Blog: In between lines of code

Artificial, or simulated intelligence?
AI
genAI
education
I am very much interested in Artificial Intelligence (AI), both in general, and in what it means for (higher) education. My focus is mostly on Generative AI, such as Large…
February 3, 2026

Scaling Participatory live coding in an undergraduate computational biology course
BIOS1100
teaching
live-coding
This post is about the course BIOS1100 - Introduction to Computational Modelling in the Biosciences, that I have taught at the University of Oslo, Norway since 2017. I…
April 2, 2020
 
Announcing canvasCourseCli
canvas
teaching
I wrote a small command line tool (in Python) for retrieving, adding and updating content, pages and files exposed to students and teachers, for a Canvas course.
March 4, 2020
 
FWIW: abbreviations useful to know for reading posts on Twitter
twitter
I may happend that you, like me, come across abbreviations when reading tweets that I have no idea of what they mean. I have collected the ones I see the most and that I…
December 17, 2018

Welcome to my new website!
site
A while ago I decided that I wanted a website that
October 30, 2018
 
Experiences with the first edition of “Introduction to Computational Modelling for the Biosciences”
Teaching
BIOS1100
December 21, 2017
 
A new 1st semester bachelor course ‘Introduction to Computational Modelling for the Biosciences’
Teaching
BIOS1100
March 8, 2017
 
Instructor training at the 2017 Data Intensive Biology Summer Institute at UC Davis
Bioinformatics
Next Generation Sequencing
Teaching
Software Carpentry
March 6, 2017
 
The Roche/454 Life Sciences GS FLX and GS Junior: an obituary
Next Generation Sequencing
newbler
October 21, 2016
 
Developments in high throughput sequencing – July 2016 edition
Next Generation Sequencing
454
Illumina
Ion Torrent
oxford nanopore
pacbio
July 8, 2016
 
​From now on, I will only do open science
Miscellaneous
open science
May 27, 2016
 
A video introduction to instructing by means of live coding
Carpentry
Data Carpentry
Software Carpentry
Teaching
May 13, 2016
 
Carpentry week 2016 at the University of Oslo
Carpentry
Data Carpentry
Software Carpentry
Teaching
April 11, 2016
 
On being an instructor for Software and Data Carpentry
Carpentry
Data Carpentry
Software Carpentry
Teaching
April 5, 2016
 
How to sequence and assemble a large eukaryote genome with long reads in 2015
Bioinformatics
assembly
pacbio
October 1, 2015
 
Notes from the ”FEBS-IUBMB workshop on education in molecular life sciences”
Bioinformatics
Teaching
September 23, 2015
 
Active learning strategies for bioinformatics teaching
Bioinformatics
Experiences
Software Carpentry
Teaching
August 31, 2015
 
Developments in high throughput sequencing – June 2015 edition
Next Generation Sequencing
454
GS FLX+
GS Junior
HiSeq
Illumina
Ion Proton
Ion Torrent
Ion Torrent PGM
MinIon
MiSeq
NextSeq500
oxford nanopore
pacbio
sanger
SOLiD
June 17, 2015
 
A hybrid model for a High-Performance Computing infrastructure for bioinformatics
Bioinformatics
Next Generation Sequencing
HPC
April 13, 2015
 
On graph-based representations of a (set of) genomes
Bioinformatics
Next Generation Sequencing
assembly
graphs
April 9, 2015
 
Thoughts on a possible Assemblathon3
Bioinformatics
Next Generation Sequencing
assembly
March 4, 2015
 
My review of ‘MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island’
Bioinformatics
Next Generation Sequencing
Reviews
MinIon
oxford nanopore
reproducible science
December 10, 2014
 
My review of ‘Long-read, whole-genome shotgun sequence data for five model organisms’
Next Generation Sequencing
Reviews
pacbio
November 27, 2014
 
On the benefits of ‘open’ for teaching
Experiences
assembly
Teaching
November 4, 2014
 
Our review of ‘Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data’, aka the HGAP paper
Bioinformatics
Next Generation Sequencing
Reviews
hgap
pacbio
June 19, 2014
 
Developments in next generation sequencing – June 2014 edition
Next Generation Sequencing
454
GS FLX+
GS Junior
HiSeq
Illumina
Ion Proton
Ion Torrent
Ion Torrent PGM
MiSeq
NextSeq500
pacbio
SOLiD
June 11, 2014
 
My review of ‘Automated ensemble assembly and validation of microbial genomes’
Bioinformatics
Reviews
assembly
June 5, 2014
 
Make Newbler open source: the Roche response and the future of Newbler
Bioinformatics
Next Generation Sequencing
454
newbler
March 17, 2014
 
Looking back at AGBT 2014
Bioinformatics
assembly
Illumina
Ion Torrent
oxford nanopore
pacbio
February 18, 2014
 
