Jan 18-20, 2016
9:00 am - 5:30 pm
Instructors: Martin Callaghan, Grace Cox, Andrew Walker
Helpers: George Taylor, Jon Mound, Andrew Evans, Jo Leng
Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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".
The workshop is funded by NERC as part of the Advanced Training Short Courses programme. Priority will thus be given to NERC-funded PhD students and early career researchers from the environmental sciences who should register below or contact Jon Mound for further information. Some funding to cover travel and accommodation costs of these participants is avalable. Any unallocated spaces will be made generally avalable in early December.
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.
This is the second of two workshops in January aimed at the NERC community and funded by the ATSC scheme. This one is aimed at participants with very little (or no) prior knowledge of programming but who want to develop some knowledge of python, and an understanding of good practice in scientific computing and the tools that make this possible. The workshop to be held in Bristol earlier in January will be more appropriate for those with more background knowledge. If you are not sure which workshop is best for you please get in touch with us.
Contact: Please mail J.E.Mound@leeds.ac.uk for more information.
|09:00||Arrival and Welcome|
|09:30||Using the shell to do more in less time (1)|
|10:45||An introduction to python (1)|
|13:30||An introduction to python (2)|
|15:15||An introduction to python (3)|
|09:30||Using the shell to do more in less time (2)|
|10:45||Using version control to manage information|
|13:00||Using version control to share information|
|15:15||Open science and good programming practice|
|09:30||Python and environmental data|
|16:30||Pulling it all together|
We will use this Etherpad 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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option. This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is bash, so no
need to install anything. You access bash from the Terminal
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing
bash. There is no need to
Git is a version control system that 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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git.
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.
nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).
We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).
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).
We have gathered together the various links you will need and useful information below. These will remain accessable after the workshop and we will add to this list as the workshop progresses. Please read and abide by the code of conduct.
Much of the material we will be using during the workshop can be found online and you will need copies of this on your laptop. In order to download the material for the first session on bash (and to check you have a working system with internet access) please start a new shell and type the following commands:
(typing return after each line). You should see something like "repository successfully cloned". Let us know if this does not work for you.
cd cd Desktop git clone https://github.com/gracecox/2016-01-18-leeds-bash.git cd 2016-01-18-leeds-bash
The python material is is avalable in the same way. To get hold of the data (and the files we created during the workshop) type:
cd cd Desktop git clone https://github.com/callaghanmt/2016-01-18-leeds-pystudents.git cd 2016-01-18-leeds-pystudents
If you find yourself in a shell that you don't recognise, or in an editor that you can't get out of then see recognising prompts and how to exit.
Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745.
Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285.
Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424.
Ram K (2013) "git can facilitate greater reproducibility and increased transparency in science", Source Code for Biology and Medicine 2013, 8:7 doi:10.1186/1751-0473-8-7.
Glass, R. (2002) Facts and Fallacies of Software Engineering, Addison-Wesley, 2002. (PDF).