carpentries-incubator / life-sciences-workshop

Life Sciences Workshop

Life Sciences Workshop

Data Carpentry provides workshops on fundamental data concepts, with the aim of proving the required skills to get started with modern data analysis. This workshop uses a collection of results files from a typical lab-based plate-reader, as seen in most life sciences labs.

The workshop primarily involves spreadsheet software (such as Microsoft Excel) and R, but assumes no prior knowledge of the latter. Basic familiarity with spreadsheets is expected.

Note that although the dataset used throughout these lessons is scientific, the ideas and principles explored could easily be applied to other data analysis scenarios outside of a life sciences context.

Motivation

The ability to load data into Excel, perform calculations and create plots is widespread. However, this 'mouse-click' driven approach to analysis, combined, perhaps, with a lack of good data management principles, can lead to analytical results that are ambiguous, non-reproducible, and unusable in the long term.

By applying basic data management ideas, combined with the ability to load, explore and analyse data in a code-based environment like R, your research efforts will be significantly improved.

Structure

Day 1 is aimed at a general audience of anyone who uses spreadsheets for their work. The material does not cover how to use a spreadsheet in terms of calculations, loading data, etc, as such knowledge is generally widespread. Instead, the focus is on how to organise and arrange data files and the data within those files, in order to maximise the transparency and reproducibility of your work.

Day 2 is for those who wish to go beyond the use of spreadsheets for their data analysis, with the introduction of R. The basics are covered, leading to the fitting of a 4-parameter logistic regression (4PL) curve to typical enzyme-linked immunosorbent assay (ELISA) data.

Day 3 is an introduction to statistics using R, focused on 'before and after' scenarios, which are typical in life science scenarios (e.g. evaluating results before and after a reagent change).

life-sciences-workshop's Issues

update links to episodes

in the index file, it looks like you replaced the default table with direct links to the github version of the episodes.

With the template, your lesson is currently rendered at https://carpentries-incubator.github.io/life-sciences-workshop/

Once the Rmarkdown files will be recognized by the template, the Rmd files will be knit into Markdown files in the _episodes folder and the default table that comes with the template will list all the episodes.

If you prefer to keep your customized version of the index file, you'll need to replace the links to: {{ page.root }}{% link _episodes/01-project-organisation-introduction.md %} for instance.

Tangentially related, for lessons that rely on Rmarkdown, I can set you up with Continuous Integration (we've been using Travis, but I'd like to start setting up new repositories with GitHub Actions) to render automatically the Rmd files into Markdown in the episodes folder so you don't have to render these files locally and keep both the md and the Rmd versions in the repository.

move all content to this repository?

hi @RobHarrand,

thanks for transferring your lesson to the Carpentries Incubator!

It looks like this repository is used a pointer to other lessons. I'm wondering if it would make sense to move the lessons you link to in this lesson directly in this repository and include in the index page how the episodes are intended to be distributed over the 2 days of the content you developed?

Let us know what you think!