OmicsNet

Update History

Migrated from Java EE to Jakarta EE (09/21/2024);
Code refactoring for improved performance (07/27/2024);
Harmonized curation from different TF databases (ENCODE, ReMap, Enrichr, GTEx, ARCHS4), and updated the CHEA TF-target database to version 3 (06/27/2024);
Updated PPI databases - STRING from v11 to v12.0, and IntAct 2022 to 2024 (Release 247) with more species added (06/27/2024);
Updated the microRNA and their gene targets databases - Tarbase 8.0 to 9.0; and miRTarBase 8.0 to 9.0 (06/27/2024);
Added support to label all nodes in the network (06/06/2024);
Code refactoring for improved performance (04/29/2024);
Upgraded R version to 4.3.2 and PrimeFaces 13.0.1 (12/20/2023);
Fixed the issue for enrichment analysis on the highlighted module in 3D network (10/25/2023)
Code refactoring for better performance (10/10/2023)
Minor text updates and interface improvements (08/18/2023)
Code refactoring and feature enhancement based on user feedback (04/05/2023)
Fixed the issue with PNG image export (02/21/2023)
Upgraded R version to 4.2.2 (12/09/2022)
Enhanced ID mapping for miRNA input list (11/22/2022)
Upgraded to PrimeFaces 12.0.0 (10/15/2022)
JS code refactoring for improved performance (06/07/2022)
Fixed an issue with peak network generation (05/15/2022)
Upgraded R version to 4.1.3 (05/14/2022)
Improved messages based on results from database searching and API calls (04/25/2022)
Added support for genomic coordinates for SNP input (04/19/2022);
Updated FAQs and Gallery, added a new tutorial on IBD case study (04/05/2022);
Added support to allow users to browse, search and manually remove edges or nodes from individual omics networks (04/01/2022);
Added support for adding only edges when using PPI databases (03/25/2022);
Added support for R command history for more reproducible analysis (03/17/2022);
Added support for tissue-based filtering to improve network accuracy (03/15/2022);
Fixed a bug for network file upload based on user feedback (03/01/2022);
Improved interface for network building (02/15/2022);
Updated tutorials for MS peak and taxon list inputs (01/21/2022);
Improved SNP-gene mapping functions for better performance (01/18/2022);
Enhanced LC-MS peak-to-metabolite interface for better user experience (01/12/2022);
Code refactoring and bug fixing based on user feedback (01/07/2022);
Added support for microbiome metabolite prediction based on comprehensive genome-scale metabolic models (GEMs) (12/20/2021);
Upgraded to PrimeFaces 11 (12/18/2021);
Added support for global annotation of untargeted metabolomics data based on the NetID approach (12/10/2021);
Code cleaning and interface updates (10/15/2021);
Added support for topological distributions in Network Tools (09/15/2021);
Users can now save an unique URL to share dynamic network with collaborators (08/12/2021);
Users can now stop GIF animation at any time after it starts (07/05/2021);
Consolidated interface and functions between 2D and 3D network visualization (06/08/2021);
Fixed the issue in creating secondary network and improved 2D network visualization (06/02/2021);
Upgraded to PrimeFaces 10 (04/27/2021);
Bug fix for network upload and enrichment analysis (03/22/2021);
Added support for node and edge adding feature (02/18/2021);
Enhanced node labels for PNG export (11/30/2020);
Enhanced Network Tool for network customization (11/18/2020);
Enhanced support for PNG export - up to 3X larger (10/28/2020);
Fixed the background update issue (08/07/2020);
Users can now select the original database for miRNA gene target analysis (07/06/2020)
Click the to share interactive visual analytics results with your collaborators! (05/18/2020);
Added support for the Human Reference Interactome (HuRI) map (05/13/2020);
Updated Java (from Java8 to Java11) and Primefaces (from PF7 to PF8) (04/08/2020);
Fixed the issue with pie chart node disappearing after network customization (03/25/2020);
Added support to upload both genes and proteins in the network and display nodes as pie charts (03/05/2020);
Code cleaning and performance enhancement for Steiner Tree computing (02/05/2020);
Added support for integrative analysis of gene and metabolites (11/18/2019);
Added a new layout method force-module to create "bubbles" around modules for better visual exploration (08/07/2019);
Added support for one more layer to support a total of 4 layers in 3D perspective layout (06/07/2019);
Added support for fog effects for improved 3D experience (06/06/2019);
The 3D view now supports two drag movements - rotating around center and moving around on the plane (06/04/2019);
OmicsNet now supports both 2D and 3D network views (05/27/2019);
Upgraded the web framework to Primefaces 7.0 (05/19/2019);
Added support to project currently highlighted nodes into a different layer (03/27/2019);
Detailed protocols on how to use OmicsNet is now available in Current Protocols in Bioinformatics (12/17/2018);
Minor bug fixing for more informative error messages (10/15/2018);
Code cleaning and feature enhancement (07/30/2018);
Fixed the issue with HMDB ID mapping (07/10/2018);
Updated OmicsNet logo and code cleaning (06/20/2018);
Enhanced color scheme and added better graphML example for demo (06/18/2018);
Fixed issue with mouse metabolite list upload (06/10/2018);
Added more browser detection method for incompatible versions (05/20/2018);
Updated home page for better user experience (05/12/2018);
Added a gallery page to show visual effects (05/07/2018);
Added animation functions for layered and sphere layouts (05/05/2018);
Bug fixes for edge bundling and performance improvement (05/03/2018);
Fixed issues with node deletion and size change after switching between different subnetworks (04/30/2018);
Added feature to allow batch selection and highlighting of arbiturary list of nodes (04/28/2018);
Updated FAQs and tutorials to synchronize with recent changes (04/25/2018);
Added parameter summary for network building and customization (04/24/2018);
Minor bug fixes and interface improvement (04/21/2018);
Added support for uploading plain .txt file containing edge lists (04/19/2018);
Added support for halo effect for highlighting seed nodes (04/18/2018);
Implemented premade shading models for improved user experience and performance (04/15/2018);
Added support for edge bundling to reduce edge crossing in large networks (04/10/2018);
Added support for expression values in graph files (03/18/2018);
Fixed bugs when users upload graphML files (03/12/2018);
Updated Network Builder page to allow fine control over the composite network (03/04/2018);
Fixed issues with computing arc (edge) height for spherical layout (02/20/2018);
Added support for setting background color and dragging each layer (02/10/2018);
Minor interface updates, code cleaning and performance tuning (01/20/2018)
Added support for shortest paths analysis and visualization (01/15/2018)
Added functions for communicty detection and shortest paths analysis (12/20/2017)
Added Tutorials and updated FAQs (12/12/2017)
Added support for edge opacity adjustment (11/25/2017)
Enhanced Error Message Display when WebGL is not supported (11/20/2017)
Added support for edge thickness adjustment (11/15/2017)
Added support for adjusting node colors based on different topological measures (10/25/2017)
Added support for spherical layout (10/02/2017)
Code cleaning and performance tuning for large network rendering (09/10/2017)
Added support for graphML and SIF data upload (08/25/2017);
Added support for layered layout for multiple omics data (08/15/2017);
Refactoring the JavaScript code to reduce memory consumption (07/20/2017);
Added support for dynamic search for drugs and TFs from current network (06/24/2017)
Added support for node shading effect (05/31/2017)
Interface updates and code cleaning. Added Reset function (05/24/2017)
Initial prototype of OmicsNet and website setup (05/21/2017)