Bika Lab Blog

Worthy. Laboratory management system for public health laboratories

2010-06-09T10:03:00.000+02:00

You might be aware of the success of me and my colleagues at Bika Lab Systems in building open source laboratory management solutions. Well not quite financially, but in the project's popularity, glory, feel-good and reach. Our software has been downloaded a whopping 30 000 times, near 10 000 in the last year

One tragic omission remains, a branch of the system for public health laboratories active in the prevention and treatment of HIV, Malaria, TB and curable cervical cancer amongst others

Because of health ministry and big sponsorship involvement, this sector is awash with hot air, inertia and totally f*cked up agendas, never mind suffering people. Commercial systems for hospitals cost millions

IMHO, not that of Bika Lab Systems or Health Foundation which would be a bit more civilised I guess

We need R750k ($100k) to customise Bika's robust water quality system and make it available as Bika Health for public download. We received a 50% grant to this effect from DTI's Innovation fund and we are sure to make up the rest from commercial sponsorship or community contributions - in May we had a Bika enthusiast at a big commercial lab contribute a fully developed SQL database back-end, worth thousands...

The need is urgent and we are now rushing up an alpha version to present to further prospects and make available on-line for review. The Alpha, version 0.3, will cost us approximately R75k, translating neatly to $10 000. We kicked non-profit fund raising and distribution vehicle, The Bika Health Foundation, est. 2008, into gear to collect this and pledged $5000 of work for free

We are trying to raise the residual $5000 via micro pledges with one of the web tools designed to this purpose, Chip in. Please see the widget at www.bikalabs.org, home of the Bika LIMS open source community

And please contribute should you have the odd $10 bill floating around in cyber space - the widget uses PayPal mainly but allows for credit cards. In which case you'll be provided with a PayPal account if you don't have one - a little irritating, please blame the local banking cartel. The account will however save you on-line banking costs in the long run, PayPal will be represented in ZA by FNB locally soon

I tested with $25 and it seems to work. Please chip in! And forward this e-mail to prospects in your network. The campaign kicks off in all earnest next week

We do get receipts and I'll be listing contributions - if agreed to by the contributor - linked to your nominated site for some Google brownies, Bika is nogal heavily weighted

More about this campaign and The Bika Health Foundation

Where's the catch? For one I am intrigued by this kind of social experiment - note that Diaspora, a Facebook like project but with principles and superior architecture, appealed for $10 000 in a similar campaign and was sitting at $120 000 barely a week later... Secondly, when Bika Health takes off, i might get to see some more of the exotic developing world, Africa, South East Asia, the Caribbean and Latin America where the need is biggest. Doing so from 3rd world hospitals will keep me sober i am sure

Bika Mail 9. Born free. Open-source software in the recession

2010-06-09T10:02:00.002+02:00

Latest newsletter released, for full details:
http://www.bikalabs.com/article/bikamail/9bornfree/view

Bika Health pilot in Suriname

2009-11-03T15:32:00.000+02:00

A project to pilot Bika Health 0.2 interfaced to OpenERP and EMR Medical on a project at the University Hospital in Paramaribo, Suriname has been started

From a post by Chris Larsen at the Bika OS Health LIMS discussion group

Due to a series of fortunate circumstances, we have been able to close ranks with the Bika group, as well as the OpenERP/Medical developers in order to launch both applications in the course of a pilot project with the Academisch Ziekenhuis (University Hospital) in Paramaribo, Suriname
As the above programs are Python-based, we even hope to make them talk to each other, which would provide an important step towards a reasonably holistic framework for health facilities
This holds even more true, as the OpenERP backbone of Medical offers great potential to facilitate everyday health facility management

A test platform is nearing completion. Interfacing the laboratory instruments will be the only major customisation to Bika Health required for the pilot. Functional and design discussion continues at the Health group
The interface to OpenMRS completed earlier will be complemented with interfaces to Medical and OpenERP, open source medical and enterprise record keeping and management systems respectively
The Bika developer team thanks all the participants, Health group members, Medical, the Academisch Ziekenhuis and Chris for glueing the project together, it is difficult to contain our excitement
Project Concept Paper: Piloting Bika, OpenERP and Medical with the Academisch Ziekenhuis in Paramaribo (Suriname)

(as posted on Bika Lab Systems)

