Category Archives: Liberia

Open Source vs. Free

I am working with a group of developers who have built a Laboratory Information Management System (LIMS) based on the Open Source principle.  I spent a lot of time researching the availability of inexpensive, flexible LIMS that we might deploy as part of the project in Liberia.  There were about 30 variants of Open Source LIMS and about half that many commercial versions including some SAAS.

Recently there’s been a blog that was brought to my attention about the ‘cost’ of an Open Source solution.  The blog was focused on LIMS and so it was worth reading.  The author came to a similar conclusion that I did about open source LIMS in general, in that there have been very few successes.  Of the 30 or so I looked at most had been abandoned after the grad student left the institution where they worked or the organization’s funding stream evaporated or the single author decided to pull the plug and abandon the effort.  There are a few that continue including the one I selected for our project in Liberia, Bika.Lims and Bika.Health.   I’ll cover that selection process in some other posting.

What I wanted to focus on here was the disconnect between ‘free software’ and an ‘open source based solution’ which I think the blog author missed.  The blog author’s point was that the bulk of the cost of a system implementation of something as complex as a LIMS isn’t in the cost of the software but rather in the cost of implementation.  In general, the author got that part correct.  Implementation of any system involves a lot of challenges, a lot of people, and a lot of costs.   The actual cost of the software license for a piece of commercial software may be a fraction of the overall cost of implementation when you factor all the labor for training, physical implementation, support networks, etc., etc.  The point is well taken but may miss one of the really important issues around Open Source, namely flexibility.

Let’s take the work I am doing in Liberia right now.  We have very difficult circumstances for our deployment.  We have a very tight budget, difficult environment (poor power, lack of internet, no air conditioning, low computer literacy rates, etc., etc….), lack of continuation funding, and a challenging model to try to fit the LIMS into.  Liberia is recovering from two civil wars and the horrendous Ebola outbreak.  The outbreak exposed the poor health care system within the country and was a wake-up call to the rest of the world at what a risk that puts everyone in.

The LIMS that was needed had to be able to operate in this environment.  It also had to be tailor-able, it had to be able to be adapted to the specific needs of the health care system of Liberia. Most importantly, it had to be sustainable.  When I evaluated commercial applications for LIMS what I found were very sophisticated systems, a fairly high startup cost, a high annual support cost, and an inflexible system.   Given that both an ‘Open Source’ and a ‘Commercial Licensed’ software package would have the same implementation costs (i.e. the training, etc. I mentioned earlier), the cost associated with licensing and annual updates/support was a significant factor in my decision making.  Why?  Because I knew we had to customize the software to make it fit for Liberia.  Even if the commercial system vendor would agree to do the customization, that cost would be above the cost of licensing.   What if instead, I could take those costs for software (LIMS, database, operating systems, etc.) and instead apply that budget line item to customization?   To go even further, what if instead of paying licensing fees I instead took some of that money to train local Liberian’s on how to customize the LIMS and become contributors to the Open Source project itself?

In fact that is what we are doing.  We selected the Open Source Bika.Health platform not just for its functionality, its zero cost for licensing, and its developer network but also because it is Open Source, meaning it is growing and accepts contributions to the software from developers around the world trying to solve problems.  Additionally being Open Source meant we were allowed, actually encouraged to experiment with the software, with the platform it runs on, with pretty much everything to make it work for Liberia.

Yes, we are incurring some additional costs in developing our own implementation for Liberia.  Yes, we do not have a corporation behind the software development adding new features (which we probably won’t use in Liberia anyway) and yes we have to think about support but we have to think about support anyway as the funding for running the LIMS is based on a grant and that grant will expire.  So focusing on that eventuality it became clear that if we can train Liberian staff to support and grow the system, to adapt and contribute to the project, then they may even become the regional experts on the project in West Africa and support others in implementation.

Yes, implementing a software system is not inexpensive, easy, or free and so you must be careful of what your actual objectives are.  Are they to deploy and run?  Are they to provide a quick win and then leave them in the lurch or are they to provide a tailored system that fits the current needs and the capabilities to grow that system themselves in the future.  If that’s the objective, then an Open Source solution might be exactly what is needed.

A Year without Windows – the hardware

When you sit in an office in Liberia working, you are faced with a multitude of problems, poor power, little or no air conditioning, bad Internet (think 3G… as long as it is not raining and when it rains, there’s no connection), and hot sticky weather mixed with salt-laden air in the capital city of Monrovia.   Perfect setup for IT equipment?

