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.

Why you should never use a spreadsheet in place of project management software

When you work in IT, especially as a systems engineer or manager you end up at some time in your life needing to run a project. If you have and/or if you ever went to college for business or IT management or to get some kind of project management certificate you probably ended up using MS Project. It is a good program, a really complex program. There are both single user and enterprise versions for teams. Unfortunately it is also expensive, Project Standard lists for $599 per license. Not exactly affordable for an NGO organization.

After searching around I noticed there are a bunch of online, web-based project management software as service systems out there. This might be a very good option for a team where you have reliable Internet capabilities but what about the requirement I have, the ability to work on the software no matter if I am working from my US office, here in Africa, or a 30,000 feet somewhere above the Atlantic Ocean?

I spent a lot of time examining the limited offerings that are out there and came up with one, Project Libre ( This product is not associated with the Libre Office group but an independent company that has as its focus an opensource desktop project and a paid web-service product.


So how good is the tool for project management. Well, it is not an exact knock-off of MS Project although it can import MS Project files according to documentation, I have not tried it. To test it I took our Bika.Health Laboratory Information System (LIS) implementation for the Ministry of Health in Liberia and built the project out. I needed to product a gantt chart and figured “well, I might as well build it right.” The interface is similar to Project, there are resources, there are tasks, it is easy to indent the tasks to make subset and milestones. Overall I’d say if you are comfortable with Project, within an hour you will be comfortable with Project Libre. Like MS Project, allocating resources is more art than science and Project Libre seems to follow the strategy of MS Project in much the same way. Interpreting the resource terminology took me a while (hours vs. days, availability, percent utilization) and I am still sure I over allocated half my resources (just like I used to in Project). I miss a simple zoom feature on the Gantt, there is one on the task bar but it is not granular enough. I still haven’t quite got printing a gannt across multiple pages right either but I think that’s more about me than the tool.

If I had to pay for Project Libre I’d give it a B+ as a replacement. If you factor that it costs nothing, then it is of course an ‘A.’ It is light years ahead of using a spreadsheet template simply because of the way it has integrated resources, a critical fail point for way too projects I have seen that mistakenly try to force Excel to be a project management tool.


A year without Windows (almost) – The applications

In our connected world it seems that you can do almost everything you need on a computer with just a browser.  Well, that’s what Google thought when they created their ‘Chrome’ O.S. and hardware vendors followed with a series of ‘Chrome books’ which were basically diskless netbooks.

That works great in a world where no matter where you are there is a connection via WiFi.  In my work in Liberia, well that just doesn’t really work at all.  Whether it is sitting in the cramped economy seat on another 11 hour flight or at the apartment in Monrovia or even our office, there just isn’t always a connection.

Of course Microsoft made their fortune on not only the Windows OS but also on the MS Office suite (which has gone the way of Chrome with connection requirements) and the big three applications that come with MS Office are: Word, Excel, and Power Point (I’ll get to Outlook and Access in another posting).   These application are the defacto norm for business, education, governments, etc.  and so without their equivalent capability Linux is D.O.A.

In 2014 I loaded the Libre Office suite of tools on my little Ubuntu Ace V5.   At first I was a bit confused by the interface, I thought the suite was a clone of MS Office.  No, it was a branch of Open Office and so it inherited the interface.  I am not saying the interface is bad, it was just like the big leap I needed to take from MS Office, which pretty much used the same legacy interface from MS Office 2000, to Office 2013 and now 360.  It was different, not bad.

Example of Calc User Interface

Example of Calc User Interface

Word = Writer

I do a lot of writing, a lot of technical writing and when I used Word I used a lot of the features for constructing a document all the way from outlining to footnotes.  I never used the forms feature but I still managed to create my Masters Thesis in MS Word.   When I was at my work at Saint-Gobain I lead a team and we did a lot of collaborative writing and so markups, change tracking and comments were a big deal.  In 2014, when I started using LibreOffice Writer, there were some challenges including an annoying habit of freezing the PC requiring a hard reboot.  Turns out that was mostly a Ubuntu problem in memory management.  Anyway, the good news is that since 2015 I can say there is nothing I have found lacking in the Writer program.  True, some of the Windows fonts don’t quite match  but that’s true even for the Office version on a Mac, if you are careful it all works out.   Writer uses the open document standard as its norm but just as happily read and write in the XML DOCX format Microsoft uses.  No one will know you are using a free software program!

