Folders on the visual interface

We have introduced support for folders on the CGC. To complement our existing API functionalities, now you can organize your project files into folders through the CGC's visual interface, which allows you to have a better overview of your files and manage them more easily.

Smart Variant Filtering

The variant filtering process consists of selecting highly confident variants and removing the ones that are falsely called. This process used to be mostly left out from deeper testing in secondary genomic DNA analyses, even though it can boost precision of variant calls significantly. After developing graph genome alignment tool and reassembly variant caller, we are now launching the Smart Variant Filtering tool used for filtering germline variants.

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SUPPORTED INSTANCES UPDATE

We now support the use of new generation AWS EC2 Compute Optimized instances (C5) and General Purpose instances (M5) in task executions and Data Cruncher analyses on the CGC.

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DATASETS API UPDATE

The ICGC dataset is now available on the CGC and is queryable via both the Datasets API and the Data Browser.

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CASE EXPLORER

The Case Explorer now utilizes TCGA GRCh38. Learn more from our documentation.

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TCIA, CPTAC, AND TARGET IN THE DATASETS API

You can now query TCIA, CPTAC, and TARGET data via the Datasets API.

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AMAZON KMS SUPPORT FOR VOLUMES

You can now use Amazon KMS with your Amazon S3 volume. Simply provide your KMS ID when configuring your volume for the CGC. Learn more from Amazon's documentation about using a KMS ID.

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SEVEN BRIDGES COMMAND LINE INTERFACE

We are rolling out the release of Seven Bridges Command Line Interface (version 0.5.0) which will make our public API accessible through the command line as well.

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RABIX BETA RELEASE ON CGC

When you create or edit a tool or workflow on the CGC you’ll see a message asking if you want to try our beta release of Rabix, our new Software Development Kit for the Common Workflow Language (CWL). Rabix consists of two tools.

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TCGA GRCH38 DATASET UPDATE

The CGC is committed to providing its users with the most up-to-date version of the TCGA GRCh38 dataset that is available from the NCI Genomic Data Commons (GDC). In keeping with this commitment, the CGC transitioned from hosting version 5.0 of this dataset to version 7.0 on August 17, 2017.

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SUPPORT FOR AMAZON WEB SERVICES SPOT INSTANCES

Seven Bridges has introduced support for Spot instances on the Amazon Web Services (AWS) deploy of the Cancer Genomics Cloud. Spot instance support can be selected as a default for projects and and an option for each task execution. By selecting a spot instance execution costs can be dramatically reduced. Our testing indicates an execution cost savings of over 75% on common workflows.

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DATASET IMPROVEMENTS

TARGET GRCh38 Dataset

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset provides genomic, transcriptomic, and epigenomic data from patients representing several childhood cancers and serves as a valuable complement to the existing genomic and multi-omic datasets available on the CGC. The complete TARGET GRCh38 dataset, which includes both Open Data accessible to all researchers and Controlled Data, to which access is regulated by the Database for Genotypes and Phenotypes (dbGaP), is now available on the CGC. This dataset can be queried using the Data Browser to generate custom cohorts from within this dataset as well as cohorts derived from multiple similarly aligned datasets such as the TARGET GRCh38 and TCGA GRCh38 datasets.

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ELASTIC BLOCK STORAGE CUSTOMIZATION FEATURE

Overview

On August 1, we released a feature that provides you with the ability to customize the amount of Elastic Block Storage (EBS) disk space attached to different Amazon instance configurations. EBS customization is useful for bioinformatics workflows because it provides the ability to optimize your computation by giving you greater control over requirements and costs.

To learn more about EBS customization, please see our documentation.

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PARALLEL INSTANCE LIMITS AND TASK QUEUING

Individual users on the CGC now have a default usage limit of 80 parallel instances. Seven Bridges sets this upper bound because the number of parallel instances used in total by the CGC Platform is limited by Amazon Web Services (AWS), the CGC’s underlying cloud service provider. While this means that tasks using more than 80 instances can take longer to complete, it also helps ensure that instances are available for all CGC users to run their analyses.

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HARMONIZED DATASET ON THE CGC

Datasets on the CGC are now categorized as "harmonized" and "legacy" in accordance with the GDC.

In 2016, the GDC started hosting and distributing previously generated data from The Cancer Genome Atlas (TCGA). Additionally, for all submitted sequence data (FASTQs and BAM alignment files), the GDC generated new alignments (BAM files) to the latest human reference genome, GRCh38, using standard workflows. Using these alignments, the GDC generated derived data, including normal and tumor variant and mutation calls, gene and miRNA expression, and splice junction quantification data. The GDC refers to this process of data generation through standard workflows as data harmonization.

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EXPORT TO VOLUMES: COPY-ONLY PARAMETER

We've added an Advance Access copy-only parameter to the Start an Export job request for Volumes. This means that, while it is fully operational, it is subject to change. If this parameter, copy_only, is set to true, the specified file will be copied to a volume but the source file will remain on the CGC. Learn more from our documentation.

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SEARCH VIA THE DATASETS API

Use the Datasets API to search across datasets hosted on the CGC, such as TCGA and CCLE. First, use a free-text search to find all exact matches in metadata across all databases. Then, use the URIs obtained in the initial search to obtain further details, including individual members matching the designated resource. All responses are provided in the JSON format.

Learn more about searching via the Datasets API.

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SEVENBRIDGES-PYTHON 0.7.0

We've released a new version of the Python bindings for our API, sevenbridges-python 0.7.0, which includes some major updates.

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DATA BROWSER: COPY ALL FILES

Choose to copy files from a specific File node or from all File nodes on the Data Browser canvas. Learn more about this feature.

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