Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct
research. Its target audience is researchers who have little to no prior computational experience,
and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly
apply skills learned to their own research.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
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:
Norwich Research Park Innovation Centre, Colney Ln, Norwich NR4 7UZ.
Get directions with
OpenStreetMap
or
Google Maps.
When:
December 10.
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
Data Carpentry's
Code of Conduct.
Accessibility: We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
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.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Setup
To participate in a Data Carpentry workshop,
you will need working copies of the software described below.
Please make sure to install everything and try opening it to make sure it works
before the start of your workshop. If you run into any problems,
please feel free to email the instructor or arrive early to your workshop on
the first day.
Participants should bring and use their own laptops to insure the proper setup of
tools for an efficient workflow once you leave the workshop.
Platform-specific Notes
This workshop will be using the software outlined in the install instructions below.
Please see the section for your operating system for those directions.
Please go through all the installation steps below and make sure that
you not only installed them, but start them up to make sure they're working.
If you have any problems, don't hesitate to email the instructors to
ask for help, or arrive early on the first day of the workshop to
get help.
A spreadsheet program
For this workshop you will need a spreadsheet program. Many people already have
Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet
program, there are a few other options, like OpenOffice and LibreOffice. Install
instructions for LibreOffice, which is free and open source, are here.
Download the Installer Install LibreOffice by going to the installation page. The version for Windows
should automatically be selected. Click Download Version 6.0.3 or later. You
will go to a page that asks about a donation, but you don't need to make one.
Your download should begin automatically.
Install LibreOffice Once the installer is downloaded, double click on it and it should install.
To use LibreOffice, double click on the icon and it will open.
Putty
You will need a terminal program to access the AWS Cloud/HPC cluster.
Chose the download link appropriate to your system
To use it, double-click on the downloaded file
Follow any installation instructions, if any
At the workshop we will give you additional information (e.g. host, username, port) to connect
R
In the workshop, we will use RStudio. RStudio is a nice interface to the
programming language R. To use RStudio, you need to install both R and RStudio.
Under Installers select RStudio 1.1.447 or later - Windows XP/Vista/7/8
Double click the file to install it
Once it's installed, open RStudio to make sure it works and you don't get any error messages.
IGV If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for
looking at SAM and BAM files, SNPs, and variant calls.
To download IGV, please visit
this page
and log in. Please register if you do not already have a login.
Click on the large button for the Download Binary Distribution
Find the zip archive on your computer and expand it
To run IGV, double-click on the IGV.bat file.
Mac
Please go through all the installation steps below and make sure that
you not only installed them, but start them up to make sure they're working.
If you have any problems, don't hesitate to email the instructors to
ask for help, or arrive early on the first day of the workshop to
get help.
A spreadsheet program For this workshop you will need a spreadsheet program. Many people already have
Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet
program, there are a few other options, like OpenOffice and LibreOffice. Install
instructions for LibreOffice, which is free and open source, are here.
Download the Installer Install LibreOffice by going to the installation page. The version for Mac
should automatically be selected. Click Download Version 6.0.3 or later. You
will go to a page that asks about a donation, but you don't need to make one.
Your download should begin automatically.
Install LibreOffice Once the installer is downloaded, double click on it and it should install.
To use LibreOffice, double click on the icon and it will open.
FTP Client (Filezilla) An FTP client will help you transfer files easily between your computer and the cloud.
Chose the download link appropriate to your system
To use it, double-click on the downloaded file
Follow any installation instructions, if any
At the workshop we will give you additional information (e.g. host, username, port) to connect
R In the workshop, we will use RStudio. RStudio is a nice interface to the
programming language R. To use RStudio, you need to install both R and RStudio.
Under Installers select RStudio 1.1.447 or later - Mac OS X 10.6+ (64-bit) to download it.
Once it's downloaded, double click the file to install it
Once it's installed, open RStudio to make sure it works and you don't get any error messages.
IGV
If time permits, we will use The Broad Institute's IGV (Integrated Genome Viewer) for
looking at SAM and BAM files, SNPs, and variant calls.
To download IGV, please visit
this page
and log in. Please register if you do not already have a login.
Click on the large button for the Download Binary Distribution
Find the zip archive on your computer and expand it
To run IGV, double-click on the IGV.bat file.
Linux
Please go through all the installation steps below and make sure that
you not only installed them, but start them up to make sure they're working.
If you have any problems, don't hesitate to email the instructors to
ask for help, or arrive early on the first day of the workshop to
get help.
A spreadsheet program For this workshop you will need a spreadsheet program. Many people already have
Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet
program, there are a few other options, like OpenOffice and LibreOffice. Install
instructions for LibreOffice, which is free and open source, are here.
Download the Installer Install LibreOffice by going to the installation page. The version for Linux
should automatically be selected. Click Download Version 6.0.3 or later. You
will go to a page that asks about a donation, but you don't need to make one.
Your download should begin automatically.
Install LibreOffice Once the installer is downloaded, double click on it and it should install.
To use LibreOffice, double click on the icon and it will open.
FTP Client (Filezilla) An FTP client will help you transfer files easily between your computer and the cloud.
Chose the download link appropriate to your system
To use it, double-click on the downloaded file
Follow any installation instructions, if any
At the workshop we will give you additional information (e.g. host, username, port) to connect
R In the workshop, we will use RStudio. RStudio is a nice interface to the
programming language R. To use RStudio, you need to install both R and RStudio.
R is available through most Linux package managers.
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).