# Foundational Open Science Skills (FOSS)

> A self-paced course that teaches researchers core open-science skills: open science, data management, the command line, LLMs, version control, software environments, containers, HPC, and CyVerse cloud computing. The source repository is an Open Knowledge Format (OKF v0.2) bundle: every page carries YAML frontmatter with type, provenance (generated/sources), and lifecycle (status/stale_after) fields.

Full corpus for ingestion: https://unm-carc.github.io/foss/llms-full.txt

Every page's Markdown source (OKF frontmatter included) is served at its URL plus `index.md` — for example https://unm-carc.github.io/foss/course/setup/index.md.

## Course

- [Before FOSS Starts](https://unm-carc.github.io/foss/course/setup/): Accounts to create and software to install before the first FOSS session, including notes for Windows users.
- [Weekly Schedule and Communications](https://unm-carc.github.io/foss/course/schedule/): Week-by-week schedule of the Fall 2025 FOSS offering, with lesson topics and links to each session's HackMD notes.
- [Code of Conduct](https://unm-carc.github.io/foss/course/code-of-conduct/): Expected conduct for FOSS participants and how to report a violation.
- [Glossary & Acronyms](https://unm-carc.github.io/foss/course/glossary/): Definitions of the computing, open-science, and cyberinfrastructure terms and acronyms used throughout FOSS.

## Lessons

- [Introduction to Open Science](https://unm-carc.github.io/foss/lessons/01-open-science/): What open science is, its six pillars (open access, data, educational resources, methodology, peer review, and source software), and why researchers practice it.
- [Data Management and Documentation](https://unm-carc.github.io/foss/lessons/02-data-management/): The data life cycle, FAIR and CARE principles, data management plans, licensing, and tools for documenting research projects.
- [How to Talk to Computers](https://unm-carc.github.io/foss/lessons/03-talk-to-computers/): An introduction to the Unix shell: navigating directories, working with files, and automating tasks with shell scripts.
- [How to Talk to LLMs](https://unm-carc.github.io/foss/lessons/04-talk-to-llms/): How large language models work, prompt-engineering techniques such as priming, chaining, and the CRAFT framework, and AI coding tools for research.
- [Reproducibility I: Version Control](https://unm-carc.github.io/foss/lessons/05-version-control/): Version control with Git and GitHub: repositories, the commit-push-pull cycle, branching, pull requests, and handling large files.
- [Reproducibility II: Software Environments](https://unm-carc.github.io/foss/lessons/06-software-environments/): Computing environments, the system PATH, and using Conda, pip, and renv to create, share, and reproduce software environments.
- [Reproducibility III: Containers](https://unm-carc.github.io/foss/lessons/07-containers/): Why containers matter for reproducible research, core Docker commands, running an example container, and writing, building, and pushing a Dockerfile.
- [Remote Computing: HPC](https://unm-carc.github.io/foss/lessons/08-hpc/): Logging in to a high-performance computing cluster, submitting Slurm batch and interactive jobs, loading modules, and running Apptainer containers.
- [Remote Computing: CyVerse](https://unm-carc.github.io/foss/lessons/09-cyverse/): An overview of the CyVerse cloud platform: the Discovery Environment, Data Store, Data Commons, analysis apps, and the analysis dashboard.
- [10. AI models & where to find them](https://tyson-swetnam.github.io/intro-gpt/): External resource.
- [Extra: Workflows with Nextflow](https://unm-carc.github.io/foss/lessons/extra-nextflow/): A comparison of the Nextflow and Snakemake workflow managers and a hands-on RNA-seq tutorial that runs a Nextflow pipeline in a Conda environment.

## Capstone

- [Capstone Project Overview](https://unm-carc.github.io/foss/capstone/overview/): Objectives, example projects, and presentation prompts for the FOSS capstone, in which learners apply a course skill to their own work.

## About

- [Credits and attribution](https://unm-carc.github.io/foss/about/credits/): The CyVerse origin of FOSS, its authors and instructors, funding, how to cite the course, and the CC BY 4.0 attribution for this adaptation.
- [Contributing](https://unm-carc.github.io/foss/about/contributing/): How to edit pages, the OKF frontmatter contract, verifying adapted content, and building the site locally.
- [For AI agents](https://unm-carc.github.io/foss/about/ai-agents/): How agents and harnesses should consume this site: llms.txt, per-page Markdown with OKF frontmatter, and trust signals.

## Meta

- [Documentation update log](https://unm-carc.github.io/foss/log/): dated history of changes to this bundle.
- [For AI agents](https://unm-carc.github.io/foss/about/ai-agents/): endpoints and trust signals for agents.