Oct 17 - 18, 2015
9:00 am - 5:00 pm
Instructors: Nasťa Zidkova, Filip Sedlák, Mira Hédl, Stefan Negru
Helpers: Petr Šimeček, Vašek Gergelits, Martin Jahn, Petr Švarný, Tomáš Laube, Charles Bajeux
This course will help you to use the computer more efficiently during your research. We'll show you how to automate repetitive procedures like manipulating files, computing statistics and creating charts from your data. This will help you make your analyses less error prone and reproducible.
If you're eager to learn but you don't see the use of such skills in your research, don't worry. The more you know, the more cases you'll see where you can apply your newly acquired skills.
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.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Price: This course is offered to you at courtesy of the instructors and helpers. Please smile at them. :-) There is no budget for food and beverages. If you'd like to return the favour, you're more than welcome to bring in any meal or snack.
Contact: Please mail firstname.lastname@example.org for more information.
Registration: Registration is closed now :(
Don't take the schedule too seriously, it may change.
|09:30||Introducing the Shell, Files and Directories|
|10:40||Combining Shell Commands, Finding Things|
|13:00||Analyzing Patient Data in Python|
|14:50||Making Choices, Combining Things, Understanding Errors|
|09:00||Defensive Programming, Debugging, Command-line programs|
|10:40||Libraries in Python|
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.
Software Carpentry organization maintains 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
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.
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 an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 2.x and not version 3.x (e.g., 2.7 is fine but not 3.4). Python 3 introduced changes that will break some of the code we teach during the workshop.
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).
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 workshop.)
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).
Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.