KBase Documentation
  • KBase Documentation
  • KBase Terms & Conditions
  • Getting Started
    • Signing Up and Signing In
      • Step-by-Step Signup Guide
      • Authentication Update
    • Supported Browsers
    • Narrative Quick Start
    • Narrative Interface User Guide
      • Access the Narrative Interface
      • Tour the Narrative Interface
      • Narrative Navigator
      • Create a Narrative
      • Explore Data
      • Add Data to Your Narrative
      • Browse KBase Analysis Tools
      • Analyze Data Using KBase Apps
      • Job Browser
      • Revise Your Narrative
      • Format Markdown Cells
      • Share Narratives
      • Linking Static Narratives to ORCID
      • Access and Copy Narratives
      • Organizations
    • FAQs
  • Manage Your Account
    • Linking Accounts
    • Linking KBase to ORCiD
  • Working with Data
    • Data Upload and Download Guide
      • Data Types
      • Importing Data
        • Bulk Import Limitations
      • Assembly
      • Genome
      • FASTQ/SRA Reads
      • Flux Balance Analysis (FBA) Model
      • Media
      • Expression Matrix
      • Phenotype Set
      • Amplicon Matrix
      • Chemical Abundance Matrix
      • SampleSet
      • Compressed/Zipped Files
      • Bulk Import Specification
      • Downloading Data
    • Searching, Adding, and Uploading Data
    • Filtering, Managing, and Viewing Data
    • Linking Metadata
      • Ontologies and Validated Terms
    • Public Data in KBase
    • Transfer Data with Globus
  • Using Apps
    • Analysis Apps in KBase
      • Assembly & Annotation
      • Comparative Genomics
      • Metabolic Modeling
      • Metagenomics & Community Exploration
      • Data Matrices - Amplicon, Stats
      • Chemical Abundance
      • Expression & Transcriptomics
    • Apps in Beta
  • Running Common Workflows
    • Assembling & Annotating Microbial Genomes
      • FAQ: Assembly and Annotation
    • Comparative Genomics & Phylogenetic Analysis
      • FAQ: Comparative Genomics
    • Metagenomic & Community Analysis
      • FAQ: Metagenomics & Community Analysis
    • Transcriptomic Analysis
      • FAQ: RNA-seq Analysis
    • Constructing Metabolic Models
      • Constructing and Analyzing Metabolic Flux Models of Microbial Communities
      • FAQ: Metabolic Modeling
  • Community Developed Workflows and Tools
    • Functional Annotation
    • Functional and Taxonomic Profiling of MAGs
    • Taxonomy
    • Viral
    • Random Walk with Restart Toolkit
  • Troubleshooting
    • Problems with the User Interface
    • Help Board
    • How to Report Issues
    • Job Errors and Their Meanings
      • Common Job Errors
        • The Job Log
      • Import Job Errors
      • Assembly App Errors
      • Annotation App Errors
      • Functional Genomics App Errors
      • Modeling App Errors
  • Developing Apps
    • The KBase SDK
    • Create a KBase Developer Account
    • KBase GitHub Repository
  • External Links
    • KBase Narrative Interface
    • KBase web site
    • KBase App Catalog
  • kbase.us
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On this page
  • Is KBase free to use?
  • I'm getting an error. What do I do?
  • Is it possible to obtain publication-quality figures by using these tools?
  • I have too much data to move.
  • Can I import more than one file into a Narrative at the same time?
  • How many users can view a Narrative?
  • I work with datasets with many samples, outputs from each step often mixed together and often hard for me to select the ones for the next step. How do I keep them organized?
  • What languages are supported in code cells?
  • How does KBase compare with the standalone tools available with command line interface? Does KBase always use the most recent version?
  • How do I access advanced parameters?
  • How do I get a tool I like added?
  • What pipelines does KBase provide?
  • Will my data be made public?
  • What organisms are available in KBase?
  • Is there an API to allow access to the methods from the command line?
  • Can I get an in-person KBase workshop at my institution?
  • Can I see the background code for KBase?
  • What is the difference between Public and Private organizations?
  • Why can't I open a Narrative in an Org?
  • What if I lose access to my account?

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  1. Getting Started

FAQs

Frequently Asked Questions about KBase.

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Last updated 1 year ago

Was this helpful?

Is KBase free to use?

