Bioinformatics

Query a Postgres DB from a Python Application By the end of this blog post you will have all the tools you need to query a Postgresdatabase, with some dummy data, from a python application, all without installing a single thing besides docker onto your computer! Learning Curve If you

Learning Curve The Pain The first time I setup an app to connect to a mysql database I spent at least a full hour fiddling with that connection string, before throwing my hands up in frustration and taking a walk. I find walking to be very therapeutic, so I calmed

Overview If you've ever worked with scientific software you will know that installing them is not necessarily straightforward. I think this is changing quite a bit with tools like conda and docker, but sometimes we need to just sit down and debug an installation. There is hope here,

Overview If you are anything like me, you heavily rely on a debugger. Likewise, you install all your development environments into a docker container because installing things on your own computer is FOR THE BIRDS. I cannot tell you what a relief it is to have all my development environments

Containers, Compose, Swarm, Desktop? Docker isn't simply a container or a virtual machine, its an entire ecosystem. Luckily, each component is a layer that builds upon its previous layer. There are definitely a lot of moving pieces, but from a birds eyes perspective there are three main components.

Recap Up until this point we covered: * Building a custom docker container using the official python miniconda container as our base. * Interactively running commands in our custom image * Giving docker build time instructions and run time instructionswith RUN and CMD. * Spinning up a webserver that we can access on our