iVariantGuide Release Notes
On January 12, 2018, Advaita released a major update to its platform, with improvements to iPathwayGuide, iVariantGuide, and iBioguide.
IMPROVEMENTS
The Advaita Knowledgebase was updated to version 1711 and now includes:
- 3 organisms: homo sapiens, mus musculus, rattus norvegicus
- 213,390 Genes
- 1,933 Diseases
- 44,976 GO terms
- 4,791 Drugs
- 955 Pathways
- 5,710 miRNAs
- 3,161,730 References
- For a complete list of databases and versions, please see report information within each application.
NEW FEATURES
- iVariantGuide: API Client now accepts multi-sample analyses
- Improvements to account registration page to ensure proper organization affiliation.
BUG FIXES
- iPathwayGuide: Improvements to parsing of CuffDiff-formatted files to maintain association of phenotype labels. Fold changes and p-value parsing remains untouched.
With Advaita’s latest update to its applications and knowledge base, Advaita updated its API for iVariantGuide and iPathwayGuide.
An API or (Application Program Interface) is a set of routines, protocols, and tools for building software applications. An API specifies how software components should interact. Advaita’s API is designed for advanced users of iPathwayGuide and iVariantGuide who would like to streamline their data processing and bypass the UI for submitting data.
Advaita’s API is designed to take advantage of the AWS EC2 environment and allow users to submit one to several datasets in rapid succession. Results from the application are still viewed in the application and are just as informative.
The API documentation and links are viewable at: https://hub.docker.com/r/advaitabio/api-client/
API access and support is available to subscribers who have opted for API access to either iPathwayGuide or iVariantGuide customers. If you would like to add API access to your existing annual subscription, please contact us at sales@AdvaitaBio.com for additional information.
On February 27, 2017, Advaita released a major updates to its platform. These are the release notes.
IMPROVEMENTS TO: iPathwayGuide, iVariantGuide, iBioguide, and the Advaita Knowledge Base
- Changes to AWS services in preparation for HIPAA compliance
- Updated knowledge base to version Advaita KB v1702, which includes the following data sources and versions:
| Database | Version | iPG Annotations | iVG Annotations |
|---|---|---|---|
| KEGG | Release 81.0+/01-20, Jan 17 | Pathways, Diseases, Drugs | Pathways |
| Gene Ontology | 2016-Sep26 | GO Terms | GO Terms |
| Targetscan | Targetscan v7.1 | miRNA Target Genes | miRNA Target Genes |
| MIRBASE | MIRBASE v21,06/14 | miRNA Sequences | |
| dbSNP (incl 1k genomes) | Build 149 | Minor Allele freq. | |
| RefSeq | Release 71 July 2016 | Impacted Transcripts | |
| ClinVar | Dec 1, 2016 | Clinical Significance | |
| SNPEff | v4.1L | Predicted Impact |
IMPROVEMENTS TO iPATHWAYGUIDE
- NEW FEATURE! Onboarding carousel with top user benefits
- NEW FEATURE! API (Premium feature)
- Bug fix: genes selected in Genes Table on Pathways page are now highlighted on pathway map
IMPROVEMENTS TO iVARIANTGUIDE
- Improved error messaging for sample upload & report creation
- NEW FEATURE! Versioning: each report now shows which version of the Advaita Knowledgebase was used to annotate the sample. Outdated reports may be updated when viewing Report Info: either on the Reports page or from within the report itself. As is true for other Advaita applications, only the report owner may update it.
IMPROVEMENTS TO iBIOGUIDE
- Updated to use AKB v1702
11/1/2016
The Commercial Release of iVairantGuide is here! With this commercial release we now have the following enhancements from the last Beta:
- Redesigned uploading and intake navigation work flow with onboarding queues
- Improved navigation and selection on visual filters/graphs
- Improved sharing capabilities:
- View share history
- autofill prompts for often-used email addresses
- Ability to associate filter presets to shared report
- Ability to associate filter presets to public link (anyone can see what you see)
- Improved tooltips and onboarding
- Improved pathway and GO analysis with p-value ranking and advanced correction factors
- UI improvement
- User profile page
- API credentials
- Initial API (Premium Feature)
- Printable Summary (Premium Feature)
- Improved Pathway and GO Analysis (Premium Feature)
- Harmonization of labeling and naming conventions
- Numerous bug fixes and security enhancements
9/6/2016
In the pre-commercial release of iVariantGuide the following issues have been addressed:
- Redesigned uploading and intake navigation work flow with onboarding queues
- Improved navigation and selection on visual filters/graphs
- Improved sharing capabilities:
- View share history
- autofill prompts for often-used email addresses
- Ability to associate filter presets to shared report
- Ability to associate filter presets to public link (anyone can see what you see)
- Improved tooltips
- Improved pathway and GO analysis with p-value ranking and advanced correction factors
- UI improvement
- User profile page
- Introduction of subscriptions (free during beta) to see premium features
- Redesign of processing engine to paralellize analyses
- Improved filtering speed
- Harmonization of labeling and naming conventions
- Numerous bug fixes and security enhancements
- Redesigned uploading and intake navigation work flow
- Improved navigation and selection on visual filters/graphs
- Improved tooltips
- Redesigned notification of filter presets when navigating away from variants page
- Harmonization of labeling and naming conventions
- Numerous bug fixes and security enhancements
4/11/2016
- Analyses are currently limited to single sample analyses. Multi-sample analyses are in development.
- Input file size is limited to ~100mb for now.
- Input files must be .vcf or .vcf.gz version 4.1 or later; reference genomes hg19 (GRCh37) and GRCh38 are supported.
- Supported filters include by quality, read depth, genomic region, variant class, predicted effect, clinical significance, and impact score.
- Filter combinations may be saved as “Presets” for later use with new data sets.
- Detailed variant view includes links to: iBioGuide, dbSNP, OMIM, MedGen, PubMed, and more.
- View variants in context of impacted pathways. Pathway view highlights affected genes and provides ability to model miRNAs and drugs.
- View variants in relation to GO terms. Navigate upstream and downstream to identify specific ontology terms.
- Share reports with individuals or publicly.