I learned a lesson from the install at the medical school, equipment corrodes here very quickly.  I also learned not to get too attached to your personal workstation.  Two of my coworkers had very expensive MAC’s stolen out of their bedrooms in a guarded apartment while they were sleeping.   One of the thefts was done by a guard.

The last thing I think about is what kind of image I want to portray.  If I show up with a $2,000 laptop what does that mean to the people I am here to help?   Does a $2,000 laptop really get my email any faster?  Do I do some kind of exotic work with super powerful software requiring hyperspeed processing?  The answer is almost always no.  So what kind of equipment do I carry (and it has to run Ubuntu really well).

I ended up picking a low end Acer Aspire V5 – it cost me $259 new.  It’s small, light, uses little power and has a pretty good processor.  What I did next was to ‘enhance’ it a bit.  I replaced the harddrive with a 500GB SSD and upgraded the ram to 16gb.

acerv5

I decided to leave the WIndow OS on its own partition in case I needed to run Windows (now running Windows 10) and loaded Ubuntu 14.04 LTS.  I added a small external shell to the unit as a bit of protection plus it provides a little bit more venting when on my lap.  It also helped it survived several dops by the TSA when checking through various airports.

The Acer will run for about 8 – 10 hours on battery which is really plenty.  The power supply is pretty small and lightweight and has the added bonus of interchangable plugs so you can go from US to Euro without a separate adapter.  The WiFi chip appears to pickup and hold signals as good as anything else I have ever used.

My total investment on this unit was: $259 + SSD ($139) + ram ($69) = $467.  So I could buy three more of these and give them away to my co-workers in Liberia for the price of one high end laptop.   Yes, it has a small screen but I find that easier than a big screen to handle in a cramped economy class seat flying across the Atlantic for 10 hours.  As for power to run applications, once i replaced the hard drive and added memory, I am able to run everything including VM instances so I can test new software.

The day when Rick and WPI grad student Chris go to the US Embassy

bead retriever

Bead Retriever

That picture is of a working Thermo Fisher Scientific ‘Bead Retriever’ running in a lab.  Our lab in Tappita had two of these at a cost of $18,000 each.  They cut by 2/3’s the amount if time it takes to prepare samples for analysis.  With the unit running we could run maybe 60 samples (as in potential Ebola patient samples) a day.  Without, 20.   Trouble was, both units stopped working so they were sent back to the CDC at the US Embassy here.  It might be three to five weeks to get replacements.  So Chris and I offered to take a look.  We called Thermo Fisher and got a tentative nod, unfortunately tech support was not available.  Working off each other (ok, we got a little loud so they put us in our own room) for about 2 hours (did I mention that Chris is a robotics expert? Handy to have when working on a robotic system like this) we had one of the moments.  We had the little units apart and were taking it apart piece by piece when we said, “what if that little motor was supposed to have that screw running through it?”   Another 20 minutes and when we pressed ‘start’ we got the message indicating it was ready to run the samples (we actually did not have any samples).   We did the same thing on the other unit, same result.  Next step… Tuesday the lab guys (the ones that know how to use this thing) will do a dry run with fake samples to see if we really fixed.   Just goes to show you what two engineers with a screwdriver and a Leatherman can do.

It all starts tomorrow

Tomorrow morning, I won’t be driving to UMass Medical School and dropping off Julie, instead I’ll be getting out of the car and going to my new office in the Office of Global Health.  Tomorrow I begin the task of bringing innovative, sustainable information technology to the ACCEL project in Liberia!   I am excited for this opportunity to work towards strengthening the health services inside Liberia as part of the great team that has been brought together by UMass.

You can read more about the ACCEL program here ACCEL Global Health website  and you can also follow the work of the Medical School as WE continue to build the health care capabilities in Liberia at the UMass Global Health site.  UMass Medical School, office of Global Health   of course you can also follow Julie and I here on this blog as we return to Liberia this summer!

A time for cautious celebration

Good news arrived at the end of last week.  Liberia was declared Ebola free by the WHO (WHO – The Ebola Epidemic is over in Liberia) .   I am thinking about all those that made this possible, all the health care workers that risked their lives, some losing their lives to the disease.  All the Liberians who came forward to help, again putting themselves at risk.  To the churches for spreading the word throughout the country.

And now, we need to roll up our sleeves and repair the damages and rebuild the health care organizations throughout the country.  I am pleased to still be working with the University of Massachusetts Medical school on their continuing efforts there.  I’ll post new updates about the renewed efforts soon.