Carpentries style materials

Here are a collection of Carpentries style lessons. These are not part of the official carpentries curriculum, but are a good source of inspiration whenever you need them. Remember to acknowledge the authors according to their license.

Would be awesome if you could add examples! please contact me for questions.

If you want your lessons to be part of the Carpentries curriculum you can propose them to The Carpentries Incubator: The Incubator will serve as a single point of entry for lessons or ideas at any stage in the development process. Some of the lessons here are transitioning to the incubator.

R

• Git using Rstudio by Stijn van Hoey recently (Oct 2019) moved to The Carpentries Incubator! https://carpentries-incubator.github.io/git-Rstudio-course/. This is a short lesson to teach git from RStudio using The Carpentries style version 9.5.0. developed by Stjin van Hoey, you can contact me @orchid00 if you have questions or @stijnvanhoey on github and @SVanHoey on twitter.
• https://tibhannover.github.io/FAIR-R/ – Fork of r-novice-inflammation that focusses on function documentation, packaging & testing. Was used in https://tibhannover.github.io/2018-07-09-FAIR-Data-and-Software/
• https://uomresearchit.github.io/r-tidyverse-intro/ –a condensed version of the Software Carpentry intro to R lesson, with tidyverse and a bit of modeling thrown in. Put together by Research IT, University of Manchester, UK
• Data Harvesting for Agriculture https://data-carpentry-for-agriculture.github.io/trial-lesson/, Contact Lindsay Clark or Neal Davis for more information at data-harvesting [at] illinois [dot] edu.

R Genetics and Genomics

• Quantitative Trait Mapping https://smcclatchy.github.io/mapping/. This lesson introduces genetic mapping using qtl2, a R package for analyzing quantitative phenotypes and genetic data from complex crosses like the Diversity Outbred (DO).

Python

• Numpy https://afdataschool.github.io/numpy/ by AF data school.
• Python for Atmosphere and Ocean Scientists https://data-lessons.github.io/python-aos-lesson/ Using Data Carpentry template Contact Damien Irving @DrClimate
• Plotting and Programming in Python using Spyder instead of Jupyter Notebooks - http://scw-aberystwyth.github.io/python-novice-gapminder/
• Software Testing in Python https://neurohackweek.github.io/software-testing-for-scientists/ by neurohackademy.
• Python Testing and Continuous Integration https://katyhuff.github.io/python-testing/ by Katy Huff.
• High performance Python https://neurohackademy.github.io/high-performance-python/ by neurohackademy.
• Convolutional Neural Networks https://neurohackademy.github.io/convolutional-neural-networks/ by neurohackademy.
• Image processing with Python - This lesson is under development (not yet official) for use in the Digital Imaging and Vision Applications in Science (DIVAS) Image Processing summer workshop https://datacarpentry.org/image-processing/.
• Introduction to Python for Data Science https://kaust-vislab.github.io/python-novice-gapminder/.
• Introduction to Conda for (Data) Scientists https://kaust-vislab.github.io/introduction-to-conda-for-data-scientists/.
• Publication ready scientific reports and presentations with Jupyter notebooks https://annefou.github.io/jupyter_publish/index.html.

Machine Learning with Python

• A carpentry style course on machine learning with Python and Scikit Learn https://scw-aberystwyth.github.io/machine-learning-novice/
• C3DIS 2019 - Introduction to Machine Learning with Python https://injeans.github.io/c3dis-intro-to-ml/ Using The Carpentries style version 9.5.3.
• https://machinelearningcarpentry.github.io/machine-learning-novice/

