Team work opens all the ports

Lana Vogrinec, 30. januar 2023

It’s Monday and my week is starting the same way as usual – I’m drinking chamomile tea and making an outline of what I need to do in the upcoming days. Suddenly, my colleague Živa appears at my office and starts explaining something to me excitedly. Before I realize what is happening, I already agree with what she is asking me – I will be the deputy administrator of our new server with a funny name, Rosina.

You may be wondering why a server needs an administrator and let me tell you, before starting this job, I had no idea such a thing existed. But at our institute, each laboratory and every single piece of equipment (even the coffee machine!) has its administrator. And the administrator has a deputy. This super-team is responsible for writing instructions on how to use it, maintain it, and interfere if problems arise.

Rosina is not a physical instrument, like your average old centrifuge. It’s a very powerful server, which will be the home of a fancy program package called CLC Genomics. Our experiments are often based on analyzing nucleotide sequences of viruses, which are long strings of four letters (A, C, T, G) that contain information about how the viruses function. So kind of like a viral instruction manual. We are usually dealing with enormous amounts of these letters, much too big for the human mind to comprehend. And this is where the CLC program comes in – it helps us organize and analyze all of the data gathered from lab experiments. We all heavily depend on it, so setting it up ASAP is of vital importance. Sounds like the perfect job for a newcomer who knows next to nothing about computers and programming (me). Thankfully, I don’t have to tackle it alone – my good friend Anja is the person in charge and I am just her apprentice who will take over once she goes on maternity leave in 3 months. Anja is very capable and smart, but her field of expertise is next-generation sequencing, not computers.

Here’s the catch – Rosina is essentially a computer, but one without a screen or a keyboard. On top of that, it runs on a Linux operating system, which means that everything that we want her to do has to be written in computer language through the command line. What a fun challenge for two girls, who are both absolutely clueless about this particular language. If only Rosina spoke Italian.

And so we started the process. At first, things went smoothly, we just followed the not-so-very-clear instructions and crossed our fingers every time we entered a command. We managed to get through the manual and were excited to see if it works – but of course, it didn’t. We googled like mad, contacted the support services, called every person we know who could help, and bothered Živa with a million questions. We tried every possible solution, but the message ‘Error’ continued to appear on our screens. As time progressed, we were getting more and more confident that our next solution will work – but of course, it didn’t. Days passed and we were nowhere close to solving this issue.

On Friday I had an online meeting and suddenly an excited Anja appears at my door. She sees that I am busy, but she is holding a post-it note, which she sticks to my window – it says: ‘Check if the ports are open’. What in the world are ports and why would they not be opened? Of course, they weren’t.

A few google searches later, I manage to find the command that opens specific ports, which, as their name suggests, serve as a passageway for programs to connect (or so I understand). I try opening these imaginary ports and after a few mistakes caused by reckless typos, I finally succeed. After my meeting, I run to Anja (okay walk, her office is next door) to try it out. It’s a miracle, the program WORKS! At first, we can’t believe it, but soon, excitement settles in. Although it’s already 5 pm and we both have other places to be, we cannot resist the urge to walk down the hall and excitedly tell everyone who will listen that we finally did it.

In the end, this week was an unexpected but very interesting detour from what I usually do – there were no lab coats or pipettes involved – and still I had a lot of fun. As for the final result, we now have a fully functional CLC Genomics Workbench that everyone can use and I have a new set of skills, which will undoubtedly be useful at some point in the future. After all, the program needs to be updated every now and then, and knowing our luck, the updates will probably come out next week (spoiler alert: they did!).