Oct 12, 2016
8:30 am - 5:00 pm
Instructors: Joslynn Lee, Camille Avestruz
Adapted from Software Carpentry and Data Carpentry workshops, which are for any researcher who has data they want to analyze with no prior computational experience is required. This abridged hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.
In short form of the traditional 2-day workshops, we will cover The Unix Shell, Programming with R, and Programming with Python. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.
Who: This free workshop has a morning and afternoon session. The workshop is aimed at undergraduate, graduate students, faculty and other researchers.
Where: 300 E Ocean Blvd, Long Beach, CA 90802. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software and Data Carpentry's Code of Conduct.
Contact: Please mail Joslynn Lee jolee@cshl.edu for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 08:30 | Overview of Agenda and Instructors |
| 08:40 | Introduction to CyVerse Infrastructure |
| 08:55 | Introduction to Software & Data Carpentry and Reproducible Research |
| 09:00 | Scaling data skills training for researchers |
| 09:05 | Good Enough Practices |
| 09:15 | Computer check for software/downloads |
| 09:30-11:30 | The Unix Shell |
| 09:30 | Introducing the Shell |
| 09:35 | Navigating Files and Directories |
| 09:50 | Working with Files and Directories |
| 10:05 | Pipes and Filters |
| 10:30 | Break |
| 10:40 | Loops |
| 10:55 | Shell Scripts |
| 11:10 | Finding Things |
| 11:30-12:00 | Wrap-up |
| 04:30 | Large scale computing + CyVerse |
| 11:50 | Questions |
| 01:30 | Overview of Agenda and Instructors |
| 01:35 | Introduction to CyVerse Infrastructure |
| 01:40 | Introduction to Software & Data Carpentry and Reproducible Research |
| 01:45 | Why I became an instructor? |
| 01:50 | Computer check for software/downloads |
| 02:00-3:15 | Programming with R |
| 02:00 | Intro to RStudio and Data Analysis |
| 03:15 | Break |
| 03:30 | Programming with Python |
| 03:30-4:30 | Demo Notebook |
| 04:30-5:00 | Wrap-up |
| 04:30 | Large scale computing + CyVerse |
| 04:50 | Questions |
To participate in this workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. In addition, an up-to-date web browser is necessary.
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.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]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
(found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
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
install anything.
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.
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.
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
Others editors that you can use are Text Wrangler or Sublime Text.
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 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).
jupyter notebook
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear.
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).
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.