why.qmd

# Open source: the what and why 

'Open-source' software is software covered by a license that legally allows 
access and inspection of the software's source code. The many varieties of 
open-source licenses determine what you can then do with the software's source 
code, i.e.  copy, modify, contribute or redistribute. Being able to view and 
then do something with source code wasn't always so. The term 'open-source' has 
been in use at least since the 1990's [@Peterson2018] and the principles behind
the term pre-date computer software. Thus, as long as there has been source 
code there have been efforts to make it 'open-source'. 

As computing systems became widely adopted in universities and beyond, the 
value of freely accessing the IT's source code became apparent. This effort 
was described as making software 'free' by Richard Stallman and formalised 
by the creation of the Free Software Foundation in 1985, including the creation 
of a legally enforceable licenses (the GNU Public License) to enshrine source 
code as 'free', that is, having the freedom to access. Although this effort was 
the genesis of today's open-source communities, many people mistakenly 
understood 'free' to mean gratis, which was incorrect: most open-source 
licenses allow the software to be sold for a fee [@OSI]. As is the case, 
even if the main goal of open source is not creating software gratis, it 
so happens that the majority of open-source software is made available at no 
cost.  Regardless of whether it is sold for a fee or not, the term 'open-source' 
is the preferred term by most with respect to software with a license that 
allows access to the source code.

Readers coming from the pharmaceutical industry probably perceive a 
contradiction here: how can software which is typically gratis to use, have any 
intrinsic value to either business or private users? Fair enough: this industry 
depends on capital investment which then depends on retaining the details of 
their drugs and production secret. The difference lies in the utility of (some) 
software, versus, in this example, a drug or therapy. Certain categories of 
software enable the creation of new value. Obvious examples being programming 
languages enabling creation of specialized applications which can support a 
specific business process, e.g. C, Python, R and many others. The ability to 
use and improve these open source languages freely accelerate in multiple 
dimensions the ability to create business value, e.g. specialized smart phone 
apps that offers a service to end-users. Imagine if you have an idea for a smart 
phone app, but before you can write a line of code, you need to buy a license 
to install that language. And after investing the time and money to access this 
language you realise it doesn't work as well as you need for your particular 
app. Or worse yet, it has a bug which renders it unfit for your purpose. 
Little chance you can resolve this quickly. Open-source software does not 
have these restrictions so you can focus all your resources on end-user value,
 not the tools needed for creation. 

Open-sourcing software solutions is also a mindset approach. As you use 
available open-source code, you are using bits and pieces to create a piece 
of software/analytics that is greater than the individual parts. By 
open-sourcing your solution, you give others the opportunity to build on top of 
your work, as well as improve your work itself by contributing. Ultimately, 
this comes back around to yourself: What you have available at your disposal 
is now greater, than if you worked in a silo.

Open-source is also a step towards ensuring reproducibility. Consider an 
analysis done in a propriety language by a pharmaceutical company. An academic 
accessing the same data through a data sharing initiative may find results 
that contradict those done using the propriety tool. Such a researcher would 
not be able reproduce the results nor investigate the source of the 
discrepancy---and in fact any attempt to reproduce results is dependent on 
the for-profit company providing a license to generate that 
insight [@Rodrigues2022]. 

The drugs and therapies manufactured by the pharmaceutical industry are the 
equivalent of a smart phone app: they provide end-user value. It’s sound 
business logic to open source the tools used to create these products: remove 
the restrictions to creating drugs and enable each company to sharpen their 
focus on developing and delivering them.