Laurent Gatto on The Carpentries

Celebrating The Carpentries Workbench

Mon, 21 Aug 2023 00:00:00 +0000

In May 2023, a significant milestone was reached as The Carpentries transitioned all 43 of its official lessons to a new lesson infrastructure, The Carpentries Workbench. This project, led by Zhian Kamvar our Lesson Infrastructure Developer, was a three-year coordinated effort requiring input and contributions from many members of our community. We asked six of them to provide their reflections on the project, its impact, and Zhian’s leadership.

Jennifer Stubbs, Assistant Professor, Bradley University

Community Roles: Community Session Host, Instructor, Maintainer

Incubator Lesson Spotlight: Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

Tue, 13 Jul 2021 00:00:00 +0000

The Incubator Lesson Spotlight highlights a lesson under development by our community in The Carpentries Incubator. In this edition, we look at the progress being made on the {{page.lesson_title}} lesson, and hear from the authors about how The Carpentries community can get involved with the ongoing development of this lesson.

Lesson Profile

Title: {{page.lesson_title}}
Lesson Pages: https://carpentries-incubator.github.io/bioc-rnaseq
Lesson Repository: https://github.com/carpentries-incubator/bioc-rnaseq

Learning Objectives

After following this lesson, learners will be able to:

choose an appropriate design for a bulk RNA Sequencing experiment.
import and annotate quantified RNA-Seq data in R.
assess the quality of experimental results represented as a gene expression matrix.
run a standard differential expression analysis and interpret the output.
execute a gene set analysis.

Target Audience

This lesson is aimed at researchers who are already aware of what Bioconductor is and how it can benefit their data analysis. They are comfortable with basic operations in R, such as creating numeric, character vector, and data frame variables, installing and loading packages from CRAN and Bioconductor, and visualising data in common formats such as bar and scatter plots. These researchers want to learn how to use R and Bioconductor to explore and analyse data produced in bulk RNA sequencing experiments, and visualise and interpret the results of these analyses.

Cambridge Instructor Training 19-20 September 2016

Thu, 20 Oct 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Last month, Steve and Karin taught an instructor training workshop at the University of Cambridge, sponsored by the R Consortium. The event was organized by Laurent Gatto, a Software Sustainability Institute Fellow, with help from Paul Judge and Gabriella Rustici from the University of Cambridge Bioinformatics Training facility. 25 trainees from a diverse set of backgrounds spent two days getting to know each other and learning how to teach, and several have already completed the checkout process. You can read a full write-up on the SSI website, and we hope to be able to organize a repeat in the new year.

R Instructor Training Applications Open

Mon, 16 May 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Thanks to generous sponsorship from the [R Consortium](https://www.r-consortium.org/), Software Carpentry is running a two-day R instructor training class in Cambridge, UK, on September 19-20, 2016. If you are active in the R and/or Software and Data Carpentry communities, and wish to take part in this training, please fill in [this application form](https://docs.google.com/forms/d/1py7-vm6ZGHKZD_lixAlaAeQnWk9llEnK5sOEydI2Ipc/viewform). We will select applicants, and notify everyone who applied, by June 30, 2016; those who are selected will be responsible for their own travel and accommodation. If you have any questions, please mail [training@software-carpentry.org](mailto:training@software-carpentry.org).

Please note that as a condition of taking this training:

An R-based Instructor Training Sponsored by the R Consortium

Mon, 28 Mar 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

The R consortium Infrastructure Steering Committee awards have been officially announced and we are happy to confirm that our proposal to organise an R-based instructor training was successful.

We will organise an in-person instructor training that will focus on R. While the content of the training will not change as such, code-related exercises and examples that the participants will be working with will be focused on R, and will be made available to the R instructor community to help them improve their teaching. The full proposal is available here.

Running a Remote Workshop in South Africa

Sat, 13 Jun 2015 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

Last month we ran a workshop at Stellenbosch University in South Africa. The workshop instructors were Laurent Gatto (from the UK - coming in as remote instructor), and two local instructors - David Merand and Anelda van der Walt. We had four helpers in the room and 32 participants.