CGHub News

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:

  1. Speed Improvements. Faster response time-up to 50% improvement in display time.
  2. 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.
  3. Download URLs Available. An easy to parse list of BAM URLs now available for downloading, to support user-scripting of downloads.
  4. 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.

  1. Order and naming of columns has been changed to be consistent with the CGHub Data Browser downloadable manifest
  2. 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

Nov 7th, 2013 - CGHub Data Browser 1.2

CGHub is happy to release the latest version of the CGHub Data Browser. This release includes a new hyperlink connection to the TCGA Data Portal, providing access to Data Matrix Dataset information for TCGA barcodes.

Also included are new filtering capabilities that allow identifying FASTQ files and whether sample types are frozen or FFPE.

CGHub Data Browser Release Notes 1.2.

Aug 29th, 2013 - CGHub Data Browser 1.1

CGHub is happy to release the latest version of the CGHub Data Browser. This release includes several performance and stability improvements, as well as a user requested feature, Batch ID Search.

The new “Batch ID Search” function allows users to paste a list of multiple genomic IDs (barcode, and/or UUIDs) to an input text box, or upload a file with multiple genomic IDs. The Batch Search option facilitates building a downloadable manifest.xml file from a list of IDs that users may have obtained from some other source.

CGHub Data Browser Release Notes 1.1.

Aug 26th, 2013 - National Cancer Institute Cancer Genomics Cloud Pilots

The NCI is soliciting comments from the cancer research community to help design the next generation of cancer research infrastructure.

Because CGHub is a repository, data needs to be downloaded for analysis. In the next iteration, downloading would be unnecessary. Researchers would use a data browser to select both data and analysis tools from the same repository and compute cloud system.

You can learn more about the NCI's cancer cloud pilot program from their blog.

Please let your voice be heard at: NCI Cancer Cloud Pilots.

May 30th, 2013 - CGHub Data Browser 1.0

CGHub is proud to release CGHub Data Browser 1.0, a web application that assists users in performing a visual search of the CGHub database and in creating a manifest file that is then used, by GeneTorrent, to download desired files.

Please visit the CGHub Data Browser located here: CGHub Data Browser

CGHub Data Browser Release Notes 1.0

March 14th, 2013 - Cancer Genomics Hub wins 2013 Innovations Award in Networking

Awarded by the Corporation for Education Network Initiatives in California (CENIC). Please see this press release located on the UCSC News Center page for more information on the CENIC awards. In addition, please see the links below for presentations given by CGHub staff at the annual CENIC conference.

CENIC Pioneering
Linda Rosewood's presentation
CENIC NTPGD
Chris Wilks' presentation

Feb 26th, 2013 - GeneTorrent 3.8.3 released

CGHub is happy to release Windows, Macintosh, and new Linux versions of GeneTorrent client. With the release of GeneTorrent 3.8.3, different clients will be used for downloading or uploading, thus simplifying installation and support.
To current CGHub users: This is not a mandatory upgrade. Your current version of GeneTorrent will function normally.

Dec 11th, 2012 - CGHub releases CCLE data sets

CGHub is happy to announce the release of Cancer Cell Line Encyclopedia (CCLE) data sets. This data set is available for public download with the GeneTorrent software, and more information can be found here: CCLE Data Sets page.

Oct 2nd, 2012 - CGHub updated to GNOS 3.3

New Features in 3.3:

  1. -k minutes, --inactivity-timeout minutes. Ex: "-k 45" for a 45 minute timeout. Allows uploader and/or downloader, to specify an inactivity time out. The default stting is to never time out. However, you may find it useful to set a timeout, if you have experienced issues while running GeneTorrent.
  2. Various security and bug fixes, which can be found in the release notes located here:Release Notes 3.3.
  3. Added "OR" function to cgquery. Please see users guide for more information.

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