16 articles News

Breaking news from ggKbase.

Replaced listed_features with Elasticsearch

In this upgrade of ggKbase, we replaced the listed_features table (which is the core component that supports lists, genome summaries, and binning) with the Elasticsearch search engine. Is this a big deal? It’s HUGE! Lists are automatically updated to all projects, even the newly added ones. No need to update lists when you are adding more projects…

Lists Upgrade

The lists system is a useful tool in ggKbase – it allows users to categorize genes on associated annotation. As the number of lists has increased from the contribution of our users as well as by adding the HMM lists, we have realized the need to be able to access and edit lists more easily.…

Memberships and Permissions

Building on the agile permission framework that was adopted at the end of last year, ggKbase 5.3 brings more granular control over memberships and permissions to the owner of the resources on ggKbase. For this rollout, project owners now can not only add members to their projects, but also provide their members fine-grained control over…

Genome Summary Upgrade

Genome Summary, an important tool in ggKbase, has been significantly upgraded in its user interface (UI), user experience (UX) and system performance. For the UI/UX improvement, the Project Selection page has been removed. Instead there is now a Project Selection menu, similar to the Organism Selection and List Selection menus you are already familiar with. This change…

Batch Rebin from File

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…

Feature and Contig Notes Associate Lists

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…

ggKbase on Rails 5

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.

File Downloads Configuration Updates

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…

Modernizing ggKbase

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…