Software Carpentry @ Oxford University's Department of Biochemistry

5-7 December 2016

9:00 am - 5:00 pm

Instructors: Krzysztof Poterlowicz, Laura Fortunato, Maja Založnik

Helpers: Nadya Fursova, Katy Brown, Hania Pavlou, Aino Jarvelin, Kinga Kamieniarz-Gdula, Michal Gdula

General Information

The Biochemistry Department of Oxford University, ELIXIR-UK and the Software Sustainability Institute are proud to organise and host a data carpentry course in data analysis covering introduction to the UNIX shell, GitHub as well as programming and data visualization in R. Standard Software Carpentry workshop will be followed by the third day of hands-on next generation sequencing (NGS) data analysis in R course. 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 workshop is organised over 3 days - Day 1 and Day 2 are standard Software Carpentry workshop, while Day 3 is added to allow you to apply some of the things you were taught the previous 2 days to a real life problem. So, on Day 3 the you will learn how to do RNA-seq and ChIP-seq analysis in R to study differences in transcriptome and epigenome profiles of serum- and 2i-grown mouse embryonic cells.

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: Medical Sciences Teaching Centre, Lower Ground Seminar Rooms (LGa and LGb), Sherard Road (off South Parks Road), Oxford, OX1 3PL. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (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 Carpentry's Code of Conduct.

Etherpad: http://pad.software-carpentry.org/2016-12-05-oxford.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code during the workshop.

Contact: Please email a.nenadic@manchester.ac.uk or michal.gdula@bioch.ox.ac.uk for more information.

Sponsors and supporters

This workshop has been sponsored and supported by:

ELIXIR-UK
SSI

Schedule

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
11:00 Automating tasks with the Unix shell
12:30 Lunch break
13:30 Version control with Git/Github
15:00 Coffee
15:30 Version control with Git/Github
16:00 Introduction to R and RStudio
17:00 Wrap-up of day 1

Day 2

09:00 Programming in R- Data Structures
10:30 Coffee
11:00 Programming in R - Functions explained
12:30 Lunch break
13:30 Programming in R - Creating Publication-Quality Graphics
15:00 Coffee
15:30 Programming in R - Creating Publication-Quality Graphics
17:00 Post-workshop questionnaire and wrap-up of day

Day 3

09:00 RNA-seq, ChIP-seq analysis overview
10:00 Introduction to the data
11:30 Prepartion of read count table
12:00 Coffee
12:30 Differential expression analysis with Deseq2
13:00 Lunch break
14:00 Visualization of RNA-seq results
15:00 Coffee
15:30 Relation of gene expression data to ChIP-seq data
16:30 Wrap-up

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Using R from the command line
  • Reference...

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
  • Reference...

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.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected 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.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

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). 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.

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).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Windows

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

Mac OS X

Video Tutorial

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.

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

Video Tutorial

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. 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.

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.

R

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

Windows

Video Tutorial

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.

Mac OS X

Video Tutorial

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.