Why LIMS? & New Bika Health Mailing List

Why LIMS?
To facilitate the adoption of open source software in laboratories, and to help motivate the use of Bika in laboratories aimed at their decision makers, we created this thorough document. This document includes the following sections; Summary, Totaling the Cost of LIMS Ownership, Benefits through resource optimization, Key benefit areas, So Why LIMS?, Why web based? (web based vs web enabled), Why professional open source?, Why Bika?
I recommend it as a must read for any laboratory considering their next LIMS purchase, and considering lowering their total cost of ownership. Who wants to pay licenses, if there's an alternative? ;-)

New Bika Health Mailing List
Over the last year and a bit, we've had at least 40 solid requests for a medical or health LIMS/LIS, recently the activity has intensified, with even a couple of sponsors lining up. To better organize the discussion about this next project of Bika Lab Systems; Bika Health, we have created a specific group for it. The group is open to the public, but posting requires membership, you can apply directly at the group, or send me an email. The purpose of this group? The following intro says it all:

"This discussion group is to establish requirements and development plans for Bika Health, an open source laboratory information management system (LIMS) for medical laboratories, based on feature rich Bika LIMS 2

For more information please visit the Bika Health project page at www.bikalabs.com/health, the central repository for project deliverables"

Ooh yeah, here is the group's URL: http://groups.google.com/group/bika-health

Microsoft bashing?

No fortunately, they (Bill Hilt and his colleagues from Microsoft) are making it easy enough for us not having to motivate or substantiate our antipathy for MS. They are doing it all by themselves!

This morning I came across this excellent article (Microsoft's open-source rhetoric remains dangerously inconsistent written by Ryan Paul on the ars technica website) and apart from scratching my head, trying to figure out how they actually want/plan to be involved with Open Source. Bill comes out with quite some contradictory statements in his interview with InformationWeek (Microsoft's Bill Hilf Reveals Its Open Source Strategy ~ what strategy one wonders....).

Ach, I guess nothing new here :-)

Seen as it's Friday (or if you're in the US, you're probably on leave already), you may be looking for some additional reading, then I can recommend heading straight to the discussion pages on this article.

Finally, I want to wish our US readers a happy thanksgiving, and the rest of you a good week-end.

Open Source ~ just Marketing or the Real thing?

It has come to my attention through several mailing lists, that the term: 'Open Source' is more and more used to further some companies' marketing work, without necessarily backing it up with a generally accepted FOSS licenses and are reluctant to make the source available (specifically to non-clients of that product).

From the word go, we at Bika Lab Systems tried to implement the OS philosophy as well as we could, and to the best of our understanding. Therefore seeing other software companies (whether developers or implementors) trying to vie for attention through shady marketing tactics, does not go down well with us.

I guess having a clear OS license should do the trick, but the last couple of days I have kept on wondering whether there shouldn't be some form of certification issued by a proper (governmental or not) FOSS 'referee'. What do you think?

Now, Bika Lab Systems, has tried to poll its users and developers through its Mailing Lists, to find out if we are doing enough as a company to distinguish between the Open Source Bika Community and Bika Lab systems the company. Unfortunately I got very little feedback, I guess no news is good news in this case. But it still leaves us with a little bit of insecurity...

Since having made the decision to go Open Source and subsequently releasing our software under the GNU General Public License, we had the Community website (http://bika.sourceforge.net) and the corporate Bika Lab Systems website (http://www.bikalabs.com).
We are Plone fans, that much is sure, and maintaining a static html site, seemed a bit archaic. We continually add content to the bikalabs.com website (according to one on-line tool, we have in excess of 700 public pages on the site!), which is not only directly applicable to Bika Lab Systems the company, but is the knowledge base of the Bika Community.

So here's the question that maybe readers of this blog (any?) would like to comment on; Would you be happier (feel that Bika is more FLOSS) if we moved over most of the software & help center to a new (Plone) site with the http://www.bikalabs.org URL? (the idea of the new site, would be to grant access to members of the willing community to contribute directly on the site)
And what else, could we do to make the community more involved? For example, would you be happier if Bika would be managed by a foundation (such as Plone is managed by) and if so, would you participate in that foundation?
Rolling on with the bandwagon, would you rather see a foundation for the whole of Bika, or would it be better to set-up a foundation for each industry that we are targeting, i.e. a Bika Health foundation, Bika Interlab foundation, etc?