Make Newbler open source: petition results and the meeting with Roche
Bioinformatics
Next Generation Sequencing
454
newbler
February 17, 2014
 
The one and only Oxford Nanopore talk at AGBT 2014 - with real data
Bioinformatics
Next Generation Sequencing
assembly
MinIon
oxford nanopore
February 14, 2014
 
Defending ‘no-tweeting/blogging’ requests at conferences
Miscellaneous
blogging
twitter
February 13, 2014
 
Make Newbler Open Source: an update
Bioinformatics
Next Generation Sequencing
454
newbler
February 10, 2014
 
Make Newbler open source
Bioinformatics
Next Generation Sequencing
454
newbler
reproducible science
January 31, 2014
 
Would you buy that washing machine?
Next Generation Sequencing
MinIon
oxford nanopore
October 25, 2013
 
A Software Carpentry-inspired workshop to improve the way we do bioinformatics in our group
Bioinformatics
reproducible science
Software Carpentry
Teaching
October 21, 2013
 
Developments in next generation sequencing – October 2013 edition
Next Generation Sequencing
October 1, 2013
 
Software Carpentry bootcamp: lessons learned
Experiences
Software Carpentry
Teaching
September 23, 2013
 
De novo bacterial genome assembly: a solved problem?
Bioinformatics
assembly
celera
hgap
pacbio
July 5, 2013
 
Longing for the longest reads: PacBio and BluePippin
Bioinformatics
June 19, 2013
 
On assembly uncertainty (inspired by the Assemblathon2 debate)
Bioinformatics
assembly
February 26, 2013
 
Applications for PacBio circular consensus sequencing
16s
ccs
metagenomics
pacbio
sanger
February 11, 2013
 
Developments in next generation sequencing - a visualisation
Next Generation Sequencing
454
GS FLX+
GS Junior
Illumina
Ion Proton
Ion Torrent
Ion Torrent PGM
MiSeq
pacbio
December 3, 2012
 
How to sequence a bacterial genome at the end of 2012
Next Generation Sequencing
454
assembly
GS FLX+
GS Junior
Illumina
Ion Torrent
Ion Torrent PGM
MiSeq
pacbio
November 29, 2012
 
My take on the sequencing buzz at #ASHG2012
Next Generation Sequencing
GS FLX+
Illumina
Ion Torrent
oxford nanopore
pacbio
November 8, 2012
 
Combining short and long reads: choosing between PacBioToCA and the new ALLPATHS_LG
Bioinformatics
Next Generation Sequencing
ALLPATHS_LG
Illumina
pacbio
August 6, 2012
 
Paper: error-correcting PacBio reads using high-quality short reads
Bioinformatics
Next Generation Sequencing
assembly
pacbio
July 1, 2012
 
Loman et al reflects the past, not the present - a rebuttal
Bioinformatics
Next Generation Sequencing
Ion Torrent
May 9, 2012
 
Fast genome sequencing of pathogenic bacteria - which benchtop instrument to choose?
Bioinformatics
Next Generation Sequencing
454
assembly
GS Junior
homopolymer
Illumina
Ion Torrent
Ion Torrent PGM
MiSeq
newbler
April 22, 2012
 
Ion Torrent Mate Pairs and a single scaffold for E coli K12 substr. MG1655
Bioinformatics
Next Generation Sequencing
assembly
Ion Torrent
newbler
March 2, 2012
 
Ion Torrent data on E. coli K12 MG1655 - a fairer comparison with 454
Bioinformatics
Next Generation Sequencing
454
Ion Torrent
February 1, 2012
 
What is going on with 454 GS FLX+ sequencing?
Next Generation Sequencing
454
GS FLX+
January 17, 2012
 
IonTorrent: many long reads, still longer homopolymers
Bioinformatics
Next Generation Sequencing
Ion Torrent
September 30, 2011
 
IonTorrent: longer reads, longer homopolymers?
Bioinformatics
Next Generation Sequencing
454
homopolymer
Ion Torrent
August 10, 2011
 
Overcoming the second generation sequencing mindset
Next Generation Sequencing
pacbio
July 13, 2011
 
The longest reads yet: A look at PacBio’s contribution to the assemblathon
Bioinformatics
Next Generation Sequencing
pacbio
July 4, 2011
 
Going with the flow: sequencing flow orders and longer reads - Ion sets the stage
Next Generation Sequencing
Ion Torrent
July 1, 2011
 
More, longer, longest: new reads from three NGS platforms available online
Next Generation Sequencing
454
GS FLX+
Illumina
Ion Torrent
MiSeq
June 22, 2011
 
There is more (length) to Ion Torrent reads than meets the eye (and is Ion Torrent hiding it?)
Bioinformatics
Next Generation Sequencing
Ion Torrent
sff
June 16, 2011
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