January 14-16, 2019
9:00 am - 5:00 pm
Instructors: Pariksheet Nanda, Kendra Maas, Asli Uyar, Cera Fisher, James Mickley, Timothy Moore
Helpers: Dyanna Louyakis, Dipanjana Dalui
This workshop is cancelled. Thank you for your interest! We hope to see you at a future Carpentries workshop.
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Innovation Partership Building (IPB) room 315, 159 Discovery Drive, Storrs, CT 06269. Get directions with OpenStreetMap or Google Maps.
When: January 14-16, 2019. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email pariksheet.nanda@uconn.edu for more information.
Please be sure to complete these surveys before and after the workshop.
| Before | Pre-workshop survey |
| 09:00 | Workshop Overview |
| 09:15 | Introduction to R and RStudio |
| 10:15 | Project management with RStudio |
| 10:30 | Seeking help |
| 10:45 | Coffee |
| 11:00 | Data structures |
| 12:00 | Lunch break |
| 13:00 | Exploring Dataframes |
| 13:30 | Subsetting data |
| 14:30 | Coffee |
| 14:45 | Subsetting data (continued) |
| 15:15 | Control flow |
| 16:00 | Wrap-up |
| 09:00 | Creating publication-quality graphics |
| 10:45 | Coffee |
| 11:00 | Vectorization |
| 11:15 | Functions explained |
| 12:00 | Lunch break |
| 13:00 | Writing data |
| 13:30 | Dataframe manipulation with dplyr |
| 14:30 | Coffee |
| 14:45 | Dataframe manipulation with tidyr |
| 15:45 | Producing reports with knitr |
| 16:15 | Wrap-up |
| * Bioconductor is not yet formally part of the Carpentries curriculum | |
| 09:00 | Workshop Overview |
| 09:15 | Introduction to Bioconductor |
| 10:15 | RNA-seq data analysis with DESeq2 |
| 10:30 | Coffee |
| 11:00 | RNA-seq data analysis with DESeq2 (continued) |
| 12:00 | Lunch break |
| 13:30 | Solving common bioinformatic challenges using GenomicRanges |
| 14:45 | Coffee |
| 15:00 | Introduction to Bioconductor annotation |
| 15:45 | Public data resources and Bioconductor |
| 16:45 | Wrap-up |
| End | Post-workshop Survey |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo dnf install R). Also, please install the
RStudio IDE.