Look forward to your comments and feedback!

Bika LIMS 2.0 Alpha ~ Updated

Anneline upgraded the on-line Bika LIMS 2 Alpha installation with the latest to 2.0.10 at http://bika3.bikalabs.com/bika/, where we'll continue testing. Purists might object to the unconventional numbering...

Mods:

• New representation of analysis types on Worksheets in rows
• Standards implemented on Worksheets
• Changed the implementation of Blanks - now a type of Standard
• Order number on AR
• Links to clients and contacts on AR lists
• Worksheet templating working again
• Sample point made compulsory

If you want access for a look around, please contact me at Joris@bikalabs.com - pls mention you want access to Bika LIMS 2.0.
If you manage to break it (please try) please log details in the SourceForge tracker. URLs on the front page at http://bika3.bikalabs.com/bika/

A word or two about Ubuntu Gutsy (7.10)

Not wanting to repeat many a blog about the new Ubuntu release. I would only like to mention my specific experience, although initially not too impressed, after 24 hours of running and using it, I changed my mind completely.

I have a laptop and a desktop, both running 1.5 Ghz CPU's with 512 MB of RAM. Definitely not high performance machines, but rather solid work horses :-)

I started with my laptop last Friday. I decided to do a full network upgrade, rather then downloading the alternate install CD, and starting from there.

My laptop needed to download 1.1 GB, and took about 8 hours to do so. Everything went pretty smooth, no issues, just a couple of unclear questions, about replacing certain files.
A note here; the GUI pop-up had no or little information except the question: Replace or Keep. But if you move the GUI pop-up aside so you can see the info in the terminal, more informative text and additional options were displayed, allowing me to make a better decision.

Once everything was downloaded and installed, I was a bit disappointed with the look & feel, I expected something new, but rather Ubuntu decided on furthering the 'human' theme. After a couple of days of using it, I am actually happy that they took this route. I like the brown, its soothing and easy to work with. My CPU starting crunching quite solidly (almost worrying me), until I found the 'Indexing Preferences' setting, and tweaked it a bit. And now I feel my laptop is faster and a bit smoother then Ubuntu Feisty (7.04). So with the laptop, I only had happiness.

Now, my desktop was a different story. Seen as I was happy with my laptop's results last Saturday I also decided to upgrade my desktop. I got a bit of a discount on the files to download (roughly 800 MB, rather then 1.1 GB). Installing the files took a bit longer, and had to abandon it while in process. I had to leave the installation in mid-progress as it would not have been appreciated if I had chosen the feisty upgrade over my girlfriend's birthday party ;-)

Now this is not a good idea if you live in South Africa where you can't completely rely on the electricity supply 24/7. So I came home the next morning to realize we had had a power cut from 1 am to 10-ish am.

I started up my desktop, dreading the news of a failed install, and expecting the worst by having to cleanly install it. Well it did fail. I booted up almost completely, until the login screen. Then everything went black. Panic. Help. Thanks to my MS Windows instincts I pressed 'Esc' and a text based error message popped up leading to a terminal screen. Ok, now I had a chance. I started up my laptop, went to the Ubuntu Forum, did some searching and there was the answer:

sudo dpkg --configure -a

And that was it. It started processing the rest of the install and within 5 minutes I had my login screen back. And I was into Ubuntu. Then making sure all upgrades were properly installed by running the Update Manager. Saw that the power outage had probably corrupted or broken some additional packages, so I had to do a partial upgrade which went smooth, relatively quick and it was all done. Ready to explore & play.

Now I must say, that I had a similar experience with Win2K in the past, and I had to wipe the disk and start from scratch. And there we have it. Ubuntu has saved me, once more.

