Narrative Library

Narratives are interactive, dynamic, and persistent documents that are KBase’s way of making systems biology research transparent, collaborative, and reproducible. This Narrative library showcases a curated selection of Narratives created in KBase. We hope that you will not only read these Narratives, but also copy and build on them and then share your results with the research community. If you have written a scientific Narrative or a Narrative tutorial that you would like us to consider adding to this library, please let us know!

You must sign into KBase to view these Narratives. If you do not have a KBase account, you can create a free account to access these Narratives and more.

Research Narratives

These Narratives represent computational experiments or reproducible publications. You can see the data and analysis steps, along with commentary about why the steps were performed and what the results show. Copy any Narrative to your own KBase account if you would like to try rerunning or even changing the steps.

Related links

  • Our publications page lists citations of research done in KBase, some of which are represented by Narratives on this page.
  • The Research Highlights page describes in more detail some of the science done in KBase.

 

Janthinobacterium FRC Isolate Analysis

In this study, microbes were isolated from groundwater wells. The researchers noticed Janthinobacteriums from the same well, with the same 16S sequence, that differed in their ability to produce violacein (an antibacterial, antifungal compound). They sequenced the isolates and analyzed them in KBase, finding an isolate that included all 5 violacein genes. This Narrative shows how the use of multiple genome and domain annotation pipelines and comparative genomics tools in KBase can provide clues for gene functional role assignment.

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Narrative made by José Faria.

Modeling Central Metabolism and Energy Biosynthesis across Microbial Life

Automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). In this analysis (discussed in this paper), we compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes.

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Narrative made by Janaka Edirisinghe.

BioSIMP (Biological Sampling, Inference, Modeling, and Prediction)

This Narrative presents a process called BioSIMP (Biological Sampling, Inference, Modeling, and Prediction) that models and predicts the behavior of biological organisms to aid in the field of systems biology. BioSIMP models environmental factors and then uses software testing techniques to sample, classify the results to infer influential features, and build models based on these inferences. This information can then be used to predict future behavior of biological systems.

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Narrative made by Mikaela Cashman.

Cyanobacteria-Sphagnum Metabolic Interactions

Sphagnum (peat moss) is a genus of plants (Bryophyta) that associate with nitrogen-fixing diazotrophs and are quintessential ecosystem engineers. In this Narrative, the genome sequences for Sphagnum fallax and an associated microbe are used to build a combined metabolic model based on plant-microbe interactions to show that the plant portion of the model consumes the nitrogen fixed by the microbial portion of the model.

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Narrative made by Sam Seaver.

Predicting Interspecies Interactions with Validation from Transcriptomic Data

These three Narratives demonstrate strategies (described in this paper) for constructing genome-scale metabolic networks that simulate two species in a microbial consortium exchanging metabolites to sustain life. The workflow culminates in the construction of a community model for a simple microbial community consisting of one photoautotroph (Thermosynechococcus elongatus BP1) and one heterotroph (Meiothermus ruber strain A).

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Narratives made by Chris Henry.

Community Modeling Narratives

KBase has a suite of tools and data that support the reconstruction, prediction, and design of metabolic networks in individual microbes and microbial communities. A recent review article in Hydrocarbon and Lipid Microbiology Protocols discusses and compares approaches to modeling the growth and behavior of microbial communities. The Narratives below show how to perform the analyses described in the article.

 

Single-Species Model Reconstruction

For nearly all defined microbial communities, building a metabolic flux model begins with the construction and curation of such models for the individual species in the community. This Narrative reconstructs single-species genome-scale metabolic models while demonstrating every step of the process for microbes B. thetaiotaomicron and F. prausnitzii.

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Narrative made by Matthew DeJongh.

Species Interaction Analysis

Species interaction analysis investigates species that comprise a microbial community individually. This involves constructing models of each species either from genomes assembled from metagenomic reads or of genomes sequenced from pure culture isolates. This Narrative demonstrates these approaches using models of B. thetaiotaomicron and F. prausnitzii.

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Narrative made by José Pedro Lopes Faria.

Mixed-Bag Model Reconstruction and Analysis

Mixed-bag community models are perhaps the simplest type of community model to construct and analyze, as the metabolic pathways and transmembrane transport reactions from all species in a community are combined and treated as if they were contained within a single organism. This Narrative explores two approaches for building mixed-bag models: (1) merging annotations from all species and applying the standard model reconstruction pipelines and (2) merging existing single-species models into a single-compartment mixed-bag model.

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Narrative made by José Pedro Lopes Faria.

Multi-Species Model Reconstruction and Analysis

While mixed-bag models offer many advantages in their simple capacity to predict overall metabolic capabilities of microbial communities, they fail to predict the species interactions necessary for many microbial community behaviors. This Narrative demonstrates how to construct multi-species models that can both integrate all the reactions and compounds represented in each species member of the microbial community and also preserve the functions of each species into a compartment dedicated to that same species.

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Narrative made by José Pedro Lopes Faria.

Narrative Tutorials

These Narrative tutorials provide step-by-step examples that show you how to use KBase tools and data to perform useful analyses. You can copy these Narratives and rerun the steps or try them on your own data.

 

Assemble and Annotate Prokaryotic Genome Tutorial

KBase provides multiple Apps for de novo assembly of prokaryotic Next-Generation Sequencing (NGS) reads from various sequencing platforms. These assemblies can then be annotated with RAST or Prokka, enabling you to explore structural and functional features of a Genome or use it in other analyses. This tutorial demonstrates how to assemble a set of Next-Generation Sequencing (NGS) short reads into contigs and then annotate the assembly.

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Microbial Metabolic Model Reconstruction and Analysis Tutorial

KBase has a suite of tools and data that support the reconstruction, prediction, and design of metabolic networks in microbes. Starting from genome sequence data, this Narrative demonstrates how to use KBase tools to reconstruct and analyze genome-scale metabolic models. These models are primarily reconstructed from protein functional annotations originally derived from literature and subsequently propagated from genome to genome by sequence similarity.

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RNA-seq Workflow

KBase’s RNA-seq pipeline uses Tuxedo tools (including Bowtie, TopHat, Cufflinks, Cuffmerge, Cuffdiff, and CummeRbund) to quantify gene expression from RNA-seq reads. The resulting expression matrix can be used by other KBase apps to analyze expression patterns with clustering algorithms or compare reaction flux with gene expression to identify the pathways where expression and flux agree or conflict. These Narrative tutorials demonstrate how to use the KBase RNA-seq pipeline end-to-end on microbial or plant reads.

Narratives made by Sunita Kumari.

The PlantSEED Resource in KBase

PlantSEED was designed to streamline the process of annotating plant genome sequences, constructing metabolic models based on genome annotations, and using models to predict gene functions. The PlantSEED resource is available within KBase. This Narrative tutorial demonstrates how to start with plant coding or protein sequences, annotate the sequences using the “Annotated Plant Coding Sequences with Metabolic Functions” app, and then build a metabolic model of plant primary metabolism using the annotated sequences as the input.

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Narrative made by Sam Seaver.