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Indonesia Biodiversity Research Center, Bali

Aug 3-4, 2015

9:00 am - 5:00 pm

Instructors: Areej Alsheikh-Hussain, Eric Crandall

Helpers: John Deck, Katja Lehmann, Cynthia Riginos, Patricia Cockett

General Information

These lessons are intended to give learners a general introduction to computational skills that are increasingly important for biologists to understand. Do not expect to emerge from this workshop as an expert in computational biology! Our overall goal is to give you a foundation of skills that you can extend through using them in your research.

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, 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 biology faculty from Southeast Asia

Where: Praja Hotel, Renon, Denpasar, Bali. 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.

Contact: Please mail eric.d.crandall@gmail.com for more information.

Schedule

Note that this schedule only applies to the Software Carpentry portion of the workshop (first two days)

Day 1

10:00 Introduction, software setup and troubleshooting
11:00 Automating tasks with the Unix shell
12:00 Lunch
13:30 Automating tasks with the Unix shell - continued
15:00 Break
15:30 Automating tasks with the Unix shell - continued
17:00 Wrap-up

Day 2

9:00 Programming with R
10:30 Break
10:45 Programming with R - continued
12:00 Lunch
13:30 Programming with R - continued
15:00 Break
15:30 Programming with R - continued
16:30 Wrap-up for Software Carpentry Workshop

Etherpad: https://etherpad.mozilla.org/2015-08-03-IBRC-Indonesia.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

Programming in R

Setup

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. 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. We will be using Bio-Linux as a common platform for learning. Bio-Linux is a distribution of the popular and free Ubuntu Linux operating system, but includes more than 250 useful bioinformatic programs and packages. We will be using Bio-Linux for the Introduction to the Unix Shell, but also for lessons on RAD and Metagenomic pipelines on Thursday and Friday. You may install and run Bio-Linux on your computer in a variety of ways:

Windows

We will provide Bio-Linux on USB drives (generously provided by Katja Lehmann and the UK National Environment Research Council (NERC). You may boot your Windows computer directly from these drives to run Bio-Linux. Please refer here for instructions ahead of time. You will need to figure out how to boot your computer from a USB drive ahead of time. Please do so before class starts on Monday

Alternatively, you may install VirtualBox (free emulation software) and install Bio-Linux on this. This will allow you to run Windows and Bio-Linux simultaneously. See instructions here (Running Bio-Linux as a VM with VirtualBox) as well as below. This option requires 40GB of free disk space, and a 4GB download. Eric Crandall will also have the 4GB .ova file available on Sunday and Monday morning for those who are interested in this option.

If neither of the above options work, please consider installing Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program. However, you will need to install a number of additional programs if you want to use your computer for lessons on Metagenomics and RAD pipelines.

Finally, there is the possibility of using the ResBaz platform, which will allow you to use R and Unix from your browser. Please talk to an instructor if you feel this option is for you (you are unable to install anything). If you use this option, you need to have a Twitter or Github account beforehand.

Mac OS X

The USB drives cannot be booted from a Mac. We therefore recommend that you install VirtualBox (free emulation software) and install Bio-Linux on this. This will allow you to run Windows and Bio-Linux simultaneously. See instructions here (Running Bio-Linux as a VM with VirtualBox) as well as below. This option requires 40GB of free disk space, and a 4GB download. Eric Crandall will have the .ova file available on Sunday and Monday morning for those who are interested in this option.

Fortunately, the default shell in all versions of Mac OS X is bash, so if you are not able to install Bio-Linux you can use this with no need to install anything. However, you will need to install a number of additional programs if you want to use your computer for lessons on Metagenomics and RAD pipelines. Please consult the instructors about this. 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. You will need to install a number of additional programs if you want to use your computer for lessons on Metagenomics and RAD pipelines.

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

Vim and Emacs are two basic editors that come in bash. They are a bit tricky to use. If you are booted into Bio-Linux, then use Gedit, the default windowed text editor, which is fairly user friendly. There are a number of Windows user-friendly editors that you can use, but you won't be able to use them if you are booted using a USB drive: 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

If you are booted into Bio-Linux, then use Gedit, the default windowed text editor, which is fairly user friendly. Besides Vim and Emacs, other text editors that you can use are: Text Wrangler or Sublime Text.

Linux

Besides Vim and Emacs, other text editors that you can use are: Gedit, Kate or Sublime Text.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

If R installation doesn't work for you, there is the possibility of using the ResBaz platform, which will allow you to use R and Rstudio from your browser. Please talk to an instructor if you feel this option is for you. If you use this option, you need to have a Twitter or Github account beforehand.

Windows

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

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.

Virtual Machine

Here are further instructions for downloading and installing VirtualBox

  1. Install VirtualBox.
  2. Download the Bio-Linux VM image. Warning: this file is >4 GByte, so please download it before coming to your workshop.
  3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.
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