Bika LIMS 2.2.1 Released

2009-10-13T12:52:00.000+02:00

Although the full announcement with Press Release, updated demo, updated project pages on www.bikalabs.com are still wip, here already a quick mention that the files are already available for download from SF.net:

Bika Package; download this if you want to upgrade you LIMS and already have all dependent products.
Bika Product Bundle; download this if you don't have the dependent products, all are included in the bundle.
Browse all available files and archive types

Here the installation instructions. User Manual is also wip, but most of it is already covered in the Bika LIMS 2 manual.If you want to set-up the Bika Calendar, this manual might also come in handy.
For any discussions about the system;Bika User list (archive) for all installation issues, as well as the Developer's List (archive) and the Bika OS LIMS Analysis & Design List (archive)

So What's New?

Bika LIMS 2.2.0 Changes:

Attachments permitted on analysis requests and analyses
Worksheet resequencing, and sort order for worksheet analysis selection
Worksheet deletion only available for open worksheets
Portlet to provide export of analysis services and analysis profiles
Requirement for unique analysis service names, analysis service keywords, instrument import keywords and analysis profile keywords enforced.
Report headings and formats standardized across different reports
Analysis Request import alternative layout provided with selection, including profiles
Progress bar introduced for long running processes
Updated interface with Softline Pastel (South African Accounting package)

Bika LIMS 2.2.1 Changes (minor update):

StandardSampleUID was omitted from the StandardAnalysis object

The Truth Behind the Hype Behind Softare-as-a-Service (SaaS) LIMS - Part One

2009-09-09T10:57:00.005+02:00

I was planning to only post monthly updates of interesting articles we come across and publish within our reads folder, but after reading this article from LIMSletter, I just couldn't wait.

The whole article is a worthwhile read, but the highlights for me are the following snippets :

“According to industry research, 31.1% of software projects are cancelled before they are completed. Of those software projects which have been completed, over half (52.7%) have taken twice as long or have cost twice as much as originally expected. When on-premise software applications are fully deployed, the maintenance and management costs can be ten times the original license fee.”(1) Indeed, the failure rate of commercial LIMS solutions is commonly estimated to be as high as 60% by industry analysts such as Strategic Directions and ArcWeb."

“More than 80% of scientific labs do not use a professional LIMS. Not because they don’t want to, but because implementing a LIMS has been too difficult, time consuming, and costly. That ‘perfect storm’ of daunting factors includes commercial-off-the-shelf LIMS as well as home-grown solutions.” Instead, according to Kent, most labs still rely on informal systems, such as paper-based notebooks, Excel spreadsheets, or tracking systems cobbled together using tools such as Microsoft Access or FileMaker Pro"

"One LIMS vendor has stated that “the main difference between a subscription-hosted LIMS and a direct purchase ‘on-site LIMS’ is the initial cost and total cost of ownership (TCO)”.This is not the full story. The most critical difference lies not in how it is priced, but in the underlying code and how the SaaS LIMS was developed."

"In order for a SaaS LIMS to succeed, not only must the SaaS vendor invest in a comprehensive SDP, but they must also ensure the implementation of security technologies and certification programs that govern data center operations and personnel. These certification programs can include SAS 70, ISO standards, HIPAA, Sarbanes-Oxley, etc. The Statement on Auditing Standards (SAS) No. 70, for instance, is the authoritative auditing standard that judges a service organization’s controls and safeguards over their information technology and related processes. It is important that the SaaS LIMS vendor be able to produce SAS 70 service auditor reports which validate that the service offering conforms to the guidance requirements and thus delivers a secure service."

"Fortunately, if the service does not meet the lab’s needs, it can be cancelled. The burden of success rests not with the customer but with the SaaS vendor to deliver reliable, scalable, secure services. This enables the laboratory to focus on the attributes of the SaaS solution and determine how well those features and functions meet the lab’s needs, and not on implementation, management and support."

This resonated strongly with us at Bika Lab Systems, as we have been offering SaaS since inception, as our LIMS has always been web-based rather than web-enabled. And we offer it for all our products; Bika LIMS, Bika Interlab, Bika Wine, Bika CMS and soon Bika Water.

This article has also been published in our Reads folder, which is RSS enabled.
More about Bika Lab Systems' SaaS offerings.