Now what do I like about Gutsy (I don't have a powerful enough video card to experience Compiz & Beryll);

• Tracker Search Tool is very impressive (although I can't wait until Thunderbird indexing will be enabled)
  
• My boot up time is much faster then under Feisty
• After the initial indexing of files, it seems as the whole OS is a bit faster
• It's always nice to get your main applications a face lift (Open Office, GIMP, etc)
• Thunderbird had a nice Lightning upgrade (now email and calendar are far more tightly integrated. A great step forward)
• It did not install Plone 3.0, and my Plone 2.5 instances were left untouched, saving much time re-setting my Bika demo sites.
  

My wish list (but not all of these are Ubuntu's responsibility)

• I feel that Evolution is still better integrated then Thunderbird. And I would like to see that changed. :-)
• Indexing of Thunderbird emails
• Keep improving the boot up speed
• Keep improving OS speed
• Tighter integration (out of the box) for PDA's and cellphones.
• More informative error (& installation) messages. Yes I am an end user, not a developer!

That's it. Now I just feel that the next 6 months won't pass fast enough for the next version of Ubuntu.

Bika Interlab Demo 1.2 Now Available

The Bika Interlab 1.2 Demo is now available for evaluators. If you would like to have a look, please send an email to demorequest@bikalabs.com and specifically mention you want access to Interlab (as we also offer Demo access to Bika LIMS 1.2, and Bika LIMS 2.0 Alpha).
This is the front page of the demo; http://interlab.bikalabs.com/
To make the Interlab release story complete, following the official Press Release;

------------------8<-----------------------------------------------------------------

Press Release

Bika Lab Systems

10 Constantia road

Cape Town 8001

South Africa

Date: 22 October 2007

Bika Interlab 1.2 GPL release · Web-based Open Source Proficiency Testing Software

The unique and ingenuous web based inter-laboratory proficiency testing system designed and sponsored by the South African Wine Laboratory Association (SAWLA) and developed locally in open source technologies by Bika Lab Systems, went into production February 2007 and proved very successful, eliminating the 3 week turn around experienced with the spread sheet based system it replaced

Effective proficiency testing is one of the tools employed by SAWLA towards its goal to improve the quality of wine laboratories in SA, standardise methodology and provide a forum for communication and access to information

The proficiency testing scheme (PTS) runs on a monthly basis, two different wine samples per month. The scheme co-ordinator validates bulk samples as homogeneous in an ISO 17025 accredited laboratory, bottles and distributes the samples. Member labs then have a week to analyse the samples, on 15 different parameters, and submit their results on-line

In the on-line system it works like this: The PTS co-ordinator prepares the samples and creates a testing round on-line at the SAWLA web portal. The system automatically informs members per e-mail and provides relevant information about the sample type, distribution and closing date. Member labs fetch their samples, analyse them and enter their results on-line. A senior analyst or manager verifies the data

After their results were verified, and enough verified results are available to make statistical sense, members may immediately see their comparative stats and performance indicators. They are warned though that these remain dynamic as more labs submit their data. When the testing round closes, members receive their final performances per e-mail

Analysis results are archived and presented to members graphically via distribution curves, method comparisons and chronological Z-value plots. The system delivers immediate turnaround

Since the SAWLA system is built on a Content Management System (CMS) platform, it offers benefits in a dynamic interactive web portal at www.sawla.org. The SAWLA portal currently offers a Help centre with training videos, member list and statistics explanations

The system's CMS capabilities will now be exploited to the fullest in SAWLA's drive to have the system certified ISO compliant. It will serve as document repository for SAWLA's quality control manual, year plan, complaints register, corrective and preventative action forms and register, internal audits, management reviews and skills development packages

Attention will then be directed at SAWLA's long term PTS objectives, obtaining international participation and making the analysed wine available as certified reference material

------------------8<-----------------------------------------------------------------
Proficiency Testing

The aim of Proficiency Testing - also known as Inter-Laboratory Comparison Programmes, ILCP, or Proficiency Schemes - is to provide laboratories with objective assessments of the accuracy and reliability of their test results. Proficiency Testing also provides the opportunity for laboratories to benchmark their performance within a pooled industry group, nationally or internationally
www.labchek.info

------------------8<-----------------------------------------------------------------

No license fees

Bika Interlab is licensed on the GNU General Public License and can be downloaded from the Bika Interlab Project centre at http://www.bikalabs.com/interlab. Bika Interlab is based on Bika LIMS 1.2.5 and Plone 2.5

On-line demo

An on-line demonstration installation can be accessed at http://interlab.bikalabs.com/

The Bika Team

http://www.bikalabs.com/

Bika Interlab 1.2 Released

We're complete on the file release front. Last night we released Interlab 1.2

You can get the file directly from Sourceforge.net, or though the Bika Interlab Project page on Bikalabs.com. Later today or tomorrow morning (it is week-end after all!!) you will see it popping up on Plone.org's Bika Interlab page, and on Freshmeat.net (somewhere...)

