Public Demo

Overview

We have installed a public demo at the University of Cambridge to facilitate the testing and development for all users. We have loaded and indexed five different datasets organised in 3 projects and 5 studies, these cover the most typical data use cases today such as multi-sample VCF, family exomes, and genomes; or cancer somatic data. All documentation examples and tutorials use this demo installation.

Connecting to the public demo

OpenCGA public demo REST URL is available at http://bioinfo.hpc.cam.ac.uk/opencga-prod/. You can check REST API and documentation at http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/.

Credentials

We have created a read-only user called demouser with password demouser. As in most OpenCGA installations where normal users are not the owners of the data, demouser has been given VIEW access to all demo user data, this is a very common configuration in OpenCGA where the owner of the data grant access to other users. In this demo installation the owner of the data is demo user, while demouser user is the public user created to query data.

Datasets

Genomic Data

In this demo we have indexed 5 different genomic datasets. Data has been organised in three projects and five studies. These represents different assemblies and data types such as multi sample VCF, aggregated VCF or family genome or exome. The data is organised in 3 projects and 5 studies. You can find some useful information in this table:

Project ID - Name	Study ID - Name	VCF File Type	Samples	Variants
population Population Studies GRCh38	1000g 1000 Genomes phase 3	WGS Multisample	2,504	82,587,763
	uk10k UK10K	WGS Aggregated	10,000	46,624,127
family Family Studies GRCh37	corpasome Corpas Family	WES Family Multisample	4	300,711
	platinum Illumina Platinum	GWS Family Multisample	17	12,263,246

Clinical Data

In order to make this demo more useful to users we have loaded or simulated some clinical data, this allows to exploit OpenCGA analysis such as GWAS or clinical interpretation. You can find clinical data for each study in the following sections.

1000g

We loaded the 1000 Genomes pedigree file, you can find a copy at http://resources.opencb.org/opencb/opencga/templates/demo/20130606_g1k.ped

uk10k

There is no possible clinical data in this study. This is a WGS aggregated dataset so no samples or genotypes were present in the dataset and, therefore, no Individuals or Samples have been created.

corpasome

We simulated two different disorders and few phenotypes for the different members of the family. To be documented soon.

platinum

To be documented soon.

rams_cml

To be documented soon.