Recent Releases of regulondb-browser
regulondb-browser - RegulonDB Browser 1.5.0
Changelog
Features
- Added new tools and components for genome navigation and track filtering.
- Implemented detailed entity panels, including improved gene/protein views.
- Enhanced visualization of biological information and relations.
Improvements
- Refactored component structure for better maintainability and performance.
- Updated data-fetching logic and improved error handling in UI components.
- Improved display logic for missing or incomplete data in panels.
- Enhanced user experience and detail views in several panels.
Bug Fixes
- Fixed data loading issues and missing detail information in entity panels.
- Corrected rendering bugs in navigation and information panels.
- Patched various minor UI issues affecting responsiveness and usability.
- Fixed issues related to integration between new and legacy components.
Code Cleanup
- Removed obsolete files and dead code.
- Modularized core components for clearer structure.
- Improved internal documentation and standardized code conventions.
Dependency Updates & Testing
- Updated dependencies to latest stable versions.
- Improved and added tests to ensure reliability of new and refactored features.
Summary:
This period focused on polishing and extending the browser’s core genome visualization features, optimizing components, improving the user interface and data handling, increasing code reliability, and preparing the codebase for an upcoming release.
- JavaScript
Published by andresloal about 1 year ago
regulondb-browser - RegulonDB Browser 1.4.5
Improvements and New Features
🖥 New High Throughput Datasets Page
- Redesigned Interface for High-Throughput Datasets
- The High Throughput Datasets page now organizes collections by author/lab, including:
- TF Binding Sites (e.g., Galagan ChIP-seq, Palsson ChIP-exo).
- RNAP Binding Sites, Transcription Start Sites, Transcription Termination Sites, Transcription Units, and Gene Expression data.
- Each dataset includes an information icon (📖 book icon) that provides detailed descriptions.
🌐 New Dataset Collection Pages (e.g., Galagan ChIP-seq Page)
Each dataset collection (such as Galagan ChIP-seq) now has its own dedicated page, featuring:
- Tree-structured Navigation for Datasets
- A collapsible tree menu on the left side improves dataset exploration.
- Transcription factor names now display in their abbreviated form for better readability.
- Dataset Table Enhancements
- Users can now filter, search, and customize table columns for better data exploration.
- The dataset page provides direct download options for the full collection or specific data subsets.
📊 New Features in the Dataset Web Page
Each individual Dataset Web Page (e.g., a single TF dataset from the Galagan ChIP-seq collection) has been redesigned with the following updates:
- Reorganized Transcription Factor Section
- Now a collapsible section under the dataset header to prevent confusion with the main RegulonDB TF page.
- Expanding this section reveals detailed TF information from RegulonDB.
- New WEIGHT MATRIX Section
- Displays the binding site logo and the weight matrix table related to the dataset’s peak data.
- Matrix values can be filtered and downloaded.
- Updated Experimental Details Section
- The former “Growth Condition” section has been renamed “Experiment Details” for clarity.
- Two new fields have been added:
- Experiment Title, providing a descriptive name for each condition.
- Experiment ID (GSM), with direct links to the corresponding GEO database entry.
- IGV Genome Viewer Integration
- The IGV browser has been embedded into the dataset page for direct visualization of TF binding sites.
- Refined Source Data Display
- The dataset page now includes normalized peak data alongside author-reported values.
- Tables have been updated to support searching, filtering, and improved formatting.
This version is compatible with RegulonDB v13.6
- JavaScript
Published by andresloal about 1 year ago
regulondb-browser - 1.4.0
Full Changelog: https://github.com/regulondbunam/RegulonDB-Browser/compare/1.3.0...1.4.0
- JavaScript
Published by Galarcon128 about 2 years ago
regulondb-browser - RegulonDB UPDATE!!
- The RISet datasets now include two new columns: Column 26 (tfrsPMIDS) and Column 27 (riPMIDS), which contain references for the regulatory binding sites and regulatory interactions respectively.
- We have added new functionalities to the FilterTable component, which is used for tabular data display. Improvements consist of added sorting and filtering options along with enhanced organization of tags and columns.
- Adjustments were made to the syntax for displaying evidence and references in the data tables of regulatory interactions.
- A new column, titled "Confidence Level" has been added to the Regulatory Interaction table. This column represents the confidence level of each Regulatory Interaction, and is based on its supporting evidence.
- We've fixed a bug that previously failed to display gene relative distance. This information is now properly displayed.
- For those promoter regions with special mechanisms such as inversions, we've corrected the display of the -10 and -35 boxes to ensure they are shown correctly, as exemplified with fimAp.
What's Changed
- Bump @babel/traverse from 7.17.12 to 7.23.2 by @dependabot in https://github.com/regulondbunam/RegulonDB-Browser/pull/78
- Bump graphql from 16.5.0 to 16.8.1 by @dependabot in https://github.com/regulondbunam/RegulonDB-Browser/pull/70
- Igv browser tool by @Galarcon128 in https://github.com/regulondbunam/RegulonDB-Browser/pull/79
- Se implemento la aplicación de notebooks version beta by @IsraelCS0 in https://github.com/regulondbunam/RegulonDB-Browser/pull/80
- Gene ontology beta version by @Galarcon128 in https://github.com/regulondbunam/RegulonDB-Browser/pull/82
- Bump follow-redirects from 1.15.0 to 1.15.4 by @dependabot in https://github.com/regulondbunam/RegulonDB-Browser/pull/81
- Update app by @galarcon-ccg in https://github.com/regulondbunam/RegulonDB-Browser/pull/83
New Contributors
- @IsraelCS0 implementation notebooks beta version made their first contribution in https://github.com/regulondbunam/RegulonDB-Browser/pull/80
Full Changelog: https://github.com/regulondbunam/RegulonDB-Browser/compare/1.2.0...1.3.0
- JavaScript
Published by Galarcon128 over 2 years ago
regulondb-browser - Add Confidence Level Calculator
++Confidence Level Calculator app
- JavaScript
Published by Galarcon128 over 2 years ago
regulondb-browser - The RegulonDB Browser
Hi :)
- JavaScript
Published by Galarcon128 over 2 years ago
regulondb-browser - Release Test
is a release test
- JavaScript
Published by Galarcon128 almost 3 years ago