Breaking news from ggKbase.
We have developed the Batch Rebin from File web page, located at the project-slug/organisms, to enable users to upload a tab-delimited scaffolds-to-bins file and proceed to batch rebin a project. Users can also dissolve all the bins within the project before batch rebinning. The structure of the file is required to be like the following…
ggKbase has always allowed users to add notes to a feature or a contig. In addition to adding notes to a feature, users can also manually add a new annotation to a feature. With the integration with the Elasticsearch system and the deployment of the percolation feature in Elasticsearch, we can now analyze the newly added…
Today’s upgrade is aimed at improving the overall security (through a user permissions system overhaul) and stability (numerous bug fixes) of the site and will also facilitate future development. Please let us know if you find any problems.
One of the most used features in ggKbase is to generate and download project and organism files, such as fasta files for contigs or proteins etc. The generation of these download files is handled by several background job systems. However, ggKbase can run into problems when the background job queue system gets swamped with long-running jobs, such as…
As a step toward upgrading the core Rails engine that powers ggKbase, we just upgraded the Bootstrap templating library that renders the look-and-feel for ggKbase. Some of the noticeable changes include: the buttons look more flat (monochrome), the colors are a bit more vivid, the fonts are slightly larger, and the form boxes are slightly larger as…
Download files for organisms are now titled after their names rather than their system-generated codes. The bin name inside the files is also based on the organism name and no longer on the code.
ggKbase is now using a search engine powered by Elasticsearch. The new engine is faster, more accurate, and more advanced that our previous system. It also removes many limitations (e.g. the 10,000 result cap). Not only will the searches be faster, but the new engine will act as a springboard for future developments. We’re planning on rolling…
To improve the accessibility to projects, help/instructions, and what is the latest with ggKbase for our users, I have brought back the Explore Projects button and added two more new colorful buttons: New to ggKbase? and News & Updates right on the home page after the Search banner. We hope they will catch your eyes and make…
The search functionality is now made available on ggKbase homepage, so that users can dig into the data in ggKbase right when they arrive here, making the data more discoverable.
We added the News section in ggKbase to keep our community informed about the latest additions and changes on ggKbase. We will also use this section to announce upcoming system downtime due to maintenance and upgrade. The News is located on the top navigation bar as a dropdown list of news article titles and their publication dates. You…
