this end, today a letter came across the listserve and I wanted to share it with you.

I am the IT consultant for a small lab in. They are considering installing a LIMS and Bika looks like a logical choice.
Here are some details of the systems currently in use and the first of a few questions:

1. HPLC systems are older Thermo Separation units.

2. The HPLC systems are controlled by OS/2. (That is why I am their IT guy - I use OS/2).

3. The current network is a mixture of Windows XP & 7 for general applications and the OS/2 (actually eCS v.2) PC's using
a Windows 2003 Server.

4. Several years ago I created their sample tracking database using Lotus Approach. This has worked very well.

5. Their current method of creating results reports is a combination of a series of REXX programs (used to strip text files
from the instruments) and Excel (using a VBA script I wrote).

6. While they have access to the Internet it is through a wireless system to their ISP located about 5 miles away. There
is no current way to get high-speed wired service to their location.

1. Can Bika be set up locally (I presume on a Linux box) to gather the instrument data and sample receipt information?


Bika is platform independent. It'll be interesting to hear about Windows or Mac implementations but we recommend *nix for its robustness and use FreeBSD or Ubuntu inhouse

2. If Bika can be set up locally can the lab then make daily downloads to the appropriate off-site location?

I suspect that the data will be manipulated further at your off-site location which means a simple incremental back-up of the DB mailed and uploaded there won't work as synchronisation method. Customisation to produce and export the data captured locally and then importing it off-site will be required.
I might be missing something... cross posting to the developers' list for a bigger audience
What is the wi-fi connection speed? You say you are a 'small' lab - if you have very low volumes I propose testing with an off-site server installation and browsing to it from your local site. If capturing sample information via browser sessions gets too frustrating, Bika has a facility to upload these from csv files. Its intended for bulk Analysis requesting but will suit you just fine.
And you caught me out on this one... it is the only part of the manual not completed, see overview here
Ditto, for uploading your results from the instruments, its is also done via .csv files. Not sure whether your older instruments are capable of these, you mention instrument text files?

3. Can the current sample tracking database, which contains all the information about the customer submitted samples, be imported into the Bika database?

Everything is possible in Open Source... we do this for set-up data and a few more scripts would do the transactional data too. If it is going to be a regular job, the function could be properly developed and built into the interface.


Thanks very much,

Bika-Users mailing list


15 January, 2011

Arsenic Blues - Science Music Live at Science Online 2011

and your data best be strong

Brownie pie w ice cream

As Prepared:
335 for 37 min 385 for 5 min

1 box Pilsb
2 eggs
1/4 cup oil
3 tablespoons water

package came with sealed bag of walnuts which were added. With these, I mixed in about a quarter cup of fresh crushed almonds. To chrush: I work with a ceramic bowl from Ikea (mortar) and a glass canning jar (pestle).
Adding one extra egg increases the cakiness
Whenever I've made the brownies with the amount of oil called for on the box I do not get good results from the oven. The extra nuts and the egg nicely balance the decrease in oil.


brownies are good. Brownie pie, better.

next time I'd like to shoot for this


Facebook siege status update: Robust

Working to find the mix of different content(s) here and @drowningkittens.
I am enjoying the format especially on Twitter. Towards connecting the different components: blogging, various socialmedia (Sm), and Pandora has given more evidence to some solid contentions about facebook. Fb provided a great mechanism for the ubiquitization of social media without being an end in itself. The truely novel uses and solutions for&with Sm will be neat to see; and imagined by those who never experienced the absence of fb.

Happy with the new digs : )


14 January, 2011

#Twitter Live


Drowning Kittens:
1) started as a joke between myself and a mathematician friend.
She employed it as a nonsequitur when asked after her weekend plans

2) also a Tragedy of the Commons (ToTCs)

3) working to be an informative Twit er er