Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Please note that this workshop is only for the students affiliated with EPSRC and MRC Centre for Doctoral Training in Regenerative Medicine, University of Manchester.
Instructors: Kate Lee, Mario Antonioletti, Aleksandra Pawlik
Who: The course is delivered as a part of training for EPSRC & MRC Centre for Doctoral Training in Regenerative Medicine at the Faculty of Life Sciences, University of Manchester.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Contact: Please mail firstname.lastname@example.org for more information.
|09:00||Welcome and setup help|
|09:30||Automating tasks with the Unix shell - part 1|
|11:30||Automating tasks with the Unix shell - part 2|
|13:30||Structured programming using Python - part 1|
|15:30||Structured programming using Python - part 2|
|17:00||End of Day 1|
|09:00||Version control with Git|
|11:30||Version control - working with GitHub|
|13:30||Introduction to SQL|
|15:30||Data manipulation with R|
To participate in a Software Carpentry bootcamp, 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 bootcamp.
When you're writing code, 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 ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
Git is a state-of-the-art version control system. It lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com.
Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection
After installing Python and Git Bash:
nano is the editor installed by the Software Carpentry Installer,
it is a basic editor integrated into the lesson material.
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). Please ask your instructor to help you do this.
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.
Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
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.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager, e.g. for Debian/Ubuntu
apt-get install r-base or
yum install R.
Also, please install the
sqlite3 comes pre-installed on Linux.
you may install the Firefox SQLite browser plugin described below.
We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).