Open Source & Open Source LIMS related articles

2009-09-01T11:32:00.005+02:00

Open Source, it's companies and their place in the larger software ecosystem has recently gotten attention again through a couple of interesting write ups.

At Bika Lab Systems, when we come across interesting articles we post them in our Reads folder, for which we now have also enabled an RSS feed, so you can easily stay up to date with latest postings. The articles we added in August where;

But I also wanted to mention the article 'Open Source.... not a Hippi, Commie Moveme nt' by John H. Jones, of LabLynx, where apart from linking to our website, he also says that Bika Lab Systems is one of the 'very successful companies that are based upon the Commercial Open Source business model and they provide software that your lab needs' but also 'Right now we only have 2 real commercial open source LIMS vendors and I hope more will follow.'

I don't mind such a plug at all!-)

Professional Open Source at Work

2009-08-14T14:00:00.000+02:00

To see a good example of how the Professional Open Source business model works, you should have a look at our User List, Bika-Users (register - view archives).

Take the post with subject 'File Attachments', which was initiated by Dr. Michael Kirchner (Institute of Inorganic Chemistry from the University of Duisberg-Essen, Germany) on May the 11th, with the question:

"The most important feature is to be able to attach files (raw data, crystal information files, images) as the results of a measurement. Is this possible with bika?"

This was recognised by Bika LIMS user Chris Bolton (CEO of Benchmark Laboratories Group, Canada), who replied:

"...in our case a number of our clients are now requesting that we
attach copies of our chromatograph reports (images of chemical
signatures) produced from our gas chromatographs (GC's)"

The discussion kicked off which led to a distilled specification over three months of various inputs. The final spec, which was project managed by Lemoene Smit, was as follows:

Set-up
---------

To maintain flexibility and redundancy, attachments are allowed on both
AR and Analysis level and this is configured in the LIMS setup:

Global flag in 'Laboratory information' to indicate attachments per
AR yes/no

A similar flag per 'Analysis Service' to indicate attachments per
Analysis yes/no

In both cases:

Compulsory Y?N

Set-up table of Attachment types

Title

Description

Set-up per Client Contact
-----------------------------------

For the user to decide whether to include attachments with emailed
results or links only (default)

Radio button on the contact's publication preferences

At run time, on each AR or Analysis as configured earlier, Upload
----------------------------------------------------------------------------------------

Manage results tab

Functionality to multi load attachments from the file system via
standard *nix/Mac/Windows file browsing

Add Keywords

For ARs only

Remarks field – drop down to select Attachment title and description

It'll be quite difficult to fit all of these in per analysis

NB. Workflow dependency: ARs/Analyses without compulsory attachments
cannot proceed to to_be_verified

View and download attachment
------------------------------------------

None of the attachments will be shown in views or results emails
directly, but hyper linked only to where they are kept inside the database

File sizes are displayed to warn users of the size of the download

Clicking the link will open the attachment using the user's standard
browser preferences

AR attachments only: For display / email / print functionality these
files listed at the top of the AR window

Printed reports
--------------------
Each attachment referenced by

Title

File name

URL

Upload date

Search and Queries
----------------------------

Users finds Attachments using

file name

title

file type

Chris then sponsored this development, which was managed by Anneline Sweetnam, development manager of Bika Lab Systems, on the main trunk of Bika LIMS.

This development has been finalised and is now available on a test instance to be evaluated and signed off. If you're interested send me an email, and I'll supply you with access details

This and several other developments will be released in a major upgrade of Bika LIMS 2.2 in the next quarter.

Did you miss the announcement of the small Bika LIMS 2.1.1 release and the upgrade demo?

Here is the news item that carried the announcement, and here the list of changes in 2.1.1.
You can request a demo by sending an email to demorequest@bikalabs.com and mention that you would like to try Bika LIMS.

Nominate Bika LIMS for the SF.net 2009 Community Awards

2009-05-14T10:46:00.003+02:00

Bika LIMS @ Sourceforge.net is vying for the 2009 Community Choice Awards

Nominate Bika for:

Bika open source LIS/LIMS for Best Project

Bika open source LIS/LIMS for Best Project for Academia

Bika Health @ Global LIS Conference in Hanoi, Vietnam

2008-09-29T10:46:00.004+02:00

Bika Health and it's newly formed foundation were represented in the Global LIS Conference held in Hanoi, Vietnam from the 23rd to the 26th of September, by Lemoene Smit, Project Manager and CEO of Bika Lab Systems and Director of the Bika Health Foundation.

