Aug. 26-27, 2017
8:30 - 17:00
Instructors: Uwe Hilgert, Liz Bowman, Gaius Augustus, Upendra Devisetty
Helpers: Ajin Baby, Andreina Castillo, Keling Chen, Shu Cheng, Asher Haug-Baltzell, Firoz Pathan, Julian Pistorius, Mohit Shah, Travis Struck, Anandraj Thiyagarajaperumal, Ken Youens-Clark, Wendan Zhang
Application Form: Apply for the workshop at https://cyverse-sdc.eventbrite.com/.
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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".
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.
Where: Please check your email for the workshop location!.
When: Aug. 26-27, 2017. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges to. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Links to workshop materials are being provided below. If we can provie additional resources to help making learning easier for you (e.g. large-font hand-outs, sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email hilgert@email.arizona.edu for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 08:30 | Automate tasks with the Unix shell and git/GitHub |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Scientific Analyses with R and git/GitHub |
| 14:45 | Coffee |
| 17:00 | End of Day |
| 08:30 | Scientific Analyses with R and git/GitHub, cont. |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Scientific Analyses with R and git/GitHub |
| 14:45 | Coffee |
| 16:00 | End of Day |
Schedule subject to change if necessary.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Find, create, copy, move and delete folders and filesadd, commit, ...status, diff, ...clone, pull, push, ...Syllabus subject to change if necessary.
To participate in a Software Carpentry workshop, you will need access to the software described below. Unless you prepare your laptop as described below you will be unable to follow along. In addition, you will need an up-to-date web browser, we recommend Firefox, Chrome or Safari as Internet Explorer can be buggy.
Should you encounter issues while installing the software below, please look for a solution in our Configuration Problems and Solutions wiki page. If this does not help please get in touch (using contact details above) and we will attempt to provide a solution.
Bash is a commonly-used command line 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.
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).
You will need a GitHub account for the workshop. If you don't have one already, please register for one at github.com; basic GitHub accounts are free (and can only be used for publically available content).
(Tip: Please consider what personal information you wish to reveal. For an example, please review these instructions for keeping your email address private at GitHub.)
Git should be installed on your computer as part of the Git Bash install you just completed (described above).
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.
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.
Several text editors are available that are optimized for writing code, providing features such as automatic color-coding of key words, automatic insertion of closing brackets with each opening bracket, automatic indenting, etc. Mac OS X and Linux are usually equipped with the Vim code editor, which is not famous for being intuitive. (Tip: if you accidentally find yourself stuck in Vim, hit the Escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hit Return to return to the shell.)
We will use the basic editor 'nano' in the workshop; if your computer doesn't have it, install it by downloading/saving the Software Carpentry Windows installer. Double-click the installer file to run it. (CAVEAT: This installer requires an active internet connection.)
Please contact the workshop organizer listed above if you experience difficulties installing the 'nano' editor.
If you prefer to use other editors (such as 'Notepad++' or 'Sublime Text') add their installation directories to your system path to ensure that they run correctly in Git Bash. If you are not sure how to do this, please install and use 'nano' for the duration of the workshop.
We will use the basic editor 'nano' in the workshop; it should be pre-installed. See the Git installation video tutorial on how to open nano.
If you prefer to use other editors (including 'Text Wrangler' or 'Sublime Text'), please ensure that they integrate with your bash shell/terminal.
We will use the basic editor 'nano' in the workshop; it should be pre-installed.
If you prefer to use other editors (including 'Gedit', 'Kate' or 'Sublime Text'), please ensure that they integrate with your bash shell/terminal.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo yum install R). Also, please install the
RStudio IDE.
You will not need OpenRefine for this workshop. However, OpenRefine is a promising tool to error-check and fix large data sets quickly and, time permitting, we might discuss its use at the workshop. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.
Download software from http://openrefine.org/
Create a new directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".
Go to your newly created OpenRefine directory.
Launch OpenRefine by clicking openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).
If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.
Download software from http://openrefine.org/.
Create a new directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory by double-clicking it.
Go to your newly created OpenRefine directory.
Launch OpenRefine by dragging the icon into the Applications folder.
Use Ctrl-click/Open ... to launch it.
If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
If the program still does not work, try uninstalling and reinstalling it. This time, however, first change in Security & Privacy the settings for "Allow apps download from" by selecting "Anwhere." Once you opened the software it is recommended to reset to default security settings.
Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.
Download software from http://openrefine.org/.
Make a directory called OpenRefine.
Unzip the downloaded file into the OpenRefine directory.
Go to your newly created OpenRefine directory.
Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.
If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.