Instituto Gulbenkian de Ciência

Oct 15-16, 2018

9:30 am - 6:30 pm

Instructors: Paula Andrea Martinez, Mateusz Kuzak

Helpers: Daniel Neves, Ricardo Leite

General Information

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.

For more information on what we teach and why, please see our paper "Good Enough 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: Rua da Quinta Grande, 6, Leucippus Meeting Room, 2780-156 Oeiras - Portugal . Get directions with OpenStreetMap or Google Maps.

When: Oct 15-16, 2018. 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 Data Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers 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 bicourses@igc.gulbenkian.pt for more information.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1 - Oct 15

Before starting Pre-workshop survey
Morning Setup
Morning Project organization for genomics
AfternoonShell for genomics
Evening END

Day 2 - Oct 16

Morning Data wrangling and processing
Afternoon Data wrangling and processing continuation
AfternoonCloud Genomics
Evening Post-workshop survey
END

Syllabus

Project Organization and Management for Genomics

  • Data Tidiness
  • Planning for NGS Projects
  • Examining Data on the NCBI SRA Database
  • Materials

The Unix Shell for Genomics

  • Introducing the shell
  • Navegating files and directories
  • Redirection
  • Writing scripts
  • Project organisation
  • Materials

Data Wrangling for Genomics

  • Assessing Read Quality
  • Trimming and Filtering
  • Variant Calling Workflow
  • Ignoring files
  • Automating a Variant Calling Workflow
  • Materials

Cloud Computing for Genomics

  • Why of cloud computing
  • Logging onto Cloud
  • Fine tuning your Cloud Setup
  • Data roundtripping
  • Which Cloud for my data?
  • Materials

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.

Windows

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.

  1. A spreadsheet program

    2. 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.
  2. Putty

    3. You will need a terminal program to access the AWS Cloud/HPC cluster.
    • Go to the Putty download page
    • Click on putty.exe link to download the install file
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
  3. FTP Client (Filezilla)

    4. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • 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
  4. IGV

    5. 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.

  1. A spreadsheet program

    2. 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.
  2. FTP Client (Filezilla)

    3. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • 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
  3. IGV

    4. 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.</p>
    • 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.

  1. A spreadsheet program

    2. 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.
  2. FTP Client (Filezilla)

    3. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • 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
  3. IGV

    4. 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.