SciLifeLab Voices: Pär Engström
Hello Pär, NBIS hosts bioinformatics drop-in sessions, tell us more!
Our aim with these sessions is to make it easy for researchers to get quick answers to bioinformatics-related questions. For example, questions can be about choosing analysis methods for a data set, problems running a script or tool, programming problems, or statistical considerations when interpreting results. We are also very happy to discuss study design – it’s always a good idea to plan your analyses before collecting data!
Together with all the other SciLifeLab infrastructure platforms, we are now looking into expanding the drop-in concept to offer joint consultation sessions covering multiple SciLifeLab services. We hope this will be useful in particular for researchers who are planning multi-omics studies or other projects that make use of multiple technologies offered by SciLifeLab.
Who are the sessions for?
Anyone involved in academic research in Sweden is welcome! We mostly get visits from PhD students and postdocs, but quite often group leaders as well. We are also happy to talk with staff scientists from other parts of the SciLifeLab infrastructure or other centres.
What is the most common question you get?
Most questions are unique, but currently we get many questions about single cell and spatial data. That is perhaps not surprising, as those technologies are in rapid development and analysis methods are not yet well established. Other common topics are statistics, image analysis and running bioinformatics software on the NAISS compute systems.
What has been the trickiest question so far?
We often get questions about analysis tasks that require tailor-made scripts to be written. If the user who asks the question has some programming skills, we can often help them at the drop-in. However, in cases where the user does not know so much about programming, it’s often tricky to provide a quick solution. Instead, we can refer to our courses and openly available course material. We can also refer visitors to our hands-on support tracks, where we carry out data processing/analysis in collaboration with them, either against a fee or following a peer review selection process.
When you do not provide bioinformatics support – what do you like to engage in outside the office?
I enjoy reading, running, and spending time with my family. If I feel nostalgic, I might boot up an old computer I happen to have at home, a Commodore Amiga. I spent a lot of time programming those types of machines as a teenager, and that taught me many things I still have use for today when working with bioinformatics and data science.
More about the bioinformatics support sessions
The sessions are arranged by the SciLifeLab Bioinformatics Platform (NBIS), and the bioinformaticians that take part are experts on different data types and analyses. If you come to one of the drop-ins, NBIS will try to match you with an expert who can answer your questions on the spot. If we can’t help you right away, we can set up a consultation meeting at a later time to discuss more in-depth.
The drop-ins are free of charge and there is no advance registration. Weekly sessions are arranged weekly over Zoom, as well as on site at SciLifeLab Stockholm and at Lund University. Times and locations >>
At the Zoom sessions, we also get help from experts from the SciLifeLab Genomics platform, who can provide advice about study design for high-throughput sequencing.
For those interested in investigating molecular structures with Cryo-EM, the SciLifeLab Cryo-EM unit arranges drop-in sessions on that topic, where bioinformaticians specialised in structural biology take part >>.
