Bioinformatics for Cancer Genomics 2018 Pre-Work

Install These Tools Before the Workshop:

1) A robust text editor.

2) A file decompression tool.

  • For Windows/PC – 7zip.
  • For Linux – gzip.
  • For Mac – already there.

3) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).

4) Java -The visualization program that we will be using (IGV) requires Java. Check if you have Java installed: https://www.java.com/verify/ and download Java if you do not have it installed (Java 8).

5) Integrative Genomics Viewer 2.3 (IGV) - Once java is installed, go to http://www.broadinstitute.org/igv/ and register in order to get access to the downloads page. Once you have gained access to the download page, click on the appropriate launch button that matches the amount of memory available on your laptop (if you have space, 1.2GB is good, more is better).

Note Chrome does not launch “java webstart” files by default. Instead, the launch buttons below will download a “jnlp” file. This should appear in the lower left corner of the browser. Double-click the downloaded file to run.

Windows users: To run with more than 1.2 GB you must install 64-bit Java. This is often not installed by default even with the latest Windows 7 machines with many GB of memory. In general trying to launch with more memory than your OS/Java combination supports will result in the obscure error “could not create virtual machine”.

6) SSH client - Mac and Linux users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.

7) SCP/SFTP client - We will be moving data from the servers to the student laptops for visualization. Mac and Linux users already have a command line scp and sftp program. For Windows users, please install WinSCP.

8) A PDF viewer (Adobe Acrobat or equivalent).

9) Install Cytoscape 3.5.1: http://www.cytoscape.org

10) Within the Cytoscape program, install the following Cytoscape plugins:

From the menu bar, Apps > Manage Apps

Within all apps, Search for the following and install:
• jActiveModules (should already be installed. Install if not)
• GeneMania (should already be installed. Install if not).
• EnrichmentMap
• BiNGO
• Reactome FI Plugin

Select GeneMania from Apps Manager → Choose Another Data Set.
From the list of available data sets, select the most recent and under Include only these networks:

select All → Download.

An Install Window will pop-up. Select H.Sapiens Human (2384 MB) → Install

This requires time and a good network connection to download completely, so be patient.

11) A PDF viewer (Adobe Acrobat or equivalent).

12) Sign up for a GenePattern account at Broad. When you go to this homepage, there is under the “Getting Started” section an icon for “Run analyses on the Broad public server”. Click here and sign up for an account so that in class we can use the tool on the web.

Do These Tutorials Before the Workshop:

1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.

2) Cytoscape 3.x Preparation tutorials: Complete the introductory tutorial to Cytoscape 3.x:

  • Introduction to Cytoscape3 - User Interface
  • Introduction to Cytoscape3 - Welcome Screen
  • Introduction to Cytoscape 3.1 - Networks, Data, Styles, Layouts and App Manager

3) UNIX Preparation tutorials:

4) Sequencing Terminology

Watch This Before the Workshop:

Sequencing Technology and Terminology

Read These Before the Workshop:

Database resources of the National Center for Biotechnology Information

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

Integrative genomic profiling of human prostate cancer

Predicting the functional impact of protein mutations: application to cancer genomics

Cancer genome sequencing study design

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy

The UCSC Genome Browser database: extensions and updates 2013

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

Expression Data Analysis with Reactome

Please note that these instructions may change prior to the workshop.