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Topic 16 Posts

Our computational toolbox

We use many programming languages in our daily work for doing different tasks. We advocate for open source or free software. Operating system? Debian GNU/Linux, our course.
ecological engineering to harness evolution
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GitLab CI/CD: pipeline for the R package avidaR

By Miguel A. Fortuna in Our computational toolbox on 05 Apr 2022

We have created a Pipeline for the R package avidaR which is launched every time we upload some changes to our GitLab remote repository.…

pyLODE: an OWL ontology documentation tool

By Miguel A. Fortuna in Our computational toolbox on 22 Nov 2021

pyLODE is a python tool based on LODE that makes owl ontologies human-readable. It converts an owl file into a html page where the IRIs, descriptions, domain and ranges of the classes, object properties, and datatype properties can be easily read and visualized.…

rdf4r library: build your semantic RDF database from R

By Miguel A. Fortuna in Our computational toolbox on 15 Mar 2021

We have extended the functionality of the rdf4r library, developed for working with Resource Description Framework (RDF) data in the R programming environment, to improve performance when uploading lots of RDF triples to a graphDB triplestore hosted in a remote server.…

DataCite: get your bibliographic references automatically by providing DOIs.

By Miguel A. Fortuna in Our computational toolbox on 08 Jun 2020

Getting your bibliographic references from DOIs, appropriately formatted to the journal you are planning to submit your manuscript.…

PURL: getting permanent addresses to access the files you share.

By Miguel A. Fortuna in Our computational toolbox on 25 May 2020

You should create a persistent address for sharing files with your colleagues on the web when you are not sure about where they will be located in your server.…

Docker Hub: pulling and pushing container images to a public respository

By Miguel A. Fortuna in Our computational toolbox on 18 May 2020

Learn how to use Docker's container registry (Doker Hub) to find official images and host your own for public or private use.…

Docker: software that includes everything needed to run an application.

By Miguel A. Fortuna in Our computational toolbox on 11 May 2020

Docker is a container of software that includes everything needed for an application to run isolated from the operating system. In this post we will walk you through the installation process.…

Setting up host-parasite coevolutionary experiments in Avida.

By Miguel A. Fortuna in Our research on 27 Apr 2020

Digital coevolution between hosts and parasites resembles the coevolutionary dynamics among bacteria and phages. By following this tutorial you will be able to set up and run coevolutionary experiments in Avida (i.e., the most widely-used software platform for studying evolution in action).…

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Our computational toolbox: 16 Setting up our lab: 11 Our research: 5
ecological engineering to harness evolution © 2022 Published by fortunalab • System theme