More info and a copy of the delivered presentation will be posted in the next week or so on Bikalabs.com, but here already a shot of our stand.

By all accounts, it was a great success!

Easy Setup file for Bika 2.1 Inkosi on Windows XP & Vista

2008-07-16T11:55:00.000+02:00

I want to make everybody out there aware who wants to try Bika LIMS 2.1 'Inkosi' on their Windows XP or Windows Vista machine, that there is now an easy install file (executable) for Bika LIMS, the only pre-requisite is to have Plone 2.5.5 installed. The executable was created by our partners at the University of Costa Rica, to which we, at Bika Lab Systems, owe many thanks!

Here the original mail and link copied in (originally posted on the Bika Developer Mailing List):

Recently we made an executable file that installs Bika LIMS 2.1 Inkosi directly in Windows XP (and Windows Vista) without having to change anything to have it running. The only requirement is that Plone 2 has to be installed in 'C:/Program Files/Plone 2/', but maybe later we can make an installation file that checks the plone 2 path and install bika according to it. In the meanwhile here is this file, maybe it can be helpful to someone, greetings.
Bika LIMS 2.1 Inkosi Setup
--
Andrés Oreamuno.
Centro de Investigación en Contaminación Ambiental
Universidad de Costa Rica

This news and the file will soon also appear on our website

Installation Notes:
Once you've run the set-up programme, you need to run the IDServer and Zope. Go to Zope Management Interface and add a new Plone Site, with Extension Profile 'bika'. And you should be up and running!

Release Time for Bika LIMS 2.1 & Bika Calendar 1.0

2008-05-30T11:00:00.000+02:00

Yes, we're finally there. It's release time.

We have released two new products early this week;
Bika LIMS 2.1 'Inkosi'; the latest and much improved version of our generic Laboratory Information Management System solution.
Bika Calendar 1.0; A stand-alone Plone product, that we use as an add-on to Bika LIMS to create a true working hours calendar.

Here links to Downloads and Project Pages;

You might also see us appear in various on-line media, as on the following project websites; Plone.org (LIMS, Calendar), Freshmeat.net (LIMS) and Sourceforge.net and of course on Bikalabs.com

Here also the official Press Release (which will be released early next week):

Web-based laboratory information management · Bika LIMS 2.1 Inkosi open source release
Bika LIMS 2.1 Inkosi 'The Chief' is the next major public release of the professionally supported open source LIMS by Cape Town company Bika Lab Systems and was released 26 May 2008 on a general public license, free to download, install and use.
Popular first release of Bika - pronounced bheeka and meaning 'to report' in isiZulu - has been downloaded more than 12 500 times world wide and established Bika as leading open source LIMS.
Feature rich LIMS 2 promises to become true Inkosi to the global Bika community of users and developers. It is now in production locally and being piloted in Canada, Nigeria and Costa Rica.
Also in May, Bika hosted a fellow from CICA with the aim of further customisation and implementations in pesticide residue laboratories in Latin America. The scientific exchange was sponsored by the IAEA. A Spanish translation is nearing completion

Automation
Bika Inkosi offers a host of functional enhancements, a well developed quality control suite and more automation to further improve turnaround times and eliminate human error
Regularly requested analysis sets, analysis profiles, can now be ordered with the minimum of clicks and in bulk through import files
In the lab itself, once-off worksheet template creation circumvents laborious manual work sheet management. The templates include place holders for control and duplicate samples and can be configured to closely resemble instrument trays
Upon using a template, Inkosi populates worksheets with analyses closest to their due dates but these can be manually adjusted to requirement, before exporting them to instruments and recovering results without having to manually enter any data
Results proceed through the standard Bika web based workflow - validated against client and product specific specifications, verification and publication in the client's preferred media: email, fax, digitally signed print, SMS and export file
The process is assisted by a system of alerts, prompting role players of pending tasks. A true time calendar, taking non working hours into account, makes for accurate alerts and efficiency reports. Results remain securely archived on-line, accessible via a powerful Google-like live search engine

