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@AjitPS AjitPS released this 17 Jun 15:39
v3.0
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Learn about vigilant mode.

Key Features

  • Better Gene List & Genome Region Search. You have a list of genes and no clue what they do? Just paste your gene ids/names into the Gene List box (without any keyword) and let KnetMiner provide a summary of all information it has for your genes, their location, enriched linked terms and allow you to view their knowledge network. Genes won't be ranked and only paths from gene to trait and phenotype nodes will initially be shown. If you combine your gene list with keywords, KnetMiner will be able to rank your gene list based on relevance and highlight the most interesting paths of the knowledge network.
  • New Web API access. KnetMiner knowledge networks can now be searched and visualized through API calls. For example, check out the MFT gene in araknet, wheatknet or riceknet. Adding a keyword argument to the URL will do some smart filtering and display the most interesting paths connecting genes and keywords (see example). You can embed similar code snippets into your own website.
  • Smart Publication filtering. Some genes are linked to hundreds of papers. KnetMiner will now only show the most recent 20 publications in GeneView (Evidence box) and in NetworkView. This change will help you to get quicker to most recent research papers and has significantly improved the KnetMiner loading time.
  • Deploy your own KnetMiner with Docker. KnetMiner is now available as a Docker image that can be easily deployed on your own server or in the AWS Elastic Beanstalk. To host your own private or public KnetMiner, you will need to create or clone one of the existing my_species (see example) folder. You can build your own my_species knowledge network or ask us to build one for you as a service.

All features and bug fixes

  • Search interface:
    • Improved search interface now supporting without-keyword search
    • New search-modes implemented for search with gene-list only, genomic regions only, and gene-list + region-search in addition to existing keyword-centric search-modes
    • New loading spinner to search and view network
    • New search interface layout, icons, post-search auto-scrolling
  • Deployment:
    • New deployment framework implemented using Docker
    • Dockerfiles developed to automate building Docker images for KnetMiner for AWS and local deployment.
    • Detailed documentation available at knetminer-docker-docs
    • Build scripts implemented to automate species-specific Dockerfile invocation.
    • npm config tweaked to fix bower errors
  • Gene View:
    • Enhancements to Gene Rank calculation
    • 20 most recent publications are shown when you click on a Publication icon
  • Evidence View:
    • F-test: P-value added to evidence terms when gene list is provided
    • Network links added to user genes column if gene list is provided
  • Network View:
    • 20 most recent publications are shown in network
    • If no-keyword is provided, show initially only paths from gene to Trait and Phenotype nodes
    • If keyword doesn't match any node in path, show initially only paths from gene to Trait and Phenotype nodes
    • Added network loading spinner
    • Updated KnetMaps version for npm and bioJS
  • Map View:
    • Improved scaling to fix chromosome overlaps
    • Updated version GenoMap for npm and bioJS
  • Back-end API:
    • New API endpoints for different search-modes (gene-list search, region search and gene-list + region-search)
    • Re-structured cleanup of module hierarchy
    • Corrected gene-trait transitions
    • genepage - fixed by serving KnetMaps dist/ over https
  • Client GUI
    • relative url's for header logo and ws/ api_url
  • Release notes
    • Updates to species/data release notes, fixes added to network stats displayed in release notes
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