Release Notes

November, 2021

New

  • Workspace contents like files, analyses, reports can now be sorted in workspaces based on name, created date, last modified, author, and type.
  • 15,000 Microarray and WES (Whole Exome Sequencing) datasets from PPMI have been curated and added to Polly.
  • Dataset Overview (containing Title, Publication, Abstract, Tags for the Data, sample information as summary plots and table, processed data as a table) for every dataset can be viewed using the “View Details” option beside datasets in OmixAtlases.
  • The Datasets (gct, h5ad, vcf) files can be downloaded from the Options Menu in the Card view or from the View Details Page.
  • Request for Dataset option is available at multiple places within the OmixAtlases.

Update

  • Resolved a bug in El-MAVEN instance termination.
  • Curation information of 45,000 datasets from gnomAD and DepMap has been updated.

October, 2021

New

  • In addition to Liver OmixAtlas, polly now has GDC, GEO, cBioPortal, PharmacoDB, LINCS and Metabolomics OmixAtlases.

Update

  • Added 17500 datasets on Polly
  • Genotype, age and gender annotation were added to 3,900,000 GEO samples

September, 2021

New

  • New compute machines Mi5xlarge (32 vCPU, 250GB RAM), Mi6xlarge (64 vCPU, 500GB RAM), Mi7xlarge (64 vCPU, 970GB RAM), GPUsmall (1 GPU, 8 vCPU, 60GB RAM) and GPUmedium (4 GPU, 32 vCPU, 240GB RAM) were added to EL-MAVEN.
  • Introduced Polly Files (beta version), a desktop application for transferring files between computer and Polly Workspaces.

Update

  • Resolved a bug that caused an error in SQL query on “’” expansion.
  • gnomAD was enriched with 96,000 new datasets of WES and WGS type.
  • Fixed table view bugs and enhanced UI on OmixAtlas.
  • New datasets totalling 48,000 were added to Immport, HPA, CPTAC and GTex.
  • Auto-curated tags totalling 770,000 were added to polly datasets.
  • A bug affecting folder deletion was fixed.

August, 2021

New

  • Introduced Polly Python Library facilitating powerful search capabilities across dataset, sample, and feature level metadata on any computational environment through code.
  • Introduced “View Only Access” on Polly Workspaces – an enterprise grade permission giving more control to admins.
  • Enabled Voila Dashboards within Polly Notebooks.
  • Introduced an application resource monitor on EL-Maven, enabling users to monitor the progress of a job and make decisions about requirement of a bigger machine.

Update

  • Over 155,000 datasets were added to LINCS OmixAtlas on Polly.

July, 2021

New

  • Liver OmixAltas released.

June 18th, 2021

New

  • Added 12,200 new curated transcriptomics and single cell datasets to various Data Lake.

June 4th, 2021

New

  • Made Dual Mode Visualizatopn application and Untargeted Pipeline Application lighter for heavy datasets to avoid memory leakage.
  • Added 3.350 new curated transcriptomics and single cell datasets to various Data Lake.

Update

  • Resolved issue in Lipidomics, Dual Mode and Polly El-MAVEN Applications.

May 21st, 2021

New

  • Introduced Google Slide Intergration with Polly Notebooks.
  • Added Reporting feature using Markdown in Dual Mode Visulaization Application.
  • Added 23.350 new curated transcriptomics and single cell datasets to various Data Lake.

Update

  • Added Scree Plot under Quality Check in Dual Mode Visualization Application.
  • Resolved forgot password issue.

May 7th, 2021

New

  • El-MAVEN latest beta version is now available on Polly.
  • Added 25.120 new curated transcriptomics and single cell datasets to various Data Lake.

Update

  • Added two-way ANOVA capability in Dual Mode visualization Application along with combining multiple conditions or cohorts while performing differential expression.

April 23rd, 2021

New

  • Introduced an Admin Dashboard to provide account administrators the convenience to manage their accounts.
  • Added 10,120 new curated transcriptomics and single cell datasets to various Data Lake.

Update

  • HTML as a data file can now be opened through Workspace itself.
  • Resolved an issue to make Dropbox work seamlessly with Workspaces.

April 9th, 2021

New

  • Created Shiny and Studio applicationS for feature level search of GEO Datasets.
  • Added 11,177 new curated transcriptomics datasets to TCGA Data Lake.

Update

  • PDF as a data file can now be opened through Workspace itself.
  • Resolved an issue to make Google Drive work seamlessly with Workspaces.

March 26th, 2021

New

  • 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.

Update

  • 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

New

  • 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.

Update

  • Better accessibility to datasets within OmixWiki with accessibility to metadata filtering options.

February 26th, 2021

New

  • 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

New

  • Introduced the 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.

Update

  • 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 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.

January 1st, 2021

Update


December 18th, 2020

New

  • 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.
  • Resolved a bug in Polly Docker Domain.

October 23rd, 2020

New

Update

  • Updated Workspaces user interface.
  • Added filtering interface to COVID-19 data lake.
  • Updated datasets searchability on dataset ID and description.
  • Fixed incorrect memory error in CLI.

October 9th, 2020

New

  • 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.
  • Integrated pathway visualization in Labeled LC-MS Workflow.
  • Added dilution factor and protein normalization in the Lipidomics Visualization Dashboard.

Update

  • 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

Update

  • 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

New

  • 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.

Update

  • 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

New

Update

Deprecated

  • Deprecated El-MAVEN FirstView Integration.

June 19th, 2020

New

  • 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.

Update

  • The Single Cell Downstream docker is updated with these new packages: rpy2, anndata2ri (Python packages), ExperimentHub (R package).
  • Added a GPU instance for Polly CLI.

June 5th, 2020

New

  • 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.

May 8th, 2020

New

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.