March 26th, 2021
TEDDY (The Environmental Determinants of Diabetes in the Young) and DEPMAP (Dependency Map) Data Lakes have been added on Polly.
Introduced option to directly export data to the workspace from a Studio Preset.
Added 37,177 new curated datasets corresponding to various omics to different Data Lakes.
Updated Polly Login User Interface.
Added additional filters to TEDDY Data Lake.
Resolved issue with app hosting infrastructure to increase stability of apps for better user experience.
March 12th, 2021
Introduced Docker building feature on
Polly CLI which enable users to build dockers, check their build status and logs and push dockers to Polly. Added 11,470 new curated transcriptomics and single cell datasets to different Data Lakes.
Better accessibility to datasets within OmixWiki with accessibility to metadata filtering options.
February 26th, 2021
Introduced the functionality that enables the users to host their own application on Polly by using
Polly CLI. Enabled feature level querying for GEO Data Lake.
Added Genomics docker for variant calling and annotation.
Added a new notebook environment for Genomics Variant Analysis.
Enabled partial string search for dataset id in the search bar.
Added 20,096 new curated transcriptomics and single cell datasets to different Data Lakes.
February 12th, 2021
status page for real time updates on Polly’s status, downtime, incidents, and maintenance. Added auto-run feature for selected Studio Presets.
Enabled component updating and versioning by component creator.
Added 11,580 new curated transcriptomics datasets to GEO and LINCS Data Lakes.
Updated the UI of visualization dashboard of
Data Studio for better visibility. Updated all notebook dockers with the latest version of discoverpy (0.0.10).
Added finer error and warning messages to
CLI. Removed the 1000 row limit on query results in
January 29th, 2021
Public sharing of the reports created within any Studio session is now available on Polly.
Added 14,727 new curated transcriptomics and metabolomics datasets with 9,513 transcriptomics datasets being added to the LINCS Data Lake.
Added specific error message to indicate presence of multiple groups with the same compound name in
Labeled LC-MS Workflow. Added specific error message in
Labeled LC-MS Workflow if isotopologues of the compound are spread over different metagroups in El-MAVEN output.
January 15th, 2021
GTEx Correlation and Enrichment Analysis preset is now available which can be used to identify enriched pathways based on the gene correlations.
Added TraceFinder Downstream Analysis preset with additional feature of translating the analytical insights into shareable dashboards.
Added 1,836 new curated transcriptomics and proteomics datasets to different Data Lakes.
Enabled use of retention time information for metabolite identification and updated
Untargeted Pipeline library to handle already identified metabolities.
January 1st, 2021
December 18th, 2020
LINCS(Library of Integrated Network-Based Cellular Signatures) repository with 19,520 curated datasets has been added in
Added ANOVA Test and updated Limma Test with extra filters for volcano plot and Heatmap for the differentially expressed results in the
Dual Mode Data Visulaization.
December 4th, 2020
We now support reactions from Chinese Hamster Ovary (CHO) for integrated pathway analysis in
Resolved timeout error for opening a folder containing large number of files within a Workspace.
Resolved issue with Workspace root directory redirection on selection.
November 20th, 2020
Improved OmixWiki UI for better consumption.
Added the ability to clone Notebooks within Workspaces.
Added granular error messages for Notebook functions and CLI jobs.
Resolved the issue with renaming large data files.
Resolved the issue with folder breadcrumb in Workspaces.
Fixed involuntary logout issue.
November 6th, 2020
Data transfer time limit has been extended to 8 hour enabling transfer of 1TB data through
CLI at once.
Updated user interface of Discover and
Data Studio. Added filtering interface to GEO data lake.
Added search functionality on Discover interface.
Added highlight and cumulative size feature on multiselection in
Workspaces. Updated collaborators icon to show number of collaborators.
Resolved inconsistent log
2FC values for multiple comparisons in IntOmix. Resolved sample name descrepancy in concentration plot of QuantFit.
Fixed table column resizing error on filtering interface.
Resolved a bug in Polly Docker Domain.
October 23rd, 2020
Workspaces user interface. Added filtering interface to COVID-19 data lake.
Updated datasets searchability on dataset ID and description.
Fixed incorrect memory error in
October 9th, 2020
Introduced the option to make dockers on Polly public by adding public docker domain.
Welcome screen now displays the username.
Decreased launch time for applications and notebooks through horizontal pod scaling and buffering.
Fixed landing on Discover after logging in error.
Fixed priority assignment of automated jobs error.
Fixed renaming files after upload error.
