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Setting up the Nextflow Language Server (LSP) with NeoVim
The chroot Technique - a Swiss army multitool for Linux systems
Why is R so confusing? Because it is so hard to inspect
Learning Genomics and Bioinformatics in 2025
Rewrite of Scicommander in Go with much improved algorithm
About
A few notes from the Applied Hologenomics Conference 2024
We need recipes for common bioinformatics tasks
Why didn't Go get a breakthrough in bioinformatics (yet)?
SciPipe used at NASA Glenn Research Center
Debugging inside Jinja templates using pdb/ipdb
SciCommander - track provenance of any shell command
Troubleshooting Nextflow pipelines
Random notes from installing Debian 11 with separate accounts for work and private
Installing Qubes OS
Composability in functional and flow-based programming
Crystal: Go-like concurrency with easier syntax
Viewing Go test coverage in the browser with one command
Creating a static copy of a Drupal, Wordpress or other CMS website
Basic PUB/SUB connection with ZeroMQ in Python
Table-driven tests in C#
SciPipe paper published in GigaScience
Structured Go-routines or framework-less Flow-Based Programming in Go
Setting up a reasonable and light-weight Linux-like (non-WSL) terminal environment on Windows
Linked Data Science - For improved understandability of computer-aided research
Preprint on SciPipe - Go-based scientific workflow library
Make your commandline tool workflow friendly
To make computational lab note-taking happen, make the journal into a todo-list (a "Todournal")
Semantic Web ❤ Data Science? My talk at Linked Data Sweden 2018
Parsing DrugBank XML (or any large XML file) in streaming mode in Go
Equation-centric dataflow programming in Go
What is a scientific (batch) workflow?
Go is growing in bioinformatics workflow tools
The frustrating state of note taking tools
Learning how to learn
On Provenance Reports in Scientific Workflows
(Almost) ranging over multiple Go channels simultaneously
First production run with SciPipe - A Go-based scientific workflow tool
Compiling RDFHDT C++ tools on UPPMAX (RHEL/CentOS 7)
New paper on RDFIO for interoperable biomedical data management in Semantic MediaWiki
Notes on launching kubernetes jobs from the Go API
SMWCon Fall 2016 - My talk on large RDF imports
Tutorial: Luigi for Scientific Workflows
Combining the best of Go, D and Rust?
Time-boxing and a unified trello board = productivity
The unexpected convenience of JSON on the commandline
The matrix transformation as a model for declarative atomic data flow operations
Wanted: Dynamic workflow scheduling
How to be productive in vim in 30 minutes
How to compile vim for use with pyenv and vim-pyenv
How I would like to write Go programs
Terminator as a middle-way between floating and tiling window managers
FBP inspired data flow syntax: The missing piece for the success of functional programming?
A few thoughts on organizing computational (biology) projects
Flow-based programming and Erlang style message passing - A Biology-inspired idea of how they fit together
A cheatsheet for the iRODS rule language
Workflow tool makers: Allow defining data flow, not just task dependencies
Patterns for composable concurrent pipelines in Go
The role of simplicity in testing and automation
The problem with make for scientific workflows
Dynamic Navigation for Higher Performance
NGS Bioinformatics Course Day 3: New Luigi helper tool, "real-world" NGS pipelines
Random links from the Hadoop NGS Workshop
Links: Our experiences using Spotify's Luigi for Bioinformatics Workflows
NGS Bioinformatics Intro Course Day 2
NGS Bioinformatics Intro Course Day 1
Taking a one week introductory course in Bioinformatics for NGS data
RDFIO VM
The smallest pipeable go program
Profiling and creating call graphs for Go programs
(E)BNF parser for parts of the Galaxy ToolConfig syntax with ANTLR
Partial Galaxy ToolConfig to DocBook CmdSynopsis conversion with XSLT RegEx
Answering questions without answers - by wrapping simulations in semantics
A Hello World program in SWI-Prolog