Narratives for the KBase paper

The KBase paper discusses a series of linked Narratives that illustrate a scenario wherein two scientists use KBase to perform collaborative systems biology analysis, resulting in a reproducible, interactive “publication.” These example Narratives demonstrate how KBase facilitates sharing, collaboration, and interdisciplinary research between two scientists: Alice, a wet-lab biologist with expertise in assembly, annotation, and comparative genomics, and Bob, a computational biologist with expertise in metabolic modeling. Using KBase’s tools and data, Alice and Bob collaborate to create and refine a metabolic model for a new strain of a bacterium, starting with its genomic sequence. KBase enables these scientists to accomplish more together than they could individually, with less work and in less time.

The five “Alice and Bob” Narratives described in the paper are linked below. You can copy these Narratives and rerun the steps or even try them on your own data. Please note that you will need a KBase account in order to view or rerun the Narratives.

 

Alice Narrative 1: Assembly and Annotation  https://narrative.kbase.us/narrative/ws.18152.obj.1
Alice Narrative 2: Comparative Genomics  https://narrative.kbase.us/narrative/ws.18153.obj.1
Bob Narrative: Build Metabolic Models  https://narrative.kbase.us/narrative/ws.18155.obj.1
Bob and Alice Narrative 1: Phenotype Data Analysis  https://narrative.kbase.us/narrative/ws.18156.obj.1
Bob and Alice Narrative 2: Phenotype Data Reconciliation  https://narrative.kbase.us/narrative/ws.18157.obj.1

To see other Narratives that demonstrate how to use KBase to carry out computational experiments, please visit our Narrative Library.

Reference

Arkin, A.P. et al. The DOE Systems Biology Knowledgebase (KBase).

bioRxiv preprint first posted online Dec. 22, 2016; doi: http://dx.doi.org/10.1101/096354.

Preprint: http://biorxiv.org/content/early/2016/12/22/096354

Abstract

The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology—predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system.