Genomics on Living Systems_

Learning Genomics and Bioinformatics in 2025

Tue, 12 Nov 2024 10:28:04 +0100

Bioinformatics is growing in the clinical field, and in my job in a clinical microbiology lab, I’m increasingly asked for tips about how to get into bioinformatics or genomic data science.

As I recently took the plunge into genomics from my PhD field of small molecular structures and machine learning, as part of getting into my current position, I thought to write down what I learned in the process.

NGS Bioinformatics Course Day 3: New Luigi helper tool, "real-world" NGS pipelines

Tue, 03 Mar 2015 20:45:00 +0100

It turned out I didn’t have the time and strength to blog every day at the NGS Bioinformatics Intro course, so here comes a wrap up with some random notes and tidbits from the last days, including any concluding remarks!

These days we started working on a more realistic NGS pipeline, on analysing re-sequencing samples (slides , tutorial ).

First some outcome from this tutorial

What do I mean with “outcome”? Well, as I tried to manually copy and paste the bag of hairy nasty long bash commandline strings in the tutorial pages , that all depended upon each other, I got so frustrated that I decided to try to encode them in a workflow language / tool.

NGS Bioinformatics Intro Course Day 2

Tue, 10 Feb 2015 20:44:00 +0100

Today was the second day of the introductory course in NGS bioinformatics that I’m taking as part of my PhD studies.

For me it started with a substantial oversleep, probably due to a combination of an annoying cold and the ~2 hour commute from south Stockholm to Uppsala and BMC . Thus I missed some really interesting material (and tutorial ) on file types in NGS analysis, but will make sure to go through that in my free time during the week.

NGS Bioinformatics Intro Course Day 1

Mon, 09 Feb 2015 20:44:00 +0100

Just finished day 1 of the introductory course on Bioinformatics for Next generation sequencing data at Scilifelab Uppsala. Attaching a photo from one of the hands-on tutorial sessions, with the tutorial leaders, standing to the right.

Today’s content was mostly introductions to the linux commandline in general, and the UPPMAX HPC environment in particular, an area I’m already very familiar with, after two years as a sysadmin at UPPMAX. Thus, today I mostly got to help out the other students a bit.