So, unless you are using some esoteric hidden capability or Word, you can probably do all of your work in Writer and never miss a beat.

Excel = Calc

When I came to work at the Medical School one of the big jobs I had to do was create an accounting system to track expenses by our staff and partners in Liberia.  Another big to-do was creating a payroll system that would allow for complete accountability, be run by people on the ground, and handle the complexities of Liberian Tax Law.  My prior experience with Calc in 2014 left me wondering if it was up to the task of some very quirky and complex V-lookups, and other strange calculations.  By the time I was doing this I was over the user interface issues and so I jumped in with both hands on the keyboard and started.

I can honestly say that I was able to create everything needed within Calc (even some very nice picots for reporting) and also able to save them out in Excel’s native format for exchange with others without an issue.  I still kept everything on my workstation in open document format, mostly because I had been burned by an earlier version of Calc, but never had any issues with exchanging spreadsheets between Excel and Calc.   It just works.  There are a few times still when for some reason the cursor gets lost, that may be due to the dual screens I am using.  Closing the workbook and reopening seems to fix it.

OK – long enough posting – I’ll cover PowerPoint on another posting.



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.


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.

A year without MS Windows? The Operating System

Last year as I began my new job with UMass Medical School, I knew I would need to learn Linux better, much better.   To do anything requires a commitment and a lot of practice and patience.  So, I decided I would not use a Mac or Windows machine for my job.   I also decided to see if I could use only Open Source software to complete my work.  This is important given that my ‘clients’ as it were are the people in Liberia, Africa where seemingly every workstation and laptop I encountered has an unlicensed copy of MS Windows and MS Office and is also infected with every kind of virus and malware.

Well, it will be a year on July 7th and so I think a little review of what has worked, what hasn’t, and how I see moving forward.  I am going to go over my experience with each piece of the puzzle (i.e. operating system, software packages, and even hardware) over the next few postings.  I’ll try not to get too techie, but I am an IT guy after all!

OK – let’s staubunutlogort with the basics.   There are all kinds of ‘flavors’ of Linux.  Linux is the operating system.  It is like MS Windows 8,9,10 etc. or MAC’s OSX.  It is what turns the lifeless piece of hardware that is your laptop into a usable computer.  There are a lot fo ‘flavors’ of Linux and like Mac vs. Windows, people have their favorite.  For me, I just wanted something that was well supported, looked good, supported a lot of hardware and had a lot of Open Source software I could run on it.  So I chose Ubuntu Desktop for my little laptop computer.  ( Ubuntu webpage ).

Take a look at this screenshot of a typical Ubuntu Desktop.  It has a sort of familiar feel to MACs and to Windows as well.  I have found that it is not too foreign and that both Windows and MAC users can get comfortable with most of it pretty quickly.

ubuntudesktopI am still running version 14.04 although a new version is now available.  14.04 seems to be pretty stable.  Early last year I had one or two occasions where the laptop just froze.  Not sure why.  I even had a terrible time when it froze, I rebooted and my desktop disappeared.  That brings me to my first overall observation.

Ubuntu is pretty good but it still requires some investment in learning.  I was panicked when I lost the desktop all the icons were gone).  I managed to recover after a lot of Internet searches but it was still one of those “when did I do my last backup?” moments (answer is daily, plug in the USB drive and it runs the backup without me doing anything).

I’ve since tried several other ‘flavors’ of Linux including some really tiny ones for running on really old laptops and I still prefer Ubuntu.

There are also some interesting discoveries about Ubuntu that I am still learning.  Take the example of remote access from another workstation or making it work in a Windows network with shared drives.  A lot of times I had to drop into ‘terminal mode’ to really make things work better.  That’s a window that only has text interfaces, no graphical information at all.   Interesting to not both Windows and MAC have these modes as well.

SO, my summary – I like Ubuntu.  It keeps getting better and better.  It is easy enough even for a novice who want a simple experience but as always, investing a little time educating yourself is worthwhile.