Removed the 1000 row limit on query results in CLI.
January 29th, 2021
New
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.
Update
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
New
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.
Update
Enabled use of retention time information for metabolite identification and updated Untargeted Pipeline library to handle already identified metabolities.
LINCS(Library of Integrated Network-Based Cellular Signatures) repository with 19,520 curated datasets has been added in Data Lake.
Update
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
New
We now support reactions from Chinese Hamster Ovary (CHO) for integrated pathway analysis in IntOmix.
Update
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
New
Improved OmixWiki UI for better consumption.
Added the ability to clone Notebooks within Workspaces.
Update
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
New
Data transfer time limit has been extended to 8 hour enabling transfer of 1TB data through CLI at once.
Update
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 log2FC values for multiple comparisons in IntOmix.
Resolved sample name descrepancy in concentration plot of QuantFit.
Fixed table column resizing error on filtering interface.
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.
Update
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
New
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.
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
New
Introduced 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.
Update
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
New
Introduced a metabolomics docker equipped with packages for analysis of metabolomics data.
Introduced 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.
Integrated 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.
Update
Enabled logs access functionality through Polly CLI.
Added the python package, Discoverpy to all the dockers.
Deprecated
The Project Management Dashboard has been deprecated and replaced by Workspaces.
July 31st, 2020
New
Added dot plot for Gene Ontology in the Discover application.
Added an extra layer of security in authentication.
Update
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
New
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.
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.
Update
Improved access logs throughout the platform.
Enhanced security using a secrets management service.
Implemented regular backups and versioning of data.
May 22nd, 2020
New
Introduced Polly QuantFit node in Compound DiscovererTM that allows peak picking and absolute quantification on raw data obtained from a Thermo ScientificTM Mass Spec instrument.
Phi calculation feature has been added to Labeled LC-MS/MS Workflow.
Update
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
New
COVID-19 (Transcriptional datasets for SARS viruses, viral infections, and therapeutics for novel coronavirus) repository has been added in Data Lake.