Jul 20, 2019Equation-centric dataflow programming in GoEven though computations done on computers are very often based on some type of math, it is striking that the notation used in math to express equations and relations is not always very readily converted into programming code. …Functional Programming4 min readFunctional Programming4 min read
Mar 2, 2019Structured Go-routines or framework-less Flow-Based Programming in GoThis post has previously been published at bionics.it. I was so happy the other day to find someone else who found the great benefits of a little pattern for how to structure pipeline-heavy programs in Go, which I described in a post, and a follow-up post on GopherAcademy in 2015…Design2 min readDesign2 min read
Dec 30, 2018Setting up a light-weight Linux-like (non-WSL) terminal environment on WindowsIn my new job as a consultant and developer in Machine Learning and AI at Savantic AB, although we internally have a “choose your favorite OS” policy, we’re from time to time running into situations where we need to do development on or for Windows. Being a heavy user of…Git4 min readGit4 min read
Oct 30, 2018Linked Data Science — For improved understandability of computer-aided researchOriginally posted at bionics.it — This is an excerpt from the “future outlook” section of my thesis, titled “Reproducible Data Analysis in Drug Discovery with Scientific Workflows and the Semantic Web” (click for open access full text), which aim to provide various putative ways forward towards improved reproducibility, understandability and…Data Science3 min readData Science3 min read
Sep 25, 2018What is a scientific (batch) workflow?This story was originally posted on bionics.it Workflows and DAGs — Confusion about the concepts Jörgen Brandt tweeted a comment that got me thinking again on something I’ve pondered a lot lately: “A workflow is a DAG.” is really a weak definition. That’s like saying “A love letter is a sequence of characters.” representation ≠ meaning - @joergenbr …Big Data6 min readBig Data6 min read
Jul 9, 2018Combining the best of Go, D and Rust?This post was originally published in 2016 at bionics.it. I have for years been looking for a replacement for Python and Java for developments of various data processing tools in bioinformatics / cheminformatics, which happens to be my field of study. That is, something more performant with better concurrency and…Programming2 min readProgramming2 min read
Jul 9, 2018The problem with GNU Make for scientific workflows(originally published in 2015 at bionics.it) As soon as the topic of scientific workflows is brought up, there are always a few Make fans fervently insisting that the problem of workflows is solved once and for all with GNU make, written first in the 70’s :) Personally I haven’t been…Programming5 min readProgramming5 min read
Feb 14, 2017Launching kubernetes jobs from the Go API — notes from a beginnerMy current work at pharmb.io entails adding kubernetes support to my light-weight Go-based scientific workflow engine, scipipe (kubernetes, or k8s for short, is Google’s open source project for orchestrating container based compute clusters), which should take scipipe from a simple “run it on your laptop” workflow system with HPC support…Kubernetes3 min readKubernetes3 min read
Feb 26, 2016How time-boxing and a unified trello board solved my productivity problemsI used to have a very hard time getting an overview of my current work, and prioritizing and concentrating on any single task for too long. I always felt there might be something else that might be more important than what I were currently doing. …Productivity3 min readProductivity3 min read
Dec 5, 2014Loosely coupled tasks in Luigi workflows*** PLEASE NOTE: This article is getting outdated: The presented ideas have now matured and eventually resulted in the Scientific Luigi library *** Originally posted at bionics.it on Aug 5, 2014. Some discussion on this post has happaned in this thread. In my work in the Pharmaceutical Bioinformatics group at…7 min read7 min read
