Software Carpentry: Avida Workshop - Michigan State University

General Information

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.

Where: Biomedical and Physical Sciences Building, 567 Wilson Road Room 1455A, East Lansing, MI, 48824. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

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 dolsonem@msu.edu for more information.

Schedule

Day 1

9:00	Introductions and Overview
9:30	Avida from 10,000 feet
10:00	Finding your way around the Unix Shell
10:30	Break
10:45	Using a computing cluster
12:00	Lunch break
1:00	Doing simple experiments in Avida
2:00	Version control with Git
3:15	Break
3:30	More Git

Day 2

09:00	Analyzing data with Python
10:30	Break
10:45	More Python
12:00	Lunch break
1:00	Advanced topics in Avida
2:30	Break
2:45	More Avida
3:30	Wrap up

Etherpad: http://pad.software-carpentry.org/2015-10-16-avida.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

Files and directories
History and tab completion
Pipes and redirection
Connecting to high performance clusters
Running jobs on high performance clusters
Reference...

Programming in Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals
Defensive programming
Using Python from the command line
Reference...
Matplotlib reference
Scripts from the graphing section

Version Control with Git

Creating a repository
Recording changes to files: add, commit, ...
Viewing changes: status, diff, ...
Ignoring files
Working on the web: clone, pull, push, ...
Resolving conflicts
Open licenses
Where to host work, and why
Cloning and contributing to Avida
Reference...

Avida

What is Avida and how does it work?
A brief history of Avida research
Getting Avida running on your computer
Planning, setting up, and running Avida experiments
Collecting and analyzing Avida data
Common configurations to build off of
Contributing to Avida

Setup

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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
1. Click on "Next".
2. Click on "Next".
3. Click on "Next".
4. Click on "Next".
5. Click on "Next".
6. Select "Use Git from the Windows Command Prompt" and click on "Next". 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.
7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
8. Select "Use Windows' default console window" and click on "Next".
9. Click on "Next".
10. Click on "Finish".

Mac OS X

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 in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

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 install anything.

Git

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).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, 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" available here.

Linux

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

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.

Text Editor

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.

Windows

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.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

Python

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).

Windows

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Windows.
Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for OS X.
Install Python 3 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Linux.
Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and 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.