The Julia programming language

So, I’ve started a new playlist on my YouTube® channel called The Julia Computer Language.  For now, lessons 1 and 2 are up and as (limited) time allows, I’ll add some more.

Julia is a rather new programming language for technical or scientific computing.  You will find out a lot more about it on the Julia homepage.  Unfortunately, there is not a lot of tutorials on Julia out there and if you do find them, most are by computer scientist for computer scientists.  Perhaps rightly so, as Julia is a fantastic tool, capable of some pretty impressive things when it comes to scientific computing.  It prides itself on being as simple and easy to use as Python, with speeds approaching that of C or Fortran.  It is indeed much speedier than other mathematical languages such as Matlab® and Mathematica®.

On top of this, I believe that it makes for an excellent language for a novice starting off, learning how to code.  This is especially true for those who plan to go into the fields of science and technology.  Even if you move on to other languages, Julia will stand you in good stead.  It might spoil you, though, which means you’ll come running straight back to it.

I do stick to IPython for my medical statistics, but Julia works perfectly here too.  I’ve made a lecture on the topic, which you can view here.

Go on, give Julia a spin.  There is just something about it that speaks to me.  A certain elegance and power.  Well done to the brilliant minds that came up with it and to all those who are continuing its development.

You can write Julia code in the cloud using JuliaBox, so no need to install anything at all.  At this time, I am having tremendous problems getting it (IJulia) to run in Jupyter, so much so that I am using the very nice Juno development environment.  In upcoming lessons I will look at installing Julia, Jupyter, and Juno, but for now, you can follow along without any downloads or installs.  Just use JuliaBox and your Google® account to sign in.  The notebook files that I use are in a zip file on this page.

Review of research paper on medical education

A brief report was publish in the Canadian Medical Education Journal titled Re-thinking clinical research training in residency. The authors were struggling with the same questions we have in our department. Perhaps the two most important points relate to the need for specialists to critically appraise research and to fulfil accreditation requirements.
In medicine we have well and truly departed from the era of eminence-based medicine. It is of utmost importance for specialist to be able to evaluate research evidence to inform their practice. This requirement extends well beyond simply browsing the introduction and conclusion sections in abstracts.
Furthermore, it has become necessary for postgraduate trainees in South Africa to complete a mini-dissertation towards a Masters degree in order to qualify to sit the final Colleges of Medicine exams.
The authors then asks three questions. Firstly, is mandating original research the answer? Secondly, what ought to be the central purpose of research training? Lastly, what are the alternatives to original clinical research? They quite correctly point out that there is much more to the development of a clinician-scientist than research training and bring up the necessity to focus trainee research on local patient needs as opposed the emphasis on conducting original research.
The main section of the paper attempts to answer the three question mentioned above. I’ll leave you to read the authors’ response to their first question, most of the suggested programs in aid of producing clinician-scientists are not available in this country.
On the question of the central purpose of research training, the authors focus on the (in my opinion) commendable CANMEDS initiative of placing the patient at the centre of medical education. It might be true that there exists tremendous personal fulfilment in a career in medicine, but by its nature, it is a pursuit aimed at helping patients and not a pursuit of personal gain. As in the South African academic setting, education takes place in institutions that are publicly funded and the authors express the opinion that time, effort, and resources in research education be spent on producing work aimed squarely at direct benefit to the local patient population, as opposed to original research.
As to the alternatives to original clinical research the authors once again explore pathways which they feel might benefit the patient more. They argue for the formation of teams by PhD-trained researches and feel that trainees are in a much better position to come up with relevant clinical questions which should lead to projects managed by these teams. They feel that trainees could learn much more about research in such groups.
Lastly, they raise the important issue of time available for research during training. Their situation certainly mimics our constrained environment, where it is almost impossible to release trainees for sustained periods during which they do not provide service delivery.
Certainly some food for though. Alas, it is my humble opinion that the Canadian Medical Education System, through CANMEDS, far exceeds our local effort. At this time, our dire need lies in establishing proper education in conducting research and statistical analysis. No formal education exists in this regard.

Irritating problems in medical education

This is a bird’s eye view of the most irritating problems in my opinion.  There are certainly much bigger and important issues, but these just get me down!

They are nothing new, but the more they are mentioned, the better.  My biggest peeve?  The use of PowerPoint® or other presentations.

Now, I have nothing against PowerPoint® or Keynote®, or Prezi®, or any of these presentation tools. They are all fantastic pieces of modern software and serve a definite purpose. What really gets me down, though, is how they continue to be the standard tools of medical education.

You know the deal: Clinical educator meets students in locale and time. Students whip out paper and pencil and feverishly try and make notes, whilst also keeping an eye on that social media icon on their phones; the educator standing up front, the proud owner of 36 text-packed slides.  Now, I’m not even going to mention the relevance of the content.  That’s a post for another day.

Listen up: it is not the pinnacle of teaching when your PowerPoint® slides have transitions in them.  Delivering it, even with aplomb, and walking off, is not a measure of good education. We all know by now that students’ memory of facts given during presentations rapidly decline with time. I am sure that the only slightly long-term memorized fact that students get from us when they attend a presentation-style lecture, is what we look and sound like.

As if that isn’t bad enough, what happens next to these poor students always astonishes me. We sit back in an exam and play judge, jury, and executioner regarding their knowledge.

Where is our duty between pitching up with our presentation slides and that exam? When did we bother to find out if they really knew what was going on?  In-between slides?

Saddest part?  We know how to do better.  The literature is rich in research. Read up.

Long live PowerPoint®!

Open Courseware 2014 Conference

The main conference hall at the OCW conferene in Ljubljana

The main conference hall at the OCW conferene in Ljubljana

I am in lovely Ljubljana, capital of the small  country of Slovenia, for the 2014 Open Coursware Global Conference.  The development of open edcational resources is here to stay and it is interesting to hear and see how various universities have implemented the vision of openess!

The conference kicked off with a top-down view as seen by die European Commission and the Slovenian government.  It all starts with awareness and especially with awareness of the benefits.

Must say, with some sadness, that medicine is lagging behind the mainstream STEM fields.  Most certainly, the M is for mathematics and not medicine.  Looking forward, though, to a talk about the use of the flipped classroom from the Taipei Medical University.  Perhaps I’ll corner them for some collaborative research, since my classes are all flipped.

OCW Consortium 2014 Award

OCW logo



I’m honoured  to announce that I have been awarded the Open CourseWare Consortium 2014 Award for the category Individual Educator for my work on open education.

Previous award winner, Walter Lewin, Physicist at MIT, has been an inspiration and hero of mine and to be a recipient of the same award, is a truly humbling experience for me.

World Design Capital 2014

WDC323_AcuteCareSurgeryUnitWardMakeover_Community_Primary - CopyIn 2013 during a call for submissions to the World Design Capital (WDC) 2014 campaign, I submitted a proposal to improve the health and well-being of the patients admitted to my unit at Groote Schuur Hospital by means of redesign and update.

The ward is home to the Acute Care Surgery Unit and is one of the highest volume wards in the hospital. With the financial constraint on the South African healthcare system, aesthetic and functional design can never be a priority. This does not mean, though, that our patients deserve anything less than a first world setting during their time of need.

Having been accepted as an official WDC 2014 project (Project number #WDC323), I hope to bring on board the private sector to show good will and provide them with an opportunity to showcase their commitment to social responsibility by joining in the makeover of the ward.

Watch this space for progress on this project. For more information about how you can get involved, drop me an email.