Sep 18-22, 2017
9:00 - 16:00
Instructors: Kai Blin, Henning Redestig, Nikolaus Sonnenschein
Helpers: Svetlana Kutuzova, Christian Lieven, Emre Özdemir, Simon Shaw, Pankaj Kumar Singh
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: Building 221 rooms 237-241, DTU Lyngby Campus, Kgs. Lyngby, Denmark. Get directions with OpenStreetMap or Google Maps.
When: Sep 18-22, 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 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.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email kblin@biosustain.dtu.dk for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 09:00 | Software installation help |
| 10:00 | Automating tasks with the Unix shell |
| 11:00 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Building programs with Python |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
| 09:00 | Scientific Programming with Python |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 14:15 | Coffee |
| 14:30 | Managing data with git |
| 16:00 | Wrap-up |
| 09:00 | Introduction to R |
| 10:30 | Coffee |
| 11:00 | Data visualisation with R |
| 12:00 | Lunch break |
| 13:00 | Analyzing gene expression data |
| 14:30 | Coffee |
| 15:30 | Getting help |
| 16:00 | Wrap-up |
| 09:00 | Cell factory design course I |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
| 09:00 | Cell factory design course II |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
add, commit, ...status, diff, ...clone, pull, push, ...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.
If you have problems installing any of the requirements, we'll be there Monday morning to help. If all the requirements are installed and work correctly, you can join us Monday at 10:00 instead of 9:00.
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.
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.
Git should be installed on your computer as part of your Bash install (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.
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 research computing, and great for general-purpose programming as well. Installing all of its research 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 Jupyter 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).
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
cd DownloadsThen, try again.
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).
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 >= 3.4.0 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.
Additionally, install the packages ggplot2 and dplyr from https://cran.r-project.org/mirrors.html and gage, edgeR, pcaMethods limma and org.EcK12.eg.db from https://bioconductor.org. When done, please verify your installation by running
source("https://goo.gl/J8gVWx") in R-studio.
Install R >= 3.4.0 by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
Additionally, install the packages ggplot2 and dplyr from https://cran.r-project.org/mirrors.html and gage, edgeR, pcaMethods limma and org.EcK12.eg.db from https://bioconductor.org. When done, please verify your installation by running
source("https://goo.gl/J8gVWx") in R-studio.
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.
Additionally, install the packages ggplot2 and dplyr from https://cran.r-project.org/mirrors.html and gage, edgeR, pcaMethods limma and org.EcK12.eg.db from https://bioconductor.org. When done, please verify your installation by running
source("https://goo.gl/J8gVWx") in R-studio.