22-23 March 2021
Instructors: Stacy Shinneman, Johannes De Groeve
Helpers: Marc Galland, Flavia Aschi, Tim Lenters, Morgan Brown, Jens van Erp, Elspeth Sage
This workshop is organized by the core members of the Amsterdam Science Park Study group. This small community of computational biologists aims to promote skill sharing and collaboration through the organisation of interactive workshops. It acts as the main local hub to set-up Software and Data Carpentry workshops (official workshops and Carpentry-style). All are welcome to this study group, regardless of scientific research area, affiliation or training level.
For more information on what we teach and why, see our website: "scienceparkstudygroup".
Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. 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 "Good Enough Practices for Scientific Computing".
Who: The course is aimed at masters students, PhD students, postdocs and researchers. Preference will be given to people affliated with the University of Amsterdam. It is important for the organizers to know how many participants will be there so we can make sure there are enough helpers, so please reserve your space in advance. We will restrict the course to a maximum of 30 participants. You should have a basic working knowledge of R, but you don't need to have any previous experience working with geospatial data. If you would like to refresh your R skills before the course, you can complete this lesson. You should have a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) with a solid internet connection and you should download the data and install R and RStudio on your computer before the course.
Online course: We will meet using Zoom. Each session will begin in the main room with a short presentation by the instructor to help you get started with the module. Participants will then go to breakout rooms to work together on the module in groups of 2-3. Instructors and helpers will be available at all times for questions and problem solving. Like other Carpentries workshops, you will be learning by "coding along". To do this, you will need to have both the window for R and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options: 1) two monitors, 2) two devices, or 3) divide your screen. This blog post includes detailed information on how to set up your screen to follow along during the workshop.
When: 22-23 March 2021. Add to your Google Calendar.
Accessibility: We are committed to making this workshop accessible to everybody. If we can help making learning easier for you, please get in touch (using contact details below) and we will try our best to help.
Contact: Please email s.shinneman@uva.nl for more information.
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct.This document also outlines how to report an incident if needed.
Please be sure to complete these surveys before and after the workshop.
| Morning (9:30-10:15) |
Introduction to geospatial concepts and the datasets (Stacy) |
| Morning (10:15-11:15) |
Intro to raster data (Stacy) |
| Morning (11:30-12:30) |
Plot raster data (Stacy) |
| Break | |
| Afternoon (13:30-14:30) |
Reproject raster data (Johannes) |
| Afternoon (14:45-17:00) |
Raster calculations (Johannes) |
| Afternoon (14:45-17:00) |
Work with multi-band rasters (Johannes) |
| Morning (9:30-10:00) |
Open and plot shapefiles (Stacy) |
| Morning (10:00-11:00) |
Explore and plot by shapefile attributes (Stacy) |
| Morning (11:15-12:00) |
Plot Multiple Shapefiles (Stacy) |
| Break | |
| Afternoon (13:00-14:00) |
Handling spatial projection & CRS (Johannes) |
| Afternoon (14:00-15:00) |
Convert from .csv to a shapefile (Johannes) |
| Afternoon (15:00-16:00) |
Manipulate raster data (Johannes) |
To participate in a Data 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.
The setup instructions for the Data Carpentry Geospatial workshop can be found at the workshop overview site.
We recommend the following online resources if you would like to continue to develop your skills or for problem-solving:
NEON Learning Hub data tutorials