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 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 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.…
The LaTex extension for JupyterLab allows for live-editing of LaTeX documents.…
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.…
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.…
Git, as a version control system, allows lab members to revert and go back to an older version of the code. Moreover, sometimes multiple members are working in parallel on the same code, so Git is needed to ensure there are no code conflicts between them.…
JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data. By deploying it with JupyterHub in our server, lab members can work from the office, home or their favorite coffee shop, using a desktop computer, laptop, tablet or smartphone.…