Jun 24-25, 2015
9:00 am - 5:00 pm
Instructors: Karthik Ram, Aleksandra Pawlik, Mateusz Kuzak
Helpers: Mateusz Kuzak, Philip Lijnzaad, Vincenza Colonna, Aleksandra Nenadic, Frederik Coppens, Angel Corpuz, Walid Gharib, Joris Borgdorff, Carlos Martinez Ortiz
In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. Data Carpentry is designed to teach basic concepts, skills and tools for working more effectively with data. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools.
For communication we will be using this Etherpad
Workshop Learning objectives & programme
For more information, please contact Celia van Gelder (DTL, ELIXIR-NL).
We especially encourage to register those who may be less familiar with the above topics. There is no prerequisite as to what computing skills and knowledge is required.
The workshop is supported by the ELIXIR programme. Data Carpentry is a sibling organization of Software Carpentry and is designed to teach basic concepts, skills and tools for working more effectively with data. The structure and objectives of the curriculum as well as the teaching style are informed by Software Carpentry.
|Wednesday||09:00 - 9:30||Introduction and setup help|
|09:30 - 10:30||Better use of spreadsheets (Sample dataset 1.) (Sample dataset 2)|
|10:30 - 11:00||Break|
|11:00 - 12:00||Introduction to R|
|12:00 - 13:00||Lunch break|
|13:00 - 14:30||Working with data in R - part 1|
|14:30 - 15:00||Coffee break|
|15:00 - 16:45||Working with data in R - part 2|
|16:45 - 17:00||Wrap-up|
|Thursday||09:00 - 10:30||Working with command line - part 1. (Sample dataset.)|
|10:30 - 10:45||Break|
|10:45 - 12:00||Working with command line - part 2|
|12:00 - 13:00||Lunch|
|13:00 - 14:45||Introduction to data manipulation with SQL|
|14:45 - 15:00||Break|
|15:00 - 16:30||Working with ELIXIR cloud|
|16:30 - 17:00||Wrap-up and feedback|
To participate in a Data Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your workshop.
When you're writing scripts or text, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by ':wq!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell. (This will exit Vim and save the changes you made in the file.)
Bash is a commonly-used command line interface, a so-called shell. Using a shell gives you the power to do more tasks more quickly by freeing you from having to click everything.
R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.
Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). The instructions to modify your path are available online here. Please ask your instructor to help you do this.
Install Git (version control) and a Bash shell for Windows from the msysGit project's homepage. This will provide you with Bash in the Git Bash program.
Install the Firefox SQLite browser plugin described below.
Other tools used in Data Carpentry have been packaged up by Software Carpentry in an installer. This installer requires an active internet connection.
The default shell in all versions of Mac OS X is bash,
so no need to install anything. You access bash from
the Terminal (found
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
Kate is one option for Linux users.
Alternatively, you can use
which should be pre-installed.
sqlite3 comes pre-installed on Linux.
Also install the Firefox SQLite browser plugin described below.
OpenRefine (formerly Google Refine) is a powerful tool for exploring and working with messy data. You will need a browser (Firefox or Chrome is recommended) to work with Open Refine. Once you install Open Refine, you should be able to launch it double clicking like most of the programs. Open Refine will open in the browser (but you don't have to be online)