StrepTRN - Recent Activity

patch

Patch v0.2.0-a.1.1 July 01, 2026 - 13:52 Patch v0.2.0-a.1.1:
Fixed bug where data for species with a hyphen in the name could not be downloaded from the /Downloads page.

release

Release v0.2.0-a.1 June 16, 2026 - 09:37 Release v0.2.0-a.1:
Updates:

Updated database with re-annotated target genes and intergenic label of peaks based on summit location.
Updated the /About page with information on the annotation method.

patch

Patch v0.1.0-a.6.1 June 01, 2026 - 08:39 Patch v0.1.0-a.6.1:
Bug fixes:

Hide co-regulators toggle in the Network visualisation no longer hides the query gene when the query species is not selected.
In the TF conservation matrix, individual locus tags from composite nodes are correctly parsed for orthogroup detection.

release

Release v0.1.0-a.6 May 24, 2026 - 15:57 Release v0.1.0-a.6:
Updates:

Added a /Downloads page to download the TSV files of the gene and peak annotations.

Bug fixes:

Fixed a bug where target genes regulated by regulators of the query gene were omitted from the conservation matrix compiler when species data were missing.

release

Release v0.1.0-a.5 May 03, 2026 - 15:58 Release v0.1.0-a.5: Several changes made to the back- and frontend of the website:
Database

Intragenic peaks are now included in the database
Added additional gene name annotations

UI/UX

Added ability to change minimum threshold for Fraction Reads In Peaks. Default is set to 0.
Added ability to export the regulators and target genes from the Summary tables as tables.
TF conservation matrix rows are sorted by state counts rather than alphabetical order.
Changed wording in documentation.

Performance

Network generation has been sped up by refactoring the underlying method from using NetworkX to DuckDB querying.

release

Release v0.1.0-a.4 March 17, 2026 - 14:48 Release v0.1.0-a.4: Changes made to the Overview tab:

The functional annotation of the query gene is now displayed at the top of the tab.
Interactions where the query gene is a regulator vs. where the query gene is a target are now visually separated into their own histogram and table.
Table columns for query-gene annotation have been removed to reduce visual clutter.
Retrieved results are now sorted by descending -log10 foldchange by default.

Bug fixes:

Sorting rows in the Overview in /query now sorts all retrieved results instead of only visible rows.
Numerical columns in tables are now sorted numerically rather than alphabetically.
Clicking a column header now sorts the correct column.
'nan', '-' and empty fields are now consistently displayed in the table as 'N/A'.

patch

Patch v0.1.0-a.3.1 February 24, 2026 - 13:50 Patch v0.1.0-a.3.1: Added information to the /Help page.

release

Release v0.1.0-a.3 February 20, 2026 - 08:50 Release v0.1.0-a.3: Main changes:

Performance improvements by implementing conservation matrices as native components instead of iframes.
Added an About, and Contact page.
Added a draft Help page.
Added more visual separation between S. coelicolor and other species for more emphasis on S. coelicolor.
Show gene annotations from coverage plot as persistent pop-ups rather than pop-ups that disappear when mouse is moved away.
Repositioned legend and annotation panels of conservation matrices to avoid overlap.

release

Release v0.1.0-a.2 January 29, 2026 - 10:30 Release v0.1.0-a.2: Perfomance improvements. Loading times have drastically decreased (loading time for retrieving 500 interactions: ~10 seconds, 5500 interactions: ~2 minutes. Main changes from v0.1.0-a.1.1:

Use sql-based method for initial filtering the global network on thresholds instead of networkx.
Resolved Out of Memory issues by increasing memory for docker container and restructuring database access.

patch

Patch v0.1.0-a.1.1 January 22, 2026 - 17:00 Patch v0.1.0-a.1.1: implementation of caching for data retrieval to fix out-of-memory issues. Leads to faster loading times, and queries more likely to succeed (n TFs + n TGs for query ~< 1000).

release

Release v0.1.0-a.1 January 20, 2026 - 10:00 Release alpha version (v.0.1.0-a.1) with improved UI/UX for features from prototype. Main changes made to features:

Added ability to explore binding events for all genes, regardless of type (regulator/target gene)
Added annotations to genes and binding events.
Added interactive summary visualisation (stacked histogram).
Added interactive annotations to track plots
Removed sequence viewer.

release

Release prototype September 29, 2025 - 13:31 Release of prototype within lab. Consists of TF-centric exploration features:

Network visualisation
Track plots
Sequence viewer
Conservation of interactions