Shell

• Vim and advanced bash https://afdataschool.github.io/vim-bash/

Git - Version Control

• Customised from git - https://uw-madison-datascience.github.io/git-novice-custom/ - Teaches branches and pull requests
• CodeRefinery git intro https://coderefinery.github.io/git-intro/ - Guacamole example
• Collaborative distributed version control https://coderefinery.github.io/git-collaborative/ - Working with remotes, pull requests, and code review
• Git branch design https://coderefinery.github.io/git-branch-design/ - Rebase vs. merge, avoiding conflicts, branching models
• Git - Github - Rstudio by INBO, @Stijnvanhoey https://inbo.github.io/git-course/
• Steve Bond (Biologyguy)’s Git and Github with examples that make more sense IRL: https://biologyguy.github.io/git-novice/ Two hour edition targeted at IT pros based on this version: https://dlstrong.github.io/git-novice/. I teach this as a full day lesson, and use a cut-down version for SWC workshops: http://gcapes.github.io/git-course. Writing a paper as the narrative, covers branches, revert, reset, rebase, remotes, PRs.
• Modified version of git-novice that uses Git Desktop and uses editing a carpentry data file as example: https://caltechlibrary.github.io/git-desktop/
• Git SWC extended UW Madison https://uw-madison-datascience.github.io/git-novice-custom/ - Teaches branches and pull requests
• Git beyond the basics https://m4rkd.github.io/git-beyond-the-basics/
• Introduction to Git and GitHub https://elizabeth-dupre.com/git-course/ (forked from gcapes/git-course) by @emdupre
• Git Intro https://csiro-data-school.github.io/git-intro by CSIRO data school
• Git continued https://csiro-data-school.github.io/git-continued/ by CSIRO data school

SQL

• SQL for Business https://data-lessons.github.io/SQL-business This lesson will teach you what relational databases are, how you can load data into them and how you can query databases to extract just the information that you need.

Docker / Singularity - Containers

• Reproducible computational environments using containers https://dme26.github.io/docker-introduction/. This lesson is now within the Carpentries incubator https://github.com/carpentries-incubator/docker-introduction and it is likely that ongoing development should proceed there.
• https://neurohackweek.github.io/docker-for-scientists/
• Introduction to Conda for (Data) Scientists https://carpentries-incubator.github.io/introduction-to-conda-for-data-scientists/
• Containers in HPC from the Pawsey Centre, an overview and examples for both Singularity and Docker https://pawseysc.github.io/sc19-containers/

HPC - High Performance Computing

• HPC Carpentry: https://hpc-carpentry.github.io/ Made up of 1/2 day lessons that can be combined together in different ways depending on the audience
  • hpc-shell: Intro to the shell for people using remote advanced computing systems
  • hpc-intro: intro to using HPC systems
• A one day workshop introducing parallel programming using MPI. https://rantahar.github.io/introduction-to-mpi/
• Introduction to GPU from the University of Sydney Informatics Hub.

Common Workflow Language (CWL)

• Common Workflow Language User Guide Using The Carpentries style version 9.5.3.

GAP - computational algebra

• https://carpentries-incubator.github.io/gap-lesson/ by Alexander Konovalov

Genomics

• Molecular Epidemiology of Infectious Diseases - computer practical - prerequisite Shell https://aschuerch.github.io/MolecularEpidemiology_AnalysisWGS/index.html
• Molecular Basis of Bacterial Infections course, computer practical https://aschuerch.github.io/MBBI_ComputerPracticum/ partially based on the Data Carpentry Genomics lesson. - prerequisite Shell.

Data Stewardship

• 23 (Research Data) Things https://data-lessons.github.io/23-rd-things/ 23 (research data) Things is a self-guided training concept for anybody interested in data.
• Data and the FAIR Principles http://www.repronim.org/module-FAIR-data/ This module provides a number of lessons to ensure that a researcher’s data is properly managed and published to ensure it enables reproducible research.

  Reproducibility

• Reproducible Research Things. This lesson is still being designed and assembled (Pre-Alpha version) https://orchid00.github.io/ReproducibleResearchThings/

Open Source Software

• 4 Simple recommendations for Open Source Software https://softdev4research.github.io/4OSS-lesson/

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