iPathwayGuide Support Page - Release Notes

iPathwayGuide Release Notes2018-10-06T12:18:09+00:00
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iPathwayGuide Release Notes

Release Notes – Winter 20182018-08-22T11:02:01+00:00

On January 12, 2018, Advaita released a major updates 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.
Advaita Releases API client for iVariantGuide and iPathwayGuide2018-08-22T11:03:25+00:00

3/13/2017

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.

Winter 2017 Release Notes2018-08-25T09:59:16+00:00

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
Spring 2016 Release – June 19, 20162018-08-22T11:43:46+00:00

The following components were added or addressed in this release.

  • Extensive databases updates including:
    • KEGG pathways, drugs, and diseases
    • NCBI genes
    • TargetScan miRNAs
    • Gene Ontologies
    • PubMed references
  • New EdgeR import format support
  • Improvements to several of the exported images
  • Improvements to meta analysis to preserve order of comparisons
  • Several bug fixes
  • Changes to support additional AWS features
  • Enhancements to security
Summer 2015 Release – July 13, 20152018-08-22T11:45:49+00:00

The following components were added:

  • Support for Sciex SWATH 2.0 Proteomics Expression data
  • “Trash” bin on user dashboard
  • Pathway and ontology images are now locked for scrolling. They can be unlocked in the on-screen menu.
  • In the pathway images, individual genes can now be selected if you hover over the node in the image.
  • Coherent cascades now have arrow heads so you can see directionality of the cascade.
  • The gene table in the pathway detail page is more refined. Easier to filter.
  • Bar chart of DE genes for pathways is now presented below the pathway image.
  • Meta-analysis has a new view called “Rank layout” that lets you see how genes, GO terms, pathways, etc, rank compared to each other. (accessible from the
  • lower right corner of the Venn).
  • Several other improvements on the back-end and a few bug fixes.
Spring 2015 Release – April 13, 20152018-08-22T11:48:00+00:00

Knowledge Base Updates:

  • Genes – 195,222 (increase of 23,106)
  • Pathways – 871 (increase of 12)
  • micro RNAs – 8,837 (increase of 5,268)
  • GO Terms – 39,907 (increase of 1,880)
  • Drugs – 4,389 (increase of 229)
  • Diseases – 1,411 (increase of 12)
  • SNPs – 92,169,423 (increase of 32,120,131)
  • References – 3,010,588 (increase of 51,977)

New Features:

  • Support for nSolver data from NanoString Technologies
  • QC and Normalization metrics for Affymetrix CEL files
  • Stem-loop information for miRNAs
  • Printable report summary with detailed methods and references
  • “Line-up” comparative ranking chart in meta analysis
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