Learn how KBase can help you

Learn how KBase can help you

Explore tutorials, documentation, and FAQs about the KBase platform.

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Analysis Apps in KBase

Analysis Apps in KBase

KBase Apps are analysis tools that you can use in KBase. Apps interoperate seamlessly to enable a range of scientific workflows (see figure below). Some of the apps were written by KBase scientists and developers; others are third-party tools that were integrated into KBase with our Software Developer Kit (SDK). The number of apps available in KBase increases as members of the community use our SDK to integrate their analysis tools into the KBase platform.

The App Catalog lists all of the currently available apps. The majority of them fall into the following categories:

Assembly and Annotation

KBase provides multiple Apps for de novo assembly of Next-Generation Sequencing (NGS) reads from various sequencing platforms. These assemblies can be annotated with RAST or Prokka, enabling you to explore structural and functional features.

App List
Sequence Analysis

KBase has a suite of Apps to perform various sequence analyses. They provide the ability to assess quality, search for matches within local databases, and perform multiple sequence alignments.

App List
Metabolic Modeling

KBase has a suite of Apps supporting the reconstruction, prediction, and design of metabolic models in microbes and plants. Genome-scale metabolic models can be used to explore an organism’s growth in specific media conditions, determine which biochemical pathways are present, optimize production of an important metabolite, identify high flux pathways, and more.

App List
RNA-seq and Expression Analysis

KBase offers a powerful suite of expression analysis Apps. Starting with short reads, you can use the tool suite to assemble and quantify long transcripts, identify differentially expressed genes, cluster them and analyze them as functionally enriched modules. You can also compare the expression data with the flux when studying metabolic models in KBase and identify pathways where expression and flux agree or conflict.

App List
Comparative Genomics

KBase provides multiple comparative genomics and phylogenetic analysis Apps to enable researchers to understand evolutionary relationships between organisms and explore structural and functional variance across genomes.

App List

KBase Tutorial Narratives

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

EMSL Summer School 2021

Learn how to use visualization tools, analysis, and modeling, of multi-omics data for understanding biochemical pathways in this virtual course from EMSL.

Genome Analysis in KBase Series focuses on how to use various tools to analyze genomic sequencing data in KBase. This second Narrative demonstrates a workflow for searching and identifying features within…

Genome Analysis in KBase Series focuses on how to use various tools to analyze genomic sequencing data in KBase. This first Narrative shows how to draft isolate genomes in…

EMSL Summer School 2020

Learn how to incorporate microbial metagenomic and environmental metabolite data from watershed ecosystems into metabolic and community modeling using computational frameworks in this virtual course.

Made by Ellen Dow

Join the community of educators using KBase to teach bioinformatics and computational biology!


Why KBase?

While KBase is routinely used for advanced analysis by scientists around the world,…

Made by the KBase Documentation team

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…

Made by the KBase Documentation team

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…

Made by Sam Seaver

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. This Narrative tutorial demonstrates…

Made by Sunita Kumari

KBase’s RNA-seq pipeline uses Tuxedo tools (including Bowtie, TopHat, Cufflinks, Cuffmerge and Cuffdiff) to quantify gene expression from RNA-seq reads. The resulting expression matrix can be used by other KBase…

Made by Dylan Chivian

Gene trees can provide insight when the evolutionary history of a gene family differs from vertical inheritance that tracks with a species tree. This tutorial walks through an example of…

Upcoming webinars

Upcoming webinars

Learn about using KBase for your systems biology and bioinformatics research with one of our upcoming webinars. All past webinars are also available for viewing.

02
Feb
2022
10 am PDT

Learn the basics of KBase and best practices for your research. This webinar introduces the fundamentals of the KBase platform, including data upload, using the Narrative interface, running apps, and sharing your work with collaborators. We will also showcase some of our most popular tools for genomics and systems biology. This is a great way for new users and KBase regulars to quickly become proficient using the system! 

16
Feb
2022
10 am PDT
Take your research further with KBase’s unique publishing features. Creating a Static Narrative takes a snapshot of your Narrative and renders a version visible to anyone on the internet. When you create a Static Narrative, KBase processes the steps in the workflow from all the cells in your Narrative and creates a webpage that displays markdown text, data objects, analysis information, and data visualizations. The result is a sleek, fast loading webpage that allows everyone to view your analysis. And, as they are able to receive a digital object identifier (DOI) from KBase, Static Narratives are perfect as supplementary information to ensure reproducibility in a publication. Sign up for the webinar and see how to create Static Narratives in KBase and learn about updates to the Narrative publishing process.
Previous webinars

Previous webinars

Dec 08, 2021

Janaka Edirisinghe, Argonne National Laboratory

Join this fourth installment of our Samples in KBase webinar series to learn how to upload chemical abundance data (e.g; metabolomics) into the…

Nov 10, 2021

Join our upcoming webinar to learn how to upload amplicon tables into KBase,  link them with your samples for analysis, and build visualizations of community composition based…

Oct 13, 2021

In this webinar, learn how to import amplicon and chemical abundance data and use Samples to organize environmental metadata with analytical data.

Sep 29, 2021

Register for an introductory webinar to Samples in KBase, a new way to organize and explore environmental data in KBase through linking experimental conditions with biological data. Join…

Sep 08, 2021

Join KBase and fellow educators for the second workshop for Educators using KBase. This one hour workshop will introduce the concept workflows developed by the KBase Educators Working…

Aug 18, 2021

Join KBase and fellow educators for an introduction to the tools and resources within the KBase Educators Organization. This one hour workshop includes an introduction to the Educators…

Jul 07, 2021

KBase’s collection of tools for analyzing microbial ecosystems data is growing with new apps developed through support by the Department of Energy’s Science Focus Area program. Join this webinar to…

Apr 21, 2021

Learn about tools for taxonomic profiling in KBase. Join Mark Flynn of Los Alamos National Lab, a developer with the Bacterial-Fungal Interactions Scientific Focus Area. Mark will demonstrate…

Apr 14, 2021

Want to improve metabolic annotations? KBase has new apps to combine multiple functional annotations. Join this webinar to learn about the tools and process in KBase from

Mar 31, 2021

Learn how to promote your research with Static Narratives. Static Narratives are snapshots of the content of your Narratives that are visible to anyone on the internet, even…

Looking for information on tools and resources?

Looking for information on tools and resources?

Check out KBase Documentation for our Getting Started guide and information on tools in the App Catalog. KBase is a fully open source software project available on GitHub.

Data center network maintenance 1/22-1/23

Update Jan 19: we have been told that different network maintenance will be performed over the weekend of January 22-23.  We have not been told an exact time, nor whether there will be an outage, nor a duration of any possible outages.  We will continue to post updates if we get them.

Our data center will be performing network maintenance on Monday, January 24, 2022.  This outage should last approximately 10 minutes, and will cause disruption to narrative.kbase.us, appdev.kbase.us, and possibly compute jobs.  We have not yet been notified of a specific time, if we are told a time we will update this message.

Holiday reduced support

The KBase helpdesk will have limited or no staff during the last two weeks of the year (Dec. 20-Jan. 1). There will be delays in responding to tickets.