NewQuery with search terms
We’ve improved querying datasets via the Data Browser. After selecting one or more datasets, you can use search terms to start your query. Terms will autocomplete as you type and suggest Keywords, Related queries, and Saved and example queries. Select a query from Related queries or Saved and examples. Or, enter more keywords and hit enter to choose a pre-built query from the Results page. This intuitive feature enables users to familiarize themselves with the Data Browser and lowers the learning curve to query building.
Learn more from our documentation.
NewSupported 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 Seven Bridges Platform. Note that these instances are not available on eu.sbgenomics.com.
We’ve improved the batching functionality on the visual interface. In addition to the existing batching methods, you can now toggle batching on and off for any workflow on the DRAFT task page. You can also set batching criteria by any metadata, as was previously available on the API.
Learn more from our documentation.
ImprovementsData Cruncher – Suspend time
You can now set the period of inactivity after which the instance is stopped automatically and the analysis is saved.
Learn more from our documentation.
On January 31, 2018, Seven Bridges will deprecate legacy projects and features on the Seven Bridges Platform. Apps, tasks, and data within your legacy projects will remain accessible. Port these to Version 2 projects to conduct further analyses.
Learn more from our post.
ImprovementsPhenotype visualization improvement for Sonar
We’ve improved phenotype visualizations in the Sonar Playground. Use the scatterplot to visualize up to three dimensions of your query and observe trends or refine your original query. Note that this visualization is currently available only for single queries. Learn more about scatterplots for your queries.
The Seven Bridges Platform now supports integration with third-party authentication services that are SAML2.0 compatible. We can quickly setup external authentication on a division level as requested by the client.
ImprovementsAmazon 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 Platform. Learn more from Amazon’s documentation about using a KMS ID.
ImprovementsUpdating Help functionality
Use the Help icon on the bottom of each page to access customer support, send feedback, and find contextual supporting documentation all in the same place.
NewSeven 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.
You can use the SB CLI to leverage the functionalities of our API to interact with the Platform. You can also automate your interaction with the Platform by using the SB CLI in scripts or programs.
SB CLI is available for Linux, macOS, Windows, and FreeBSD.
ImprovementsOne second billing
We’ve switched billing for AWS EC2/EBS as well as Google instances to 1 second increments. Change will also take effect on EU platform. There is also 1 minute minimum charge per-instance. Prices in pricing plans will remain the same (per hour) but will be billed per second. Learn more from our documentation.
We’ve implemented a system to help you generate queries with a meaningful sample size of data. For instance, if you add more than three entities (e.g. Case, Sample, File) without applying any filters, the Data Browser prompts you to add one or more properties with specific values to narrow your query before continuing, as shown below.
The Data Browser similarly prompts you to add filters if you create a query that has symmetrical branches without any filters applied, as shown below.
Learn more about adding filters to your query.
ImprovementsTable of results improvements
The table below the Data Browser contains further details about your query. In addition to the List view and Analytics view, we’ve introduced a Details view.
The Details view displays details about a selected entity in the context of your query and consists of three panels. The first panel details the inbound and outbound connections for the selected entity in the context of your query. The second panel displays a list of UUIDs corresponding to that entity that match your query. If a specific UUID within the second panel is selected, the third panel displays the metadata corresponding to it.
This new Details view enables you to explore the connections and relations between entities in your query more easily and thus ensure that your query is identifying the data you need to meet your research goals.
Learn more about the Details view.
ImprovementsSupport for Amazon Web Services Spot instances
Seven Bridges has introduced support for Spot instances on the Amazon Web Services (AWS) deploy of the Platform. 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.
Due to the nature of how AWS handles Spot instances, they can be interrupted while tasks are running. If a Spot instance is interrupted, Seven Bridges’ job retry functionality will automatically restart interrupted and remaining unfinished jobs on an On-Demand instance to prevent further interruptions. Such an interruption may impact the cost savings from using a Spot instance and can result in a longer overall runtime, but the reliability of task execution is unaffected.
NewSBFS [Beta release]
SBFS is a command line tool which enables interaction with Platform project files that are mounted as a local file system.
Use SBFS to make project files available on a local file system and thus as accessible as any other locally available file. This eliminates the need for downloading complete files to a local machine, which is especially useful when working with large files exceeding the size of a local disk. With SBFS, parts of a file are accessible without necessitating a complete file download and users can perform interactive analyses on a local machine (or server instance) without needing to bring their tool to the Platform.
SBFS is available for Linux and macOS operating systems, and beta version is available for download from the new Data tools page.
Learn more from SBFS documentation.
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 Seven Bridges Platform via 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 Platform. 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.
The Platform now provides access to mass spectrometry data that were generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) as part of the TCGA initiative to characterize and quantify the proteome of cancer samples. This dataset represents 335 samples from patients with Breast Invasive Carcinoma, Colon Adenocarcinoma, Ovarian Serous Cystadenocarcinoma, and Rectum Adenocarcinoma for whom matched genomic data are available. The dataset can be queried using the Data Browser to generate custom cohorts from within this dataset as well as multi-omic cohorts across the TCGA GRCh38 genomic and CPTAC proteomic datasets.
To maximize the accessibility and value of the multi-omic datasets available on the Platform, the Data Browser now enables cross-dataset queries for datasets with harmonized metadata. This allows researchers to use the Data Browser to identify cohorts of interest across multiple genomic datasets such as the GRCh38 alignments of TCGA and TARGET.
Learn more about cross-dataset queries through a sample query.