What Is KBase?

The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics.

KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

 

Key concepts driving KBase design

 

Multi-Scale Biological Modeling

A focus on predictive, data-driven biological modeling ranging from genome annotation to environmental transformation via metabolism of communities of organisms.

Data Integration

A data model that integrates genetic, genomic, and functional data types across the tree of life and is designed to support an ever-increasing understanding of biological behavior.

Analysis Tools

A growing array of bioinformatics analysis tools can be accessed from KBase’s Narrative User Interface as “Apps” that can be browsed from the App Catalog.

Provenance

All data sources and analyses in KBase are tracked, thus allowing credit to be given to data contributors, analysts, and tool developers in addition to making workflows completely reproducible.

Collaboration & Sharing

KBase supports the sharing of data, workflows and Narratives, facilitating collaboration and accelerating the pace of scientific discovery. Narratives are “active papers” that allow others to repeat computational experiments, and alter parameters or input data to achieve different results.

Open Source

KBase software is open source and is publicly available through GitHub. The KBase SDK allows open source tools from third-party developers to be seamlessly integrated and made accessible as KBase Apps.

Advanced User Interface

Our graphical user interface (the Narrative Interface), which is built on top of the Jupyter Notebook, allows users to easily customize, execute, and share (or keep private) sophisticated analytical workflows including data, results, notes, custom scripts, and visualizations.

Meta-Analysis

We aim to incentivize scientists to integrate their data, analyses, models and conclusions by providing a platform for advanced systems biology, collaboration, reusable analysis, and publication in a framework that supports both automated and manual meta-analysis across this information.

Scientific Research

A growing number of scientists are using KBase’s data and tools in their research. Some of their work is highlighted on our Research Highlights and publications pages and in our Narrative Library.

Download KBase brochure (PDF)