Latest blog posts

My perspective after two years as a research and teaching assistant at FIDIT

Photo source: Darran Shen (@darranshen) | Unsplash

My employment as a research and teaching assistant at Faculty of Informatics and Digital Technologies (FIDIT for short), University of Rijeka (UniRi) ended last month with the expiration of the time-limited contract I had. This moment has marked almost two full years I spent in this institution and I think this is a good time to take a look back at everything that happened during that time. Inspired by the recent posts by the PI of my group, I decided to write my perspective on the time that I hope is just the beginning of my academic career.

Alumni Meeting 2023 at HITS and the reminiscence of the postdoc years

Photo source: Jahanzeb Ahsan (@jahan_photobox) | Unsplash

This month we had Alumni Meeting 2023 at the Heidelberg Institute for Theoretical Studies, or HITS for short. I was very glad to attend this whole-day event and reconnect with my former colleagues as well as researchers currently working in the area of computational biochemistry at HITS. After all, this is the place and the institution where I worked for more than half of my time as a postdoc, where I started regularly contributing code to GROMACS molecular dynamics simulator, and published some of my best papers.

What hardware, software, and cloud services do we use?

Photo source: Patrik Kernstock (@pkernstock) | Unsplash

Our everyday scientific and educational work relies heavily on hardware, software, and, in modern times, cloud services. The equipment that we will mention below is specific to our group; common services used by university and/or faculty employees will not be specifically mentioned here.

Should I do a Ph.D.?

Photo source: Santeri Liukkonen (@iamsanteri) | Unsplash

Tough question, and the one that has been asked and answered over and over. The simplest answer is, of course, it depends on many factors.

As I started blogging at the end of my journey as a doctoral student, the topic of how I selected the field and ultimately decided to enroll in the postgraduate studies never really came up. In the following paragraphs, I will give a personal perspective on my Ph.D. endeavor. Just like other perspectives from doctors of not that kind, it is specific to the person in the situation, but parts of it might apply more broadly.

Publishing (Material for) MkDocs website to GitHub Pages using custom Actions workflow

Photo source: Roman Synkevych (@synkevych) | Unsplash

As you can probably see, this website is built using the Material theme for MkDocs, which we have been happily using for over one year after using Sphinx for many years prior to that. GitHub Pages offers built-in support for Jekyll, but not for MkDocs and therefore it requires the manual building and deployment of our website. However, it automates many other things, including HTTPS certificate provisioning on our domain via Let's Encrypt.

There are several somewhat related approaches using GitHub Actions for automating the deployment of MkDocs-generated sites, usually with the Material theme, to GitHub Pages. These guides are not only found on blogs written by enthusiasts; the official Getting started section of the Material for MkDocs documentation describes the usage of GitHub Actions for deployment and provides a generic YAML file for that purpose.

Don't use RAR

Photo source: Tim Mossholder (@ctimmossholder) | Unsplash

I sometimes joke with my TA Milan Petrović that his usage of RAR does not imply that he will be driving a rari. After all, he is not Devito rapping^Wsinging Uh 😤. Jokes aside, if you search for "should I use RAR" or a similar phrase on your favorite search engine, you'll see articles like 2007 Don't Use ZIP, Use RAR and 2011 Why RAR Is Better Than ZIP & The Best RAR Software Available.

Markdown vs reStructuredText for teaching materials

Photo source: Eugenio Mazzone (@eugi1492) | Unsplash

Back in summer 2017. I wrote an article explaining why we used Sphinx and reStructuredText to produce teaching materials and not a wiki. In addition to recommending Sphinx as the solution to use, it was general praise for generating static HTML files from Markdown or reStructuredText.

This summer I made the conversion of teaching materials from reStructuredText to Markdown. Unfortunately, the automated conversion using Pandoc didn't quite produce the result I wanted so I ended up cooking my own Python script that converted the specific dialect of reStructuredText that was used for writing the contents of the group website and fixing a myriad of inconsistencies in the writing style that accumulated over the years.

Mirroring free and open-source software matters

Photo source: Tuva Mathilde Løland (@tuvaloland) | Unsplash

Post theme song: Mirror mirror by Blind Guardian

A mirror is a local copy of a website that's used to speed up access for the users residing in the area geographically close to it and reduce the load on the original website. Content distribution networks (CDNs), which are a newer concept and perhaps more familiar to younger readers, serve the same purpose, but do it in a way that's transparent to the user; when using a mirror, the user will see explicitly which mirror is being used because the domain will be different from the original website, while, in case of CDNs, the domain will remain the same, and the DNS resolution (which is invisible to the user) will select a different server.

Free and open-source software was distributed via (FTP) mirrors, usually residing in the universities, basically since its inception. The story of Linux mentions a directory on ftp.funet.fi (FUNET is the Finnish University and Research Network) where Linus Torvalds uploaded the sources, which was soon after mirrored by Ted Ts'o on MIT's FTP server. The GNU Project's history contains an analogous process of making local copies of the software for faster downloading, which was especially important in the times of pre-broadband Internet, and it continues today.

Fly away, little bird

Photo source: Vincent van Zalinge (@vincentvanzalinge) | Unsplash

The last day of July happened to be the day that Domagoj Margan, a former student teaching assistant and a great friend of mine, set up his own DigitalOcean droplet running a web server and serving his professional website on his own domain domargan.net. For a few years, I was helping him by providing space on the server I owned and maintained, and I was always glad to do so. Let me explain why.

Why we use reStructuredText and Sphinx static site generator for maintaining teaching materials

Photo source: Patrick Tomasso (@impatrickt) | Unsplash

Yesterday I was asked by Edvin Močibob, a friend and a former student teaching assistant of mine, the following question:

You seem to be using Sphinx for your teaching materials, right? As far as I can see, it doesn't have an online WYSIWYG editor. I would be interested in comparison of your solution with e.g. MediaWiki.

While the advantages and the disadvantages of static site generators, when compared to content management systems, have been written about and discussed already, I will outline our reasons for the choice of Sphinx below. Many of the points have probably already been presented elsewhere.