Full Stack Bioinformatics

HPC for Bioinformatics (3/?): Head Nodes

Sun, 29 Jan 2023 00:00:00 +0000

HPC clusters can be daunting to beginners. This blog post explains the difference of compute and head nodes and goes into detail on head nodes.

Unix Sleight of Hand (2/?): Robust Column Extraction

Sat, 24 Dec 2022 00:00:00 +0000

Many Bioinformaticians spend a lot of their time handling text files. Linux (and other Unixes) excel at processing text files and offer many tools for handling it. However, extracting a particular column from text files is surprisingly hard. This blog post explores some robust solutions.

Unix Sleight of Hand (1/?): Bash Job Control

Mon, 21 Nov 2022 00:00:00 +0000

This post deals with the basics “and beyond” of job control in Bash. The Bourne Again Shell (Bash) arguably is the most widely used POSIX-compliant shell. It has been around since 1989 and is still alive and kicking.

About

Fri, 28 Jan 2022 00:00:00 +0000

This is the web site of Manuel Holtgrewe, computer scientist, bioinformatician (focus on medical genetics), scientist, engineer, technologist, nerd – not necessarily in this order.

HPC for Bioinformatics (2/?): Machine Installation

Mon, 10 Jan 2022 00:00:00 +0000

This post describes the two basic options for system installation that we have tried so far.

HPC for Bioinformatics (1/?): Introduction

Mon, 03 Jan 2022 00:00:00 +0000

This is the first entry in the HPC for Bioinformatics series.

Thoughts on Checksums

Tue, 27 Aug 2019 00:00:00 +0000

It’s 2019 and checksums are pervasive everywhere… Everywhere? No, a small community somewhere north in - agh, forget about it!

My First Post

Sun, 04 Aug 2019 00:00:00 +0000

This is the first post in this blog. I expect to be both post length and time between posts to be highly irregular.