# KBase Documentation ## KBase Documentation - [KBase Documentation](https://docs.kbase.us/master.md): Here you will find guidance for getting started with KBase, full documentation for users and App developers, and help with troubleshooting. - [KBase Terms & Conditions](https://docs.kbase.us/terms-conditions.md): For links to policies and information on KBase resource availability. - [Getting Started](https://docs.kbase.us/getting-started.md): An introduction to KBase and guide on how to get started. - [Signing Up and Signing In](https://docs.kbase.us/getting-started/sign-up.md): Sign up and get started using KBase - [Step-by-Step Sign Up](https://docs.kbase.us/getting-started/sign-up/step-by-step.md) - [Authentication Update](https://docs.kbase.us/getting-started/sign-up/auth-update.md) - [Supported Browsers](https://docs.kbase.us/getting-started/browsers.md) - [Narrative Quick Start](https://docs.kbase.us/getting-started/quick-start.md): A fast, one-page introduction to KBase's narrative interface - [Narrative Interface User Guide](https://docs.kbase.us/getting-started/narrative.md): A more leisurely introduction to KBase's Narrative interface - [Access the Narrative Interface](https://docs.kbase.us/getting-started/narrative/access.md) - [Tour the Narrative Interface](https://docs.kbase.us/getting-started/narrative/tour.md) - [Narrative Navigator](https://docs.kbase.us/getting-started/narrative/navigator.md) - [Create a Narrative](https://docs.kbase.us/getting-started/narrative/create.md) - [Explore Data](https://docs.kbase.us/getting-started/narrative/explore-data.md) - [Add Data to Your Narrative](https://docs.kbase.us/getting-started/narrative/add-data.md) - [Browse KBase Analysis Tools](https://docs.kbase.us/getting-started/narrative/add-apps.md) - [Analyze Data Using KBase Apps](https://docs.kbase.us/getting-started/narrative/analyze-data.md) - [Job Browser](https://docs.kbase.us/getting-started/narrative/job-browser.md) - [Revise Your Narrative](https://docs.kbase.us/getting-started/narrative/revise.md) - [Format Markdown Cells](https://docs.kbase.us/getting-started/narrative/markdown.md): To edit the appearance in Markdown cells for publication, teaching, and to add navigation within the Narrative, use a combination of Markdown and HTML. - [Share Narratives](https://docs.kbase.us/getting-started/narrative/share.md): How to share your KBase Narrative workspaces with individuals and Orgs. - [Linking Static Narratives to ORCID](https://docs.kbase.us/getting-started/narrative/link-doi.md): How to add KBase static Narrative DOIs to your ORCID account. - [Access and Copy Narratives](https://docs.kbase.us/getting-started/narrative/access-and-copy.md) - [Organizations](https://docs.kbase.us/getting-started/narrative/orgs.md): How to access, search, and create KBase Organizations for labs, collaborating researchers, courses, and more. - [FAQs](https://docs.kbase.us/getting-started/faq.md): Frequently Asked Questions about KBase. - [Manage Your Account](https://docs.kbase.us/manage-account.md) - [Linking Accounts](https://docs.kbase.us/manage-account/link-accounts.md) - [Sign into KBase with ORCiD](https://docs.kbase.us/manage-account/link-orcid.md) - [Link ORCiD Records with KBase](https://docs.kbase.us/manage-account/link-orcid-records-with-kbase.md) - [Working with Data](https://docs.kbase.us/data.md): Guides for working with data in KBase - [Data Upload and Download Guide](https://docs.kbase.us/data/upload-download-guide.md): This guide provides instructions for uploading different types of data to your KBase account and downloading output data from your analysis results. - [Data Types](https://docs.kbase.us/data/upload-download-guide/data-types.md) - [Importing Data](https://docs.kbase.us/data/upload-download-guide/uploads.md): Using the Data Browser in the KBase Narrative Interface. - [Bulk Import Limitations](https://docs.kbase.us/data/upload-download-guide/uploads/bulk-limitations.md): This page contains a list of the most commonly observed bugs and known limitations to the bulk import process. - [Assembly](https://docs.kbase.us/data/upload-download-guide/assembly.md): How to upload FASTA files into KBase. - [Genome](https://docs.kbase.us/data/upload-download-guide/genome.md): Formatting and uploading annotated assemblies and GenBank or GFF and FASTA files. - [FASTQ/SRA Reads](https://docs.kbase.us/data/upload-download-guide/reads.md): Formatting and uploading FASTQ and SRA reads files. - [Flux Balance Analysis (FBA) Model](https://docs.kbase.us/data/upload-download-guide/fba-model.md): Data handling to create a model to predict biomass yield given a certain amount of input nutrient. - [Media](https://docs.kbase.us/data/upload-download-guide/media.md): How to