docsCHANGELOG

CHANGELOG

v1.2.3

  • [FEATURE] Added IntAct database to show the protein-protein interactions. More to be added in the future.

v1.2.2

  • [FEATURE] Added additional provider for the LLM Chatbot from “OpenAI” to improve the response time and accuracy of the answers. You can choose between tuned “Gpt-4o” and “Llama 3.1” models in the chatbot.
  • [FEATURE|IMPROVEMENT] Now, only hovering over the edge will show the scores of the edge in the tooltip. This reduces the clutter and effort to show the edge scores without hovering over the edge. This also removes the requriement to have a checkbox to show the edge scores.
  • [IMPROVEMENT] Clustering algorithm’s colors are now more distinct and easy to distinguish. The colors are now more vibrant and have a better contrast with the background.
  • [IMPROVEMENT] Hub Genes Identification feature now shows cut-off on number of edges which is shared with seed genes, enhancing the usability of the feature showing more connected genes with the seed genes.
  • [IMPROVEMENT] Added some help tooltip Content in the dropdown menu.
  • [IMPROVEMENT|BUG] Fixed redundancy of few diseases in the dropdown list of diseases in the left panel. Also, Target Disease Association properties is now shown in consistent according to the order that was present in OpenTargets Portal.
  • [BUG] UI fix which makes it appear that hidden nodes are also selected using selection box (while in actual, it was not being selected).
  • [BUG] Fixed the issue where on using Hub Genes Identification feature, upon hovering edge or node, the highlight (using border) of the hub genes disappears.
  • [BUG] Tissue Expression data was not being displayed and tool was crashing when the user selects the tissue expression data in the node color/size section.
  • [CHANGE] “Node Degree Cut-off” is now “Candidate Prioritization Cut-off” as it does not only consider the node degree but can also consider tissue specificity for cut-off.

v1.2.1

  • [IMPROVEMENT] Removed auto-scrolling when LLM answers a query in the chatbot.
  • [BUG] Fixed overlapping of the options in dropdown in Pathway and Tissue Specificity in node color/size section.
  • [BUG] Fixed a bug where upon selecting those properties whose value is not present in the database, the color/size shows some score.
  • [CHANGE] Left and Right Panel do not disappear when tab changes to Network statistics in the network visualization page.

v1.2.0

  • [FEATURE] Added Network statistics tab in the network visualization page to show the statistics of the network using various charts like Degree Distribution, Clustering Coefficient, etc.
  • [FEATURE] Added pie chart visualization in leiden clustering algorithm to show the distribution of clusters in the network.
  • [IMPROVEMENT] Added a new feature to download the leiden statistics in a CSV file.
  • [IMPROVEMENT] Now, we accept feedback from the users to improve the tool. You can provide feedback by clicking on the feedback button on the bottom right corner of the page.
  • [REVERT] Reverted the home page UI changes made in v1.1.6 to the previous version while keeping the database statistics section.

v1.1.6

  • [FEATURE] Added some metrics in Leiden Clustering Algorithm to evaluate the quality of the clusters which can be easily exported in a CSV file.
  • [IMPROVEMENT] Overhauled the UI of the front page to make it more user-friendly. Also, added information about database statistics.
  • [CHANGE] Tutorial Videos Section is removed and all Tutorial Videos are now available on this page.

v1.1.5

  • [FEATURE] Added a new feature to download details of the selected nodes in the network.
  • [BUG] Fixed an issue where upon unclicking a node removes highlight even when this gene was in search gene textbox.
  • [BUG] Fixed an issue where legend of edge color changes on changing node color radio button.
  • [IMPROVEMENT] Added support of more diseases from OpenTargets Portal.
  • [IMPROVEMENT] In zoom control, now reset button fits all the nodes in the viewport perfectly.
  • [IMPROVEMENT] Added support of CSV file format for export all genes in the network. Removed JPEG format as it was unnecessary.

v1.1.4

  • [IMPROVEMENT] Now, you can delete all your history with just one click in the home page.
  • [IMPROVEMENT] Uploading file with same name as the previous one will now replace the previous file.
  • [BUG] Fixed issue of Edge opacity throwing error when changing the value when show edge color checkbox is checked.
  • [BUG] Fixed issue of hovering edge makes its extremities nodes’ border size to increase.
  • [BUG] Fixed ambiguous behavior of select all button in multiple selection dropdowns.

v1.1.3

  • [FEATURE] Now, dropdown in radio buttons like Tissue Specificity & Pathway in node color/size section supports multiple selection.
  • [IMPROVEMENT] You can now multiple prefix naming conventions like P-value, p-value, p value, pval, pvalue (case-insensitive) for the uploaded data in the network.
  • [IMPROVEMENT] Updated Documentation for differential expression with a caution.
  • [IMPROVEMENT] Added Delete All button in Custom Upload Files section to clear all the uploaded files at once.
  • [BUG] Fixed issue on distinguishing nodes when using Gene Search Highlight and Hub Genes Identification feature parallely.
  • [BUG] Fixed issue of property name not changing even after changing the data type in node color/size section.
  • [BUG] Fixed issue of HGNC ID uploaded via Custom Upload Files not being reflected in the value when it was written in lowercase.

v1.1.2

  • [IMPROVEMENT] Added Tutorial Videos for the TBEP tool.
  • [FEATURE] Added Description of many properties in the dropdown menu.

v1.1.1

  • [BUG] Fixed the issue of the network visualization page having unexplained client side errors when clicking those genes which do not have any values in the database.
  • [BUG] Fixed Custom Upload Files not being reflected in their respective dropdown lists immediately after uploading.
  • [FEATURE] Now, you can change opacity of the network edges in the network visualization page to make the large network more readable.
  • [FEATURE] Now, you can view neighbours of a selected node in the network visualization page when clicked.

    Note: You can also view the neighbours of a selected node by pressing Cmd/Ctrl (⌘) + Hover on the node.

v1.0.0

First release of TBEP tool. The following features are included:

  • Network Visualization: Visualize the network of genes and their interactions.
  • Network Analysis: Modify the network parameters to focus on the key drivers of the network.
  • Node Details & GSEA: Show the details of the selected nodes and perform Gene Set Enrichment Analysis (GSEA).
  • Gene Search: Search for genes and visualize the network of the selected gene.
  • Custom Upload Files: Upload your own gene expression data and visualize the network of the uploaded data, by choosing the uploaded property in the dropdown list. For file format of the uploaded csv data, please refer to the Custom Upload Files Format section.

Beta (β) Feature

  • LLM ChatBot: A chatbot to answer your queries related to the data uploaded with citations (Sometimes, the citations may not be accurate). You may track the citations and verify the information from the original source.

    Note: Currently, LLM ChatBot does note have the capability to gather context directly from the network or your data uploaded. It is a simple chatbot to answer your specific bio-medical queries. Efforts are being made to improve the chatbot capabilities.

License