If you want to install it yourself make sure you read our installation guide (windows - *nix), here.

I'm still populating and adding bits and pieces to the Interlab demo, so that will have to wait until tomorrow or Monday.

Bika LIMS 1.2.5 Released

Ok, it has happened!
Bika LIMS 1.2.5 has been released. You can find it here at Sourceforge.net.
If this is the first time you are trying Bika, make sure you d/l the bundle, if you're upgrading or already have the dependencies, just choose the bika-1.2.5.xx package.

The official release pages (on bikalabs.com, plone.org, freshmeat.net) will start popping-up here and there between now and Monday.

Interlab release; The files will be released today, project pages will be updated between now and Monday. Full Press Release and serious marketing effort will only start on Monday.
Once Interlab files have been released, I'll post a quick note here. So you can start downloading and playing if you want. Note: to install Interlab you need Bika LIMS 1.2.5 (and dependencies)

On a sporting note: Although I am not South African, I do support The Bokke, and hope that they'll bring the Rugby World Cup home tomorrow evening in Paris.
As I am an avid F1 fan, for me things are quite exciting this week-end. It's a three way battle, and hope the politics are best left to politicians this week-end. If you know what I mean...

Have a good Week-end!

Bika Interlab release: Almost there

It's been a busy few days but we are getting there...

The release should come out this afternoon or tomorrow morning (I promise), so far we've already updated the following;

• Bika LIMS Demo from 1.2.3 to 1.2.5 -> New demo is here
• Updated the Interlab project page - here
• Today we're going to populate the Interlab demo and write suitable demo notes - wip Interlab demo site (at the time of writing the records are still pointing to the old demo ahum, but this should be fixed within the next hour or so)
• Once the demo is up & populated it's time to release...yes!

What we've also been busy with during this last week is to increase our marketing efforts around our Plone hosting (BikaCMS) services, by creating this page with our offered hosting services and it's prices. Seen as South Africa is getting to the point of understanding the value of a Content Management System (especially Open Source), I foresee this could take off well.

To spell it out one more time; we host both our Bika products (LIMS, Wine, Interlab) and plain Plone with some add-ons, such as Plone Helpcenter, Plone Softwarecenter, LinguaPlone, PloneGazette and Quills Blogging. All still on Plone 2.5, but depending on our LIMS upgrade strategy to Plone 3 (still to be discussed internally), that should be forthcoming as well.

Ok back to the Interlab demo now...

Up and Coming: Bika LIMS 1.2.4 and Interlab 1.2 release

phew, finally I can announce some movement in the Bika LIMS and Interlab sphere!

Last week-end we migrated our client SAWLA to Bika Interlab 1.2. After weeks of testing and looking at the issue tracker this morning, it seems that 1.2 is a huge improvement over (non-released) Interlab 1.0. Specifically on the performance front I think we made a leap. Of course there's also some added functionality.

Following a quick list of improvements of Bika Interlab 1.2

• Upgraded; Interlab now runs on Bika LIMS 1.2.4 and Plone 2.5.x
• Enhanced;
  
• Top performers portlet - for each sample round a list of 5 top performing laboratories is shown, showing the sample, the position, and the number of participants
• Mean and Standard deviation also displayed on closing sample email
• Removed state change drop down from Analysis request manage results to prevent inadvertent verification of non-submitted results
• Fixed; we also tackled a variety of small bugs which I will fully detail in the release notes.

For Bika LIMS 1.2.4 we have made some small changes, but mainly to accommodate the improvements made for Bika Interlab.

When can you expect to see it?
This week we are compiling both packages, have already started writing up the release notes and project details. This week-end we are planning to migrate the current Bika LIMS 1.2 Demo to 1.2.4, create an Interlab 1.2 Demo. Releases for download should be available from early next week.