Yes! KBase is completely free to use and is supported by the Department of Energy.

I'm getting an error. What do I do?

You can check and refer to our . If you do not see a reason for the error there, please make a ticket on our .

Is it possible to obtain publication-quality figures by using these tools?

Some of the Apps can produce publication-quality images that can be views by opening in a separate window. We hope to add more in the future.

I have too much data to move.

Is there a better way for handling large datasets? For large files or collections of files, we recommend using Globus. We also have a .

Can I import more than one file into a Narrative at the same time?

Yes, bulk import allows you to check multiple files in the staging area and import them all by clicking "Import Selected." More instructions on this feature are .

How many users can view a Narrative?

There is no limit to the number of users that can be invited to view or edit Narratives. However, it is possible for users who are accessing the Narrative simultaneously to overwrite each other's changes. For that reason, we recommend only one person edit the Narrative at a time.

I work with datasets with many samples, outputs from each step often mixed together and often hard for me to select the ones for the next step. How do I keep them organized?

What languages are supported in code cells?

Currently we only support code cells in Python.

How does KBase compare with the standalone tools available with command line interface? Does KBase always use the most recent version?

Provided the same data, parameters, and tool version are consistent, the results are the same. We make every attempt to use the latest versions of Apps and databases, but they do not always correspond to the most recent version.

How do I access advanced parameters?

You can view some advanced parameters depending on the app by clicking the Advanced Parameters button. For some apps there are few or no advanced parameters. In creating these Apps we aim to balance configurability and usability. As a result, for some Apps we do not make certain rarely changed parameters visible.

How do I get a tool I like added?

There are a couple venues:

1. Submit a Help Desk New Feature Request. We can't promise if or when new feature requests are added, but user input helps us plan our future development.

Alternatively, a beta version of the App might already be in KBase. In the Apps panel, click on the "R" button to switch from release to beta. When a "B" appears in place of the "R", you are viewing beta Apps.

What pipelines does KBase provide?

Will my data be made public?

What organisms are available in KBase?

In KBase as a whole, anything can be uploaded, the only exception being that human data is not permitted. There are connections to some bacterial, plant, and fungal species in the Public Data tab, but any user data or data found from public sources other than those integrated into KBase can be uploaded. On an app-by-app basis, some tools may work sub-optimally or not at all with certain species.

Is there an API to allow access to the methods from the command line?

Command line is not supported for the narratives. However, you may find more flexibility with the KBase Software Development Kit (SDK).

Can I get an in-person KBase workshop at my institution?

Can I see the background code for KBase?

Yes, the relevant Github repo for each App can be found by following the links in the App Catalog. You can access the version and parameters that were used during an App run by clicking on the ellipsis button and clicking "Show code."

What is the difference between Public and Private organizations?

  • The existence and contents of Private organizations are only visible to members of the organization. The organization will not be findable by non-members.

  • Any KBase user can see a list of all Public organizations plus a description of the organization. Non-members are given the option to request membership. Members of the organization can access more information than non-members.

Why can't I open a Narrative in an Org?

Click on ‘Click for Access’ and you are automatically granted View access to the Narrative. You can then click on the linked Narrative to open.

What if I lose access to my account?

You can log into KBase through Google, Globus, and ORCiD. It is recommended to always have at least one personal account linked to your KBase account, so that in the event you lose access to an identity supplier i.e., Google, Globus, or ORCiD because of an email provider change, then you will still have another method to login.

The best way to organize many inputs is to create sets. There are Apps for building these sets, such as that allow you to group those outputs.

2. Add as a 3rd-party developer: If you are a developer of an app, you can find more information on and you can read the documentation for our . If you are not the developer, you can reach out to the developer and ask them about wrapping it for KBase.

KBase does not provide pipelines per se; we try to be as flexible as possible. We do have that replicate the paths many users follow, but we encourage everyone to plot their own course.

All user data in KBase is . You can keep all your data private if you wish. We do encourage users to make data public in the interest of FAIR - - data practices.

If you would like an in-person workshop, contact us by email at .

If you do lose access completely, please submit a ticket through the .

Build AssemblySet
the developer's page
Software Development Kit
example Narratives
private by default until you share it
Findable, Accessible, Interoperable, and Reusable
engage@kbase.us
the job log
troubleshooting guide
Help Board
guide for importing using Globus
Help Board
described in the Narrative Guide