format reaction media files for KBase to use in FBA and modeling analysis. - [Expression Matrix](https://docs.kbase.us/data/upload-download-guide/expression-matrix.md): The Expression Matrix data type contains gene expression values taken under given sampling conditions. - [Phenotype Set](https://docs.kbase.us/data/upload-download-guide/phenotype-set.md): The Phenotype Set data type represents experimental data about an organism’s ability to grow in specific media conditions, recorded as growth or no growth. - [Amplicon Matrix](https://docs.kbase.us/data/upload-download-guide/amplicon-matrix.md): Generating and handling Amplicon Matrices to link to Samples - [Chemical Abundance Matrix](https://docs.kbase.us/data/upload-download-guide/chemical-abundance-matrix.md): Metabolomics, exometabolite, and chemical abundance data can be integrated with metabolic modeling and flux balance analysis tools in KBase. - [SampleSet](https://docs.kbase.us/data/upload-download-guide/sampleset.md): A guide to importing and formatting sampling data and metadata to comply with standard templates. - [Compressed/Zipped Files](https://docs.kbase.us/data/upload-download-guide/compressed-files.md): How to handle compressed files when uploading and importing data. - [Bulk Import Specification](https://docs.kbase.us/data/upload-download-guide/bulk.md): Import multiple files at once through bulk upload using an import specification file with the extension .csv, .tsv, or .xls following the instructions below. - [Downloading Data](https://docs.kbase.us/data/upload-download-guide/downloads.md): After analyzing data in KBase, you may wish to download results to your local computer. The Narrative Interface offers the ability to download many of the data types stored in KBase in common form. - [Searching, Adding, and Uploading Data](https://docs.kbase.us/data/search-add-upload.md): Video tutorial on searching for, adding to Narratives, and how to upload data in KBase. - [Filtering, Managing, and Viewing Data](https://docs.kbase.us/data/filter-manage-view.md): Video tutorial on filtering, managing, and viewing data in KBase. - [Linking Metadata](https://docs.kbase.us/data/samples.md): How to link environmental sampling metadata with experimental data. - [Ontologies and Validated Terms](https://docs.kbase.us/data/samples/ontology.md): Make the most out of your metadata by using controlled vocabulary - [Public Data in KBase](https://docs.kbase.us/data/public.md) - [Transfer Data with Globus](https://docs.kbase.us/data/globus.md): A how-to on large file transfer into KBase. - [Transfer Data from JGI](https://docs.kbase.us/data/jgi-transfer.md): The Data Transfer Service (DTS) connects KBase and the Joint Genome Institute (JGI) to seamlessly import data from JGI into your Narratives. - [Using Apps](https://docs.kbase.us/apps.md): All about analysis tools available in KBase - [Analysis Apps in KBase](https://docs.kbase.us/apps/analysis.md) - [Assembly & Annotation](https://docs.kbase.us/apps/analysis/assembly-and-annotation.md): Some of the tools in KBase available for Assembly and Annotation - [Comparative Genomics](https://docs.kbase.us/apps/analysis/comparative-genomics.md): Some of the tools in KBase available for comparative genomics and phylogenetics - [Metabolic Modeling](https://docs.kbase.us/apps/analysis/metabolic-modeling.md): Some of the tools in KBase available for metabolic modeling - [Metagenomics & Community Exploration](https://docs.kbase.us/apps/analysis/metagenomics.md): Some of the tools in KBase available for analyzing microbial communities and metagenomics - [Data Matrices - Amplicon, Stats](https://docs.kbase.us/apps/analysis/matrix.md): Some of the tools in KBase available for rarefaction, standardization, and analyzing amplicon matrices and OTU tables. - [Chemical Abundance](https://docs.kbase.us/apps/analysis/chemical-abundance.md): Use abundance matrices with element, compound, or exometabolite data for analysis. - [Expression & Transcriptomics](https://docs.kbase.us/apps/analysis/expression.md): Some of the tools in KBase available for expression analysis - [Apps in Beta](https://docs.kbase.us/apps/beta.md): These KBase Apps are being tested and debugged. - [Running Common Workflows](https://docs.kbase.us/workflows.md): User guides on how to run different workflows in KBase. - [Assembling & Annotating Microbial Genomes](https://docs.kbase.us/workflows/assembly-annotation.md): Running assembly and annotation in KBase - [FAQ: Assembly and Annotation](https://docs.kbase.us/workflows/assembly-annotation/faq-assembly-annotation.md) - [Comparative Genomics & Phylogenetic Analysis](https://docs.kbase.us/workflows/comparative-genomics.md): Running comparative and phylogenetic Workflows in KBase - [FAQ: Comparative Genomics](https://docs.kbase.us/workflows/comparative-genomics/faq-comparative-genomics.md) - [Metagenomic & Community Analysis](https://docs.kbase.us/workflows/metagenomic-analysis.md): Running Metagenomic and community analysis in KBase - [FAQ: Metagenomics & Community Analysis](https://docs.kbase.us/workflows/metagenomic-analysis/faq-metagenomics.md) - [Transcriptomic Analysis](https://docs.kbase.us/workflows/rnaseq.md): Running RNA-seq analyses pipelines in KBase - [FAQ: RNA-seq Analysis](https://docs.kbase.us/workflows/rnaseq/faq-rnaseq.md) - [Constructing Metabolic Models](https://docs.kbase.us/workflows/metabolic-models.md): Running metabolic modeling workflows in KBase - [Constructing and Analyzing Metabolic Flux Models of Microbial Communities](https://docs.kbase.us/workflows/metabolic-models/metabolic-flux-models.md) - [FAQ: Metabolic Modeling](https://docs.kbase.us/workflows/metabolic-models/faq-metabolic-modeling.md) - [Community Developed Workflows and Tools](https://docs.kbase.us/community-workflows-tools.md): Apps and features added by the KBase Community. - [Functional Annotation](https://docs.kbase.us/community-workflows-tools/functional-annotation.md): These apps allow users to import and utilize external genome annotations that can be combined with annotations created by KBase apps such as DRAM, Prokka, or RASTtk. - [Functional and Taxonomic Profiling of MAGs](https://docs.kbase.us/community-workflows-tools/functional-taxonomic-profiling.md): These tools allow users to examine the genetic potential of a community and investigate the strain frequencies of subpopulations in those communities. - [Taxonomy](https://docs.kbase.us/community-workflows-tools/taxonomy.md): These classifier tools enable users to assign taxonomy and detect unique genomic signatures. - [Viral](https://docs.kbase.us/community-workflows-tools/viral.md): These apps allow users to identify and analyze viral sequences in assemblies within KBase. - [Random Walk with Restart Toolkit](https://docs.kbase.us/community-workflows-tools/rwroolkit.md): These apps allow users to explore networks of multiplex data in an interactive network visualization using the Random Walk with Restart Toolkit (RWRtools). - [Troubleshooting](https://docs.kbase.us/troubleshooting.md) - [Problems with the User Interface](https://docs.kbase.us/troubleshooting/narrative.md) - [Help Board](https://docs.kbase.us/troubleshooting/support.md) - [How to Report Issues](https://docs.kbase.us/troubleshooting/report.md) - [Job Errors and Their Meanings](https://docs.kbase.us/troubleshooting/job-errors.md) - [Common Job Errors](https://docs.kbase.us/troubleshooting/job-errors/common.md) - [The Job Log](https://docs.kbase.us/troubleshooting/job-errors/common/job-log.md): The Job Log contains run information from apps and other jobs, including important error information. - [Import Job Errors](https://docs.kbase.us/troubleshooting/job-errors/import.md): This is a list of error messages found within the Job Log for Import Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted. - [Assembly App Errors](https://docs.kbase.us/troubleshooting/job-errors/assembly.md): This is a list of error messages found within the Job Log for Assembly App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted. - [Annotation App Errors](https://docs.kbase.us/troubleshooting/job-errors/annotation.md): This is a list of error messages found within the Job Log for Annotation App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted. - [Functional Genomics App Errors](https://docs.kbase.us/troubleshooting/job-errors/functional-genomics.md): This is a list of error messages found within the Job Log for Functional Genomics App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted. - [Modeling App Errors](https://docs.kbase.us/troubleshooting/job-errors/modeling.md): This is a list of error messages found within the Job Log for Modeling App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted. - [Developing Apps](https://docs.kbase.us/development.md): Interested in developing an App for KBase? Here you can find information for developers. - [The KBase SDK](https://docs.kbase.us/development/kbase-sdk.md): KBase Software Development Kit for collaborators - [Create a KBase Developer Account](https://docs.kbase.us/development/create-a-kbase-developer-account.md) - [KBase GitHub Repository](https://docs.kbase.us/development/github-repository.md) - [kbase.us](https://docs.kbase.us/kbase.us.md): Specific how to edit and use constraints in WordPress. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information, you can query the documentation dynamically by asking a question. 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