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.
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
We’ve recently added some improvements to the Sequencing Runs list. These updates should help to quickly get basic quality information about each run, without needing to click into Run details pages.
For example, % reads passed filter (%PF), average %Q30, yield, and cycles (for Read1 and Read2) are now columns on the Runs list.
With the launch of the TruSight RNA Pan-Cancer panel, a targeted enrichment panel for the detection of variants, fusions, and gene expression profiles in 1385 cancer-associated genes, Illumina is pleased to provide an intuitive BaseSpace App, RNA-Seq Alignment v 1.0, that supports simple push button analysis of the data.
We are pleased to announce a new release of BaseMount, our FUSE driver to mount your BaseSpace account as a Linux filesystem.
BaseMount allows you to navigate on the command line through projects, samples, runs and app results, and interact directly with the associated files exactly as you would with any other local file system.
BaseMount allows you to download – and now upload – files, but maybe more importantly, it allows you to work interactively with your files stored on BaseSpace without having to download them. You may, for example, run samtools directly on a large BAM file, and it will only fetch the blocks needed for your query.
This update (BaseMount v0.12) includes:
- Write-mode: project and appresult creation, file upload
- Properties can be viewed and edited
- Improved documentation
- Relaxed timeout for low bandwidth
- Unmount assistance, listing blocking processes and offering lazy-unmount