Fixed 404 error in Metabolomics Data Lake.
Integrated documentation to every application.
September 25th, 2020
Introduced Labeled LC-MS Analysis preset for natural abundance correction and visualization for single or dual labeled LC-MS data combined with an interactive, customizable and shareable reporting dashboard.
Integrated pathway visualization in
Labeled LC-MS Workflow. Added dilution factor and protein normalization in the
Lipidomics Visualization Dashboard.
Added warning message to prevent duplicate folder creation in Workspaces.
Fixed nested folder creation and notebook renaming error in Workspaces.
Fixed 503 error in Metabolomics Data Lake.
Fixed a bug associated with notebooks and shiny apps opening to a blank screen.
Fixed error occurring in automated jobs.
September 11th, 2020
Data Studio that brings the tools you need to create, customize, and share your analysis effortlessly with your team across the world. Introduced
CCLE Correlation Analysis for identification of features correlated with a gene mutation such as mutations in other genes, expression and sample level metadata.
Updated the version of scanpy to 1.6.0 in single cell docker.
Fixed a bug in notebook giving error with CLI commands.
August 28th, 2020
Updated discoverpy package in all the dockers to the latest version.
Fixed CellxGene visualization loading for specific datasets.
Fixed duplicate metabolite generation issue within the
Dual Mode Data Visualization application. Fixed minor UI issues in Workspaces.
Decreased Workspaces loading time.
August 14th, 2020
Workspaces on Polly, which is a new and improved version of Polly Projects. Added GTEx app to process the filtered datasets from GTEx data lake.
Added a filtering interface for GTEx data lake that allows filtering of the data on the basis of fields within the curated dataset.
Discover and Dual Mode Visualization for processing and further analysis of transcriptomic and metabolomic and single cell filtered datasets. Integrated
Notebook to process the filtered datasets. Hosted
CellxGene for processing and visualization of single cell datasets.
Enabled logs access functionality through
Polly CLI. Added the python package, Discoverpy to all the dockers.
The Project Management Dashboard has been deprecated and replaced by Workspaces.
July 31st, 2020
Added dot plot for Gene Ontology in the
Discover application. Added an extra layer of security in authentication.
Allowed internal standards and unlabeled data to pass through the
Labeled LC-MS Workflow to generate output. Added Phantasus, Boxplot & Whisker plot along with the bar plot in the
Discover application. Fixed Polly CLI auto login error in notebooks.
Fixed unresponsive notebook with infinite loading.
July 17th, 2020
We have released the newest version of
Polly CLI v0.1.18 enabling you to run a CLI job without the need of "secret" key if the private docker is on Polly.
Labeled LC-MS Workflow has N and C as indistinguishable isotopes. Improved the stability of both Shiny and Desktop Applications.
Communication within the infrastructure is now through encrypted keys.
Shiny apps as well as shiny states are encrypted during transit as well as storage.
Added encryption for the disks running the computations.
Encrypted buckets containing credentials.
July 3rd, 2020
Deprecated El-MAVEN FirstView Integration.
June 19th, 2020
We now support reactions from
Drosophila melanogaster for integrated pathway analysis in IntOmix. Introduced
pathway enrichment and pathway view feature along with comparative analysis in Dual Mode Data Visualization. DEPMAP CCLE (DEPMAP Cancer cell line expression data and dependency scores for genes) repository has been added in
Data Lake. Implemented input file access from the sub-folders of a project for applications.
The Single Cell Downstream docker is updated with these new packages: rpy2, anndata2ri (Python packages), ExperimentHub (R package).
Added a GPU instance for
June 5th, 2020
Introduced visualization of labels in
stacked plot within Labeled LC-MS Workflow. Enabled least privilege access for stringent access policies.
Encryption of data in transit and at rest.
Improved access logs throughout the platform.
Enhanced security using a secrets management service.
Implemented regular backups and versioning of data.
May 22nd, 2020
Polly QuantFit node in Compound Discoverer that allows peak picking and absolute quantification on raw data obtained from a Thermo Scientific TM TM Mass Spec instrument.
May 8th, 2020
Changed the optimized color palette in IntOmix from a red-yellow-green scale to a more intuitive red-green scale. All upregulated metabolites or genes are represented by a shade of red and downregulated metabolites or genes as a shade of green.
Changed the non-optimized color palette in IntOmix from a pink-purple scale to a red-green scale to remove ambiguity.
April 24th, 2020
COVID-19 (Transcriptional datasets for SARS viruses, viral infections, and therapeutics for novel coronavirus) repository has been added in