Quality Control
Bika LIMS 1 is successfully used in ISO 17025 accredited labs and Inkosi builds on this heritage with granular audit trails of samples, analyses, analysis requests, worksheets, orders, invoices, and web content edits, ensuring total traceability. Analysis and work sheet re-testing work flows are incorporated and logged
Quality Control measures include the maintenance of standards, stocks and suppliers, the use of blanks and duplicate samples, instrument calibrations and graphical reporting on trends, distribution curves, relative % error and inter-laboratory proficiency schemes

CMS - Web portal content management
Bika remains one of the few web based LIMS not held back by web enabled legacy design, but developed in the cutting edge and robust web server technologies the Internet originated on. Inkosi LIMS front end can be built up to provide valuable services to clients and staff as well as marketing material to prospects and anonymous visitors
Knowledge centres and news letter tools are just two products that easily integrate with the LIMS and literally hundreds more exist, developed in the community supporting Plone, the open source CMS Inkosi is built on

POS - the professional open source model adopted by Bika
There is much media coverage about open source software models but these are often misunderstood and its potential underestimated. POS combines traditional OSS projects run by a community of software enthusiasts with a professional company, Bika Lab Systems in the case of Inkosi. The community adds strong support and world wide adoption of the software, while Bika Lab Systems backs the project with full-time engineering staff and formal contracts sponsored by fee-paying customers
Customers benefit from the increased quality of the software and design, and increased traction enabled by the product's community. Customers, partners, engineers, and open source communities are all self-motivated in ways that are beneficial to themselves and, as a side effect, to all

Future plans
Bika LIMS development is driven by client and community requirements, and if feedback from the current round of pilot projects bears fruit, complete instrument maintenance, batching, sample storage management and change request modules will be developed for release 4th quarter 2008. These will once more be best of breed designs discussed and improved in the Bika community forums. Ubuntu!

For more information please visit www.bikalabs.com. All enquiries welcome, info@bikalabs.com

For the Friday

2008-03-07T10:59:00.003+02:00

Today I wanted to share an excellent presentation on the web.

It's called "The Brand Gap - How to bridge the distance between Business Strategy and Design", although it is not about open source, or even about software specifically. I found it very stimulating from a pure marketing point of view. Enjoy!

| View | Upload your own

SaaS and further news on LIMS 2.0 'Inkosi' Training Material

2008-02-15T09:43:00.011+02:00

SaaS:

As you probably know, Bika Lab Systems, has been offering hosted Bika LIMS, Wine & Interlab solutions since its inception, initially we used to call it 'hosted LIMS', then changed it to 'ASP' (Application Service Provision) as it was called at the time, but since last year the term SaaS (Software-as-a-Service) seems to have become the new buzzword.

What does SaaS mean?

Wikipedia puts it rather well:
Software as a service (SaaS) is a software application delivery model where a software vendor develops a web-native software application and hosts and operates (either independently or through a third-party) the application for use by its customers over the Internet. Customers do not pay for owning the software itself but rather for using it. They use it through an API accessible over the Web and often written using Web Services or REST. The term SaaS has become the industry preferred term, generally replacing the earlier terms Application Service Provider (ASP) and On-Demand.' (link to original wikipedia article)

In simple terms, it means that our web-based LIMS, is hosted from our servers (currently only based in Cape Town, South Africa, but soon in a city near you), where we offer all support services, first line support to the clients' users, technical support on the system and hardware, relieving the client of any investment in IT know-how which normally would be associated with a LIMS acquisition. You pay a set-up fee, monthly rental and a per usage fee.

What SaaS solutions are we currently offering?

- Bika LIMS 1.2 (or Bika Wine, for the beverages industry)
- Bika LIMS 2.0 (still for evaluation and assessment purposes, until we release a production ready version)
- Bika Interlab 1.2
If you are interested, and would like to know more about our pricing, drop me an email

We do not only offer SaaS, but also use open source web-based solutions on our own server, many of which are available as SaaS on the Web. I use SugarCRM for my sales and marketing initiatives, Lemoene uses dotProject for as his project management tool and is currently evaluating Projity Openproj. We tried out Trac, but have reverted to Roundup as issue tracker for our commercial clients, and of course use our Plone website as a central CMS & document repository. As you can see we practice what we preach!

