CGHub News

April 17th, 2015 - CGHub Data Browser 1.4.2

CGHub is pleased to announce the release of the latest version of the CGHub Data Browser.

This release includes:

  • Two new submitting center filters: SANGER and EBI-EMBL
  • Six new disease filters: Acute Myeloid Leukemia, Induction Failure Subproject (AML-IF); Ewing sarcoma; Non cancerous tissue; Rhabdomyosarcoma; Kidney, Rhabdoid Tumor (RT); and Soft tissue sarcoma, non-rhabdomyosarcoma

January 23rd - GeneTorrent 3.8.7 released

CGHub is happy to release version 3.8.6 of the GeneTorrent client software suite.

  • Added ability to use bundled SSL CA certificates by passing the --use-bundled-certs command line switch
  • The binary .tar.gz distribution now bundles Boost, Xqilla and Xerces-C even on distributions that provide native packages for suitable versions of these three dependencies
  • Fixed: Inactivity timeout kills checksumming of very large downloads even though progress is being made
  • Fixed: Using --null-storage results in an otherwise inconsequential error message at the end of the download
  • Removed a command line option that could be used to disable certificate verification during transfers
  • Fixed: -i passes incorrect parameter to gtdownload

December 11th, 2014 - CGHub Data Browser 1.4

CGHub is happy to release the latest version of the CGHub Data Browser.

This release includes:

  • Highlighting of deprecated or redacted BAMs.
  • Partial Barcode search support added to Batch Search
  • Search text box improvement
  • "Reason" field column added to search results display
  • Additional “Reason” fields added for researcher support

October 1st, 2014 - Database: Oxford Journal Publication

CGHub is happy to announce the publication of "The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data", in the Oxford journal "Database." (Abstract) (Full Text) (PDF)

When you publish papers which use data downloaded from CGHub, please include the following citation. Thank you for your continued use of CGHub.

Christopher Wilks; Melissa S. Cline; Erich Weiler; Mark Diehkans; Brian Craft; Christy Martin; Daniel Murphy; Howdy Pierce; John Black; Donavan Nelson; Brian Litzinger; Thomas Hatton; Lori Maltbie; Michael Ainsworth; Patrick Allen; Linda Rosewood; Elizabeth Mitchell; Bradley Smith; Jim Warner; John Groboske; Haifang Telc; Daniel Wilson; Brian Sanford; Hannes Schmidt; David Haussler; Daniel Maltbie
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data
Database 2014; doi: 10.1093/database/bau093

September 30th, 2014 - CGHub Data Browser 1.3.3

CGHub is happy to release the latest version of the CGHub Data Browser. This release added additional information about the HG19_Broad_variant to the "Assembly" help page, PCAWG to the Study filter and GRCh37-lite_WUGSC_variant_2 to the Assembly filter drop down menus.

This release includes:

  • “HG19_Broad_variant" assembly help page updated.
  • New Study Added: “PCAWG 2.0”. Added filtering support for PanCan PCAWG 2.0 data.
  • New Reference Assembly: “GRCh37-lite_WUGSC_variant_2”. Added assembly GRCh37-lite_WUGSC_variant_2 per WashU request.

CGHub Data Browser Release Notes 1.3.3.

August 19th, 2014 - GeneTorrent 3.8.6 released

CGHub is happy to release version 3.8.6 of the GeneTorrent client software suite. Aside from minor stability and usability improvements, this release introduces the ability to specify a TSV or flat file with UUIDs or URLs of analyses to download. For details please refer to the release notes.

April 15th, 2014 - GeneTorrent 3.8.5a released

CGHub has released a security update to GeneTorrent for CentOS 5 and Windows platforms. This release fixes the CVE-2014-0160 vulnerability ("Heartbleed") for GeneTorrent by upgrading the bundled OpenSSL library to version 1.0.1g. Users of CentOS 5 and Windows must upgrade to this release. Users of other platforms may skip this release as it does not include any significant changes on these platforms (GeneTorrent bundles OpenSSL only on CentOS 5 and Windows). Users of all Linux platforms except CentOS 5 should ensure that all systems running GeneTorrent have been upgraded to a fixed version of OpenSSL.

Note that this security update is a precautionary measure. As per the dbGap Security Best Practices of the dbGap Data Use Agreement, systems running GeneTorrent must be firewalled, disallowing any incoming connections to GeneTorrent and making it impossible to exploit the CVE-2014-0160 vulnerability even if GeneTorrent were to use a vulnerable version of OpenSSL.

Mar 18th, 2014 - CGHub Data Browser 1.3.1

CGHub is happy to release the latest version of the CGHub Data Browser. This release fixes issues with filtering functionality discovered late in the 1.3 release process and improves on IE compatibility.

This release includes:

  • Speed Improvements. Faster response time-up to 50% improvement in display time.
  • Easier Access to BAM and DCC Sample Information. “Information” icon provides easy access to details on specific BAMs, including links to TCGA DCC for additional sample information.
  • Download URLs Available. An easy to parse list of BAM URLs now available for downloading, to support user-scripting of downloads.
  • Internet Explorer 8 Compatibility Improvements Improvements to Internet Explorer 8 testing in 1.3 revealed compatibility issues that have been repaired

CGHub Data Browser Release Notes 1.3.1.

Mar 5th, 2014 - GeneTorrent 3.8.5 released

CGHub is happy to release new Windows, Macintosh and Linux versions of the GeneTorrent client. This release contains many bugfixes and two usability improvements. For details please refer to the release notes.

Jan 9th, 2014 - Data Manifest Format Update

Extensive format changes to the "Data Manifest File TSV" file have been made on Jan 9th, 2014.

CGHub users who rely on the Data Manifest File, in TSV format, as found on this page: Summary Statistics should be aware of the changes summarized below.

  • Order and naming of columns has been changed to be consistent with the CGHub Data Browser downloadable manifest
  • Removal of redundant/unused columns and addition of other more useful data columns (e.g. "reason", "platform" fields)

The manifest columns description page has been updated to reflect the changes, which can be found here: manifest description page

The file will continue to be a tab delimited file (TSV).

Jan 8th, 2014 - Cancer Genomics Hub adds childhood cancer data

UC Santa Cruz researchers add new data and features to the world's largest cancer genomics database, providing efficient access to crucial data for cancer researchers.

Read the press release on UCSC Newscenter

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