KnetMiner 5.7 – the final fully open-source release

KnetMiner 5.7 – the final fully open-source release

KnetMiner 5.7 includes minor enhancements and bug fixes. We have made small changes to the user search limits incentivizing users to register for a free account by offering higher gene list limits to registered users. Additionally, the API and backend have seen upgrades for better performance and usability.

Key New Features

Gene View Enhancements

The Gene table in KnetMiner 5.7 now includes a filter for gene-to-evidence distance. This distance is defined by the number of hops or relations to go from a gene to a node that provides useful evidence information (e.g., trait, publication, GO terms). For example, for a search that returns too many genes, the user can set the distance filter to 1 to focus on genes with only direct evidence, and then step-by-step begin to increase the distance to include other indirect evidences e.g., from other species or interactions. This feature allows for more refined and targeted gene searches, and will be developed further in future releases.

Gene Table Filtering

Infinite scrolling has replaced the old pagination in both the Gene and Evidence tables, streamlining the user experience and providing a more seamless navigation through large datasets.

Infinite Scrolling

Updated Sample Queries

Sample queries have been tailored to the user’s plan and permissions, providing a more personalised experience. These queries are now visualised based on the currently selected species and the user’s role, with improved scaling and an extended sample query file format to support this customisation.

Sample Queries

Map View Upgrades

Genomaps in Map View are now visualised within a larger container, offering a broader and clearer view of gene locations. Additionally, new centromere locations for various species have been added, enhancing the detail and accuracy of the genemap.

Map View Upgrades

The input box for Gene List search has been updated with a visual indicator that reflects user role limits, providing clarity on the search capacity available to different user tiers.

Gene List search

UI Internals and Bug Fixes

Several internal improvements include enhanced performance of the Evidence table and refactoring of chromosome region selection code. The JavaScript handling the gene/evidence table from the API has been upgraded, and various bug fixes have been implemented to refine user interactions and prevent UI breaks.

API Enhancements

The Gene and Evidence table outputs are now in pure JSON format, optimising the coding of API clients and cleaning up the previous “CSV inside JSON” format. Additionally, the output now includes the graph distance between genes and their evidence, allowing for more nuanced data analysis.

Miscellaneous Updates

Migration to Java 17 and recent versions of Tomcat and Jetty enhances the development environment. The Neo4j mode has been updated to Neo4 5.10.x, along with various dependency upgrades. Enhancements to demo launching scripts and continuous integration scripts, as well as new example queries, are part of this release to showcase updated user limits and capabilities.

To New Frontiers

KnetMiner 5.7 signifies our last major release at Rothamsted Research. In late 2023, we have established the Knetminer spin-out company to build the next generation of the KnetMiner SaaS platform with a team of experienced designers, developers, data scientists and bioinformaticians. While we remain committed to open source, to safeguard our IP and our expanding customer base, 5.7 is our final completely open-source version. Stay tuned!

Check out the latest updates on our website and for developers, our Revision History for more in-depth details.

Happy KnetMining!