Outline of a Paper

[tmozgach]

1. Introduction
   • Motivation: Provide a comprehensive bioinformatics environment for education or research. Don't need to know how to use external tools (CWL), good for teaching and Hackton purposes.
   • General: problems: usability and reproducibility;
     reviews existing solutions: BioContainers, Bioboxes, Bioconda.
   • Use case: ORCA provides access to external contributors.
   • Isolated (no training) VS monolithic containers
   • Non Docker VS Docker solutions (sudo)
   • Linuxbrew (1 paragraph), mention new name
   • Statistics ( number of software, etc)
2. Features
   • sudo
   • package-managers (apt-get, linuxbrew, pip, R)
   • run GUI application (X11) => Case study
   • multiple shell process per container
   • load-balancing => future direction
   • resource utilization limits (-m flag) => Case study
   • tag historical images (reproducibility)
   • security: containers are isolated from each other, both processes (ps) and files
3. Architecture
   • automated build
   • external data volume => Case study
   • Continuous integration: CircleCI, Docker Hub automated build
4. Availability
   • Docker Hub
   • GitHub
   • Link to documentation, how to install and use
   • License: currently GPL-3, let's consider relicensing as MIT
5. Case study
   • Martin's class at UBC
   • HackSeq
6. Figure
   • Component interactions: GitHub, Docker, Docker Hub, CircleCI, Laptop etc.

[tmozgach]

@sjackman I added some points in the outline from the meeting, feel free to add something that I missed while it is still in your mind =)