Learn how KBase can help you

Learn how KBase can help you

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

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.

10 am PDT

Join the KBase Educators Community for our ‘Fall Orientation.’ This community-based call’s agenda will include an introduction to educator and resources, opportunity to meet the community, and allow members to learn about new workflows or resources before the Academic year kicks off.

Instructors of any level are welcome! Learn more about the Educator Program at https://www.kbase.us/engage/educators/.

Previous webinars

Previous webinars

Jun 01, 2022

Learn from KBase Principal Investigator Adam Arkin about using KBase for multi-omic analysis of environmental sampling data. This webinar will demonstrate using KBase Samples services to organize multiple…

Mar 30, 2022

Join KBase on Wednesday, March 30 at 1pm ET / 10am PT  as we demonstrate the new Bulk Import features and work with our users to import their…

Feb 16, 2022
Take your research further with KBase’s unique publishing features. Creating a Static Narrative takes…
Feb 02, 2022

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…

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.

Network maintenance Jun 24-27

Update noon CDT: the data center maintenance is complete, and we believe all systems are back to normal.  Please contact us if you have problems.

Our data center will be performing network maintenance Friday, June 24, to Monday, June 27, 2022.  All KBase services, including narrative.kbase.us, appdev.kbase.us, and all compute jobs will be unavailable during this time.  We will begin shutting down services at approximately 2pm CDT (12pm PDT) on June 24.  We hope to be able to restore service on the morning of June 27.

www.kbase.us and status.kbase.us will not be affected by this work.  We will update status.kbase.us as much as possible during the maintenance.

System maintenance May 25

We will be performing system maintenance on Wednesday, May 25, from 2-4pm PDT (4-6pm CDT).  narrative.kbase.us, compute jobs, and appdev.kbase.us may be unavailable or unstable for parts of this time.

We do not anticipate any interruption to www.kbase.us.