BaseSpace Cohort Analyzer enables users to apply complex genomic data in novel ways across the entire drug discovery and development process. Pharmaceutical and biotechnology organizations can incorporate data analysis and interpretation into biomarker discovery, translational research, and clinical trials.
We are writing to summarize recent changes to BaseSpace Cohort Analyzer and to share our plans for 2017.
Last year our main focus was on enabling you to upload basic cancer data in a quick, easy, automated and secure manner. We implemented the following features:
User upload of somatic and copy number variation data
Users can simply create a Variant Call Format (VCF) file in BaseSpace Sequence Hub, or with other software, and drag and drop the files into a secure site for automated ingestion. This functionality is enabled for panels, exomes and whole genome sequencing (WGS) of somatic mutation data and copy number variation (CNV).
Your administrators can now assign permissions to private studies uploaded into BaseSpace Cohort Analyzer to allow certain users to see one study but not another.
We recently started a major update of The Cancer Genome Atlas (TCGA), for which we are bringing in thousands of new samples for somatic mutations, CNVs and more, which will be finalized in the coming months.
Novel Cancer Outlier Algorithm (Patent Application & AACR)
We developed an improved algorithm for Cancer Outlier Profile Analysis, which was recently released as a new app. We have a pending patent application and will present our method at this year’s American Association for Cancer Research (AACR) conference.
This year we are expanding the ability to upload hundreds of clinical attributes, as well as enabling user upload of RNA-seq data. We will also continue to bring in more TCGA and other public data and increase ways to get input and feedback directly from you. Please note that this roadmap is representative of our current development plan, which may evolve and change over time.
For now, if you have any questions or suggestions, contact us at email@example.com
We look forward to an exciting year ahead and to hearing from you!
BaseSpace Cohort Analyzer Team
For Research Use Only. Not for use in diagnostic procedures.
We are pleased to announce a minor release of BaseSpaceCLI (0.8.10) with some improvements to existing tools and a new tool –
wait command for BaseSpaceCLI is analogous to the shell command wait and was designed to help connect together separate app launches. The
wait command accepts as arguments one or more appsessions and will then wait for these appsessions to finish, polling based on a specified interval (default 60 seconds). Once they have all finished,
bs wait returns the appresults that have been generated by the provided appsessions. The intention is that these appresults can then be passed into another app launch, providing some limited app-chaining capabilities.
You’re invited to an exclusive informatics event
Advancing Precision Medicine efforts relies on the ability to make sense of a growing body of genomic data. The need for robust informatics tools and an integrated approach when it comes to acquiring, storing, distributing, and analyzing data is essential.
Join us for our BaseSpace® Suite Summit in Rochester, MN on October 3 and 4. Taking place immediately before the Individualizing Medicine Conference, registration is free. Learn more about our informatics tools and how they’re designed to help you transform complex genomic data into meaningful insights quickly and easily.
- Share your perspectives on applying informatics tools in your lab
- Attend your choice of sessions on informatics topics
- Learn best practices for laboratory information management, including how an integrated approach can expedite workflows
- Connect with your peers
Venue and Format
Lodging and Summit activities take place at the Kahler Grand Hotel in Rochester, MN. All day sessions on October 3 and the morning of October 4 include a variety of hands-on, introductory, and training sessions.
If you have questions, please contact us.
The Variant Calling Assessment Tool (VCAT) v3.0 BaseSpace® App has improved usability, several new gold references, adds BED file stratification, and delivers an enhanced in-browser report.
Improved VCF file selection
- File chooser now allows multi-selection of VCFs
- Easier usage of alternative labels for VCF files
- File chooser now defaults to the current Project
- Improved VCF file tooltips now show analysis name
Gold Reference Additions and Updates
- Added Platinum Genomes reference data for NA12877 (male spouse of NA12878)
- Added NIST GiaB gold reference data for NA24385 (Ashkenazi male)
- Added gold reference data and novelty rate calculations for hg38
- Updated NIST Genome in a Bottle reference data to version 3.2.2
- Updated Platinum Genomes reference data to version 2016-01
The new Enrichment v3.0 BaseSpace® App (formerly called Isaac Enrichment) introduces major improvements and new features including:
- Improved small variant calling
- Copy number variant (CNV) calling
- Structural variant calling
- Somatic/low-frequency variant calling
- Ability to start from FASTQ or BAM
- GRCh38 reference added
- Variant table CSV file including variant frequencies
- Improved variant annotation engine
- Improved metrics engine
Early next week all BaseSpace Sequence Hub accounts will track storage and compute usage.
Our Basic tier users will continue to enjoy 1 Terabyte of storage for free. On top of that we’re crediting your account with 250 free iCredits to use over 30 days to make sure you have a chance to explore all the apps we offer*.
We offer several compute and storage options to fit your needs. Let us know if you’d like to learn more about BaseSpace Sequence Hub tiers.
* iCredits are used to pay for app (compute and license fees) and additional storage charges. Any unused iCredits will expire at the end of this 30 day period.
We are pleased to announce the third release (version 0.8) of BaseSpaceCLI, which includes a major new tool and a number of minor features. To install the new release, run this script:
$ sudo bash -c "$(curl -L https://bintray.com/artifact/download/basespace/helper/install.sh)"
With this release of BaseSpaceCLI we are introducing a new high-performance copy tool called BaseSpace Copy or bscp, which provides the following features:
- Rich and flexible URI mechanism to specify source and target for copies
- Multi-threaded for performance and to cope with high-latency connections
- Excellent data integrity, all part data is hashed and verified. Ability to export md5sum compatible sum file for future data verification.
- Resumable downloading