Where can you expect to see it?
Bika Lab Systems Project pages:

• Bika LIMS
  
• Bika Interlab

Plone Product pages:

• Bika LIMS
• Bika Interlab

Sourceforge.net download area:

• Bika Downloads (both LIMS & Interlab)
  

Freshmeat.net:

• Bika Projects
  

As soon as the above are ready and the demo's populated with test data, expect an imminent announcement on this Blog, but also as a news item on Bikalabs.com and hopefully in many other places on the web.

So, we're almost there and expect some fireworks to come with it!

Other Notes:
Plone 3.0: at this stage all of our products are compatible with Plone 2.5.x, over the next months we will investigate the migration to Plone 3.0, and thereafter plan it. I expect this to happen sometime in 2008. Unless of course we can find a sponsor and make it a higher priority ;-)
Bika LIMS 2.0: Although we've encountered delays with LIMS 2.0, work has re-started, and hope to make a release end of October/beginning of November. If you are interested, drop me an email, and I can either give you access to our LIMS 2.0 Alpha and even send you a pre-release package of LIMS 2.0.

LIMS & Laboratory Related Mailing Lists, Forums, Discussion Groups, Websites, etc.

There are increasingly more and more mailing lists, websites that list LIMS, following is a list of sites and mailing lists that we at Bika Lab Systems subscribe to. They are in no particular order

Forums, Discussion Groups and Mailing Lists:

• LIMSForum - Dscription: The Laboratory Informatics Institute, LIMSforum.com discussion group is for discussing LIMS, Electronic Laboratory Notebook systems, Chromotography Data Systems,, Scientific Data Management Systems and validation and regulatory compliance for the laboratory industry.
• LiMS.tv - Description: The Laboratory and Science Video channel
• LIMS_info - Description: Welcome to LIMS Info, online Laboratory Information Management Systems (LIMS) community for LIMS Professionals in the world. This group is designed for LIMS professionals, Mangers, Analysts, Lab person, Chemist, Systems programmer, LIMS Administrators & Process Leads who are involved in the selection, implementation and maintenance of LIMS. LIMS Info is started to congregate all levels of LIMS Professionals in one place to share information. This group is dedicated to enhance the science of laboratory information management.
• The LIMS Mailing List - Description: The LIMS Mailing List is a forum for discussing everything and anything about LIMS. It is a great place to ask any LIMS-related question and receive educated opinions from industry users and professionals from all over the globe.
• OpenHealth - Description: The purpose of this group is to discuss issues pertaining to the use of open source free software in health care settings.
• FOSS_health - Description: Mailing list about FOSS Health software. Run by OSCHA (Open Source Health Care Association)
• Plone Scientific - Description: Mailing list for the Plone community, dealing with topics around science.
  

LIMS Listings and related websites:

• ChemicalAnalysis.com
• Environmental Health and Safety Software
• LabNews.co.uk
• LaboratoryTalk
• LIMS Finder
• LIMS Network

If you feel I've missed out a few important ones, feel free to add them in the comment list below.

Joris

Bika LIMS 2.0 Alpha - Open for Evaluation & Testing

Finally, albeit with a bit of delay, we have now opened up Bika LIMS 2.0 for interested parties to trial. Please note (as the title suggests, that is is till an Alpha version, and the functionality is not complete - see Alpha To Do page)

We expect to deploy and subsequently release Bika LIMS 2.0 in either September or early October

If you don't feel like testing it yourself, but want to keep yourself informed, I can suggest subscribing to one of the following mailing lists;

• Bika User (Subscribe - Archive)
  
• Bika Development (Subscribe - Archive)
  

If you want to participate in testing, please request details from Joris (either for access to on-line system or you can also request a Bika package to install it locally).

A LIMS 2 on-line installation can be found at http://bika3.bikalabs.com/bika. These pages will be updated regularly and carry links to the user specification, issue trackers and mailing lists for technical and functional discussion

Related: Complete News Item from BikaLabs.com

1st Post

This will be the new Blog about Bika Lab Systems activities.
Content to come in early August 2007