Close

  • Latest
  • Our research
  • Setting up our lab
  • Our computational toolbox
  • Contact
Blog Logo

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.
we embrace change
Page 1 of 2 Older Posts

DataCite: get your bibliographic references automatically by providing DOIs.

Miguel A. Fortuna on Our computational toolbox | 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.

Miguel A. Fortuna on Our computational toolbox | 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

Miguel A. Fortuna on Our computational toolbox | 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.

Miguel A. Fortuna on Our computational toolbox | 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.

Miguel A. Fortuna on Our research, Our computational toolbox | 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).…

Digital evolution: Avida as a software platform for studying evolution in action.

Miguel A. Fortuna on Our research, Our computational toolbox | 20 Apr 2020

Digital evolution is a form of evolutionary computation in which self-replicating computer programs—digital organisms—evolve within a user-defined computational environment. Avida is the most widely used software platform for research in digital evolution.…

Neo4j graph databases: working from Jupyterlab.

Miguel A. Fortuna on Setting up our lab, Our computational toolbox | 13 Apr 2020

Neo4j is a graph database that uses graph structures for semantic queries with nodes, edges, and properties to represent and store data. We will briefly describe the open source packages, written in Python and R, that we use in our lab to connect Neo4j databases from our JupyterLab server.…

JupyterLab extensions: LaTeX.

Miguel A. Fortuna on Setting up our lab, Our computational toolbox | 06 Apr 2020

The LaTex extension for JupyterLab allows for live-editing of LaTeX documents.…

JupyterLab extensions: GitLab.

Miguel A. Fortuna on Setting up our lab, Our computational toolbox | 30 Mar 2020

The JupyterLab GitLab extension allows lab members to select GitLab organizations and users, browse their repositories, and open the files in those repositories. If those files are notebooks, we can run them just as you would any other notebook.…

JupyterLab extensions: GitHub.

Miguel A. Fortuna on Setting up our lab, Our computational toolbox | 23 Mar 2020

The JupyterLab GitHub extension allows lab members to select GitHub organizations and users, browse their repositories, and open the files in those repositories. If those files are notebooks, we can run them just as you would any other notebook.…

Page 1 of 2 Older Posts
fortunalab: we embrace change Miguel A. Fortuna