If you are interested further in sales and marketing related discussions about SaaS and its trends, I can highly recommend the following Blog; SaaStream

LIMS 2.0 'Inkosi' Related

Training Material:
Manual: We already started working on the new LIMS 2.0 manual, although still w.i.p. (which it will be until final release), you can find it here
Training Videos: We have started this week with writing up the various story boards and plan to start production (of the stable parts of the system next week), and will populate in our HelpCenter, a new LIMS 2 Video section.

Software:
Demo: The LIMS 2 demo is continually updated, current version is 2.0.18, and next week we are going to upgrade it with QC reports and graphs.
Alpha evaluation release: Although not officially released, if you're interested I can send you the latest Bika LIMS 2.0 and Bika Calendar 1.0 packages, if you want to test it locally on your own server. Send me an email if you're keen.

Happy New Year!

2008-01-30T12:30:00.000+02:00

To start with, very belated best compliments of the season. Although I was planning to spend more attention over the holidays on this blog and other secondary marketing efforts, the new year started very quickly, on the 1st of January with setting up an evaluation system of LIMS 2.0 for a Canadian client. This will mean that when we release LIMS 2.0 or soon thereafter we will have substantial functionality to cater specifically for the North American markets. More about this in our next Bika Mail newsletter.

Looking for Python / Zope / Plone developers
Although we're hardly a month into the new year, business is going very well. We have a variety of projects on the go, and they are all in need to varying degrees of development. So if you're reading this and would like to work for a Professional Open Source company, you have expert skills in Python, Plone & Zope, can work autonomously, and like project based work; drop me an email.

New Laptop: HP 530
Due to an astray half-full glass of wine landing on my laptop, I ended up buying a new one, as the repairs I was quoted for came close to a new laptop anyway. After some research and looking for a budget priced laptop I found the HP 530, I got the dual-core version 1.8 Ghz with 2 Gb of RAM. It's a decent machine and have little to complain about the hardware....but on the software side I was perplexed. To start with when having made up my mind about buying a new laptop, I went straight to the Dell site and hoped to be able score a laptop with pre-installed Ubuntu. Well, they're not available (I hope: yet), which disappointed me considerably. So it's all talk and no action then!
When contacting various re-sellers in South Africa, I asked what discount I would get if they gave me the laptop without any MS software on it (be it XP, Vista or Office), and to my complete shock, they told me that they were not allowed to sell the laptop without MS Windows on it. And of course that meant no discount. But also no freedom of choice for the consumer. Maybe this is something the European competition court should be looking into ;-)
So, in the end I got it delivered within 48 hours, and thought what the heck, I want to see how Vista (basic) looks and feels like. The next disappointments were; after starting up the laptop it took more then 2 hours to install Vista, if you set yourself up as admin, you want to be an admin and not have irritating warnings that your are performing admin tasks continually, and the whole MS bundle (Vista + office) hogged an unbelievable 30 GB on my drive!!
So I went for a dual boot set-up with Ubuntu Gutsy 7.10. Installation of Gutsy took exactly 35 minutes. Now that's a proper OS! I also have full support for Compiz-Beryl, and although not enhancing productivity it is quite smooth and a good laugh (especially shaking windows ;-).
I messed the partitions options up a bit, so I went to try GParted, and I must say it's an unbelievably easy tool to use, works flawlessly and allows you to resize partitions to your heart's content.

New: Bika LIMS 2.0 Alpha testing updates
In order to keep various interested parties updated with development releases and updates to our LIMS 2.0 Alpha Demo, I am going to post a small news item on the Bikalabs.com website, starting this week with the first.

That's it for the first post of 2008, more exciting news coming in the weeks and months ahead. Stay tuned!

Why LIMS? & New Bika Health Mailing List

2007-11-30T10:45:00.000+02:00

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?

2007-11-23T10:30:00.000+02:00

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?

2007-11-21T09:30:00.000+02:00

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

2007-11-20T11:00:00.000+02:00

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)

2007-10-30T10:13:00.000+02:00

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

2007-10-24T09:30:00.000+02:00

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

2007-10-20T08:31:00.000+02:00

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

2007-10-19T14:30:00.000+02:00

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

2007-10-18T08:45:00.000+02:00

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

2007-10-10T10:08:00.000+02:00

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:

Plone Product pages:

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.

2007-10-10T10:00:00.000+02:00

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:

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

2007-08-14T11:42:00.000+02:00

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

2007-07-19T13:14:00.000+02:00

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