Oct 17-18, 2015
9:00am - 4:30 pm Saturday
9:00am - 4:00pm Sunday
Instructors: Cliff Bohm, Josh Nahum, Emily Dolson
Helpers: Alex Lalejini
Avida is a free, open source scientific software platform for conducting and analyzing experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. As a very different instantiation of evolution from biological evolution, Avida can often function as a way of testing the generality of evolutionary hypotheses. In addition, Avida's fast generation times and complete information about evolutionary trajectories can make it possible to test hypotheses that would be intractable in most biological systems.
But we know Avida can have a steep learning curve. A big part of that, especially for people with a less computational background, is that there are a lot of computational skills that are necessary (or at least highly useful) for running experiments in Avida. Increasingly, these skills are also useful for scientific computing more generally. That's why we created this workshop: a Software Carpentry workshop with a focus on getting participants up and running with Avida. Software Carpentry is a series of workshops with the mission of helping scientists and engineers get more research done in less time and with less pain by teaching them these skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. We will also apply all of these general concepts to the specific case of working with Avida; over the course of the workshop, participants will configure a run of Avida, submit it to a compute cluster, and analyze the results.
For more information on what we teach in Software Carpentry and why, please see our paper "Best Practices for Scientific Computing". For more information about current work with Avida (or to read out blog!), see the Digital Evolution Lab website.
Who: This course is aimed at people of all levels, from undergraduates to professors and anywhere betwixt, between, or beyond, who are interested in learning how to use the Avida Digital Evolution platform for their research (or personal gratification!). We will also be covering skills for scientific computing more generally (see full syllabus below), which we expect will be helpful in your work beyond Avida as well. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Interested? If you want to participate in this workshop, or be notified if we do a similar workshop in the future, please RSVP here.
Contact: Please mail firstname.lastname@example.org for more information.
|9:00||Introductions and Overview|
|9:30||Avida from 10,000 feet|
|10:00||Finding your way around the Unix Shell|
|10:45||Using a computing cluster|
|1:00||Doing simple experiments in Avida|
|2:00||Version control with Git|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
Note about high-performance computing access: Since we want this to be as hands-on as possible, and running Avida experiments on your laptop is not a viable long-term strategy, we strongly encourage you to get access to your University's high-performance computing facilities ahead of time. If you're affiliated with Michigan State Univeristy, then your best bet is the HPCC. You can get an account by sending in a request with a short summary of the research that you're interested in using the HPCC to do. Note that you must be a PI to submit a request. If you are a grad student, your PI should be able to submit a request on your behalf. If you aren't affiliated with MSU or are having problems, e-mail us and we'll figure something out.
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.
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.
Filezilla is a convenient interface for moving files between your computer and a computing cluster. Regardless of which operating system you're using, you should be able to download and install a version here.
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).
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.