jvwong

List the current installed Java versions

$ /usr/libexec/java_home -V

Install the version desired

Apple provides their own version of 6 (Java for OS X 2015-001)

List the current installed Java versions

You should see the version installed

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Tracing from SIF to Source

Goal

Trace an interaction declared in EXTENDED_BINARY_SIF to the BioPAX description, visualize the BioPAX representation in the form of a network, and identify the source database record. This gist crosses many aspects of the tools and services offered through Pathway Commons.

Audience

This is aimed at a computational audience. If you know what SIF is and you have used curl you should be fine. It would help if you are familiar with BioPAX although this is not essential.

What You Need

• Access to a command line terminal to run curl

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You can add the github repository as a remote to your checked out gist repository.

$ git clone git://gist.github.com/1234.git
$ git remote add github git@github.com:ChrisJamesC/myNewProject.git

Push it to initialize the git on github

$ git push -u github master

This will also change the upstream of the branch, so github will be default.

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Pathway Commons Web Service Test Suite

This is a sample test suite for the Pathway Commons web service written in python.

Description

Each example query on the web service description page is called programmatically and a sanity test is performed on each response. A .csv report summarizing these responses is dumped to the parent directory:

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virtualenv on OSX El-capitan

$ usr/bin/python2.7 /Users/jeffreywong/anaconda/lib/python3.5/site-packages/virtualenv.py venv
$ source ./venv/bin/activate

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GDC Data Munging Scripts

This is for use in the Pathway Commons Guide TCGA Ovarian Cancer data set description.

Setup

1. Install conda

2. Create a conda environment named tcgaov. You can use the supplied environments.yml to quickly get started.

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import os
import fnmatch
import json
import pandas as pd

def writeout(output_path, df):
    """
        Write dataframe (df) to output path (output_path)
    """
    directory = os.path.dirname(output_path)

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import os
import fnmatch
import json
import pandas as pd

def writeout(output_path, df):
    """
        Write dataframe (df) to output path (output_path)
    """
    directory = os.path.dirname(output_path)

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Pathway Commons: Guide

This code is referenced in the pathway enrichment workflow step Process Data.

Use the edgeR R/Bioconductor package to analyze RNA sequencing data for high-grade serous ovarian cancer (HGS-OvCa) from The Cancer Genome Atlas (TCGA) for differentially expressed genes.

Software requirements

• R: version 3.3.1
• Bioconductor: version 3.3

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Pathway Commons: Guide

This code is referenced in the pathway enrichment workflow step Get Data.

Use the TCGAbiolinks R/Bioconductor package to query the Genomic Data Commons (GDC) data portal for The Cancer Genome Atlas (TCGA) high-grade serous ovarian cancer (HGS-OvCa) RNA sequencing count data.

Software requirements

• R: version 3.3.1
• Bioconductor: version 3.3