Frequently Asked Questions

What is the Systems Biology Knowledgebase (KBase)?

The Department of Energy Systems Biology Knowledgebase  (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data, tools, and their associated interfaces into one unified, scalable environment, so users do not need to access them from numerous sources or learn multiple systems in order to perform sophisticated systems biology analyses.

See What is KBase for more information. You can also look at a preprint of the upcoming KBase paper at http://biorxiv.org/content/early/2016/12/22/096354 or download a printable four-page KBase brochure.

Why do we need KBase?

A collaborative computational environment is needed to bring researchers together to share and integrate large, heterogeneous datasets in order to develop predictive models and drive scientific discovery. A common framework for managing and sharing the systems biology datasets, workflows, software, models, best practices, and other relevant knowledge will increase the scientific return on investment and empower researchers to reproduce published results and review projects more effectively–cornerstones of the growing Open Science movement. Achieving a systems-level understanding of biology will allow researchers to predict and ultimately design how biological systems will function under particular conditions. (See What is KBase for more information.)

What can you do in KBase?

How are researchers using KBase?

  • Our Research Highlights page shows some recent high-profile research done using KBase.
  • The Publications page lists papers that cite KBase in their methods and analysis.
  • See our growing Narrative Library for some interactive examples of how KBase can be used to answer research questions. You can copy the Narratives and try running the steps yourself, changing the parameters to see what happens, and even running the analyses on your own data.

Who can use KBase?

Anyone can use it. Signing up for an account is easy and free. You can access KBase using our Narrative graphical user interface from any web browser.

How do I get started?

Visit the “New to KBase?” page or go straight to the Narrative Quick Start to learn how to use the Narrative user interface.

How do I set or reset my password?

If you signed up for KBase and yet your password does not seem to work, you may reset your password at any time. All you will need is access to the email account you originally signed up with. The password reset function is available from this various mentions on this site (e.g. search for “reset”), or from the Narrative Interface login form.

What software do I need to install on my computer to use KBase?

None! You don’t need anything other than a web browser, which you already have (you’re reading this FAQ on it). KBase works on most modern web browsers, including Firefox, Chrome, and Safari. See the Supported Browsers page for more information.

What should I do if my Narrative freezes or won’t load properly?

  • See our list of recommended browsers to ensure yours is supported by KBase.
  • Try a hard reload (shift-reload in your browser window).
  • If you’ve used earlier versions of KBase, they may be lurking in your cache and messing things up. Try either clearing your cache or launching KBase from an “incognito” or “anonymous” window (which doesn’t use your cache).
  • Shut down and restart your Narrative by selecting this option from the top left menu of the Narrative Interface.

For additional help and guidance on reporting issues, see our troubleshooting tips.

Is KBase a database?

KBase is not just a database–it includes tools and user interfaces as well as data. We have integrated data from a wide range of public resources. It is also possible for users to upload their own data and decide who to share it with.

How do you curate the data?

We do not directly curate data; we take annotations from public resources and users’ uploaded data. KBase does, however, provide tools and services to assist in user annotation and curation.

How do I control access to my data or Narratives?

We believe that you will ultimately help both yourself and other researchers by sharing your Narratives so that others can see what you were thinking, what you did, and what you concluded from your analyses. However, rest assured that all of your data and Narratives are private (viewable only by you) until you decide to share them. You can choose to share a Narrative with specific collaborators or with everyone.

What training, such as tutorials and workshops, is available?

The KBase team presents at various conferences and conducts workshops for end users and developers. Check our calendar of events to find out when and where these will be. In the near future, KBase will be offering various types of training and collaboration with users and developers: tutorials based on current KBase tools and interfaces, bootcamps focused on educating community developers on how to develop computational tools in KBase, and webinars and workshops targeting particular scientific problems.

If you would like to host a KBase workshop at your organization, please contact us.

Do you have any online educational materials?

Yes, we do. If you’ve never used KBase before, start with the “New to KBase?” page. The Narrative Interface guide and the Data Search guide will teach you about those key KBase interfaces. The App Tutorials show step-by-step analysis examples. We are also beginning to introduce Narrative tutorials–the first of these is about the Assemble and Annotate app. Not only can you read through an example of how to assemble and annotate data in KBase; you can make your own copy of the Narrative tutorial and run the steps yourself, even changing the parameters or uploading your own datasets to analyze.

Another useful reference is the KBase Glossary, which defines terms that are used in specialized ways in KBase documentation. For more documentation links please refer to the Docs menu.

A printable four-page KBase brochure is available as a PDF.

Where can I find your source code?

Nearly all KBase software is publicly available through GitHub, where it can be reviewed and extended by the community.

KBase’s open source software license can be viewed here.

Can I add my own analysis tools to KBase?

Yes! The KBase SDK offers members of the KBase community a mechanism to add open-source, open-license (e.g., GNU Public License) tools to KBase, so that they run on KBase’s computational architecture and are available through the KBase Narrative Interface. See the Developer Information page for more information.

How should I cite KBase?

Arkin, A.P. et al. The DOE Systems Biology Knowledgebase (KBase).
bioRxiv preprint first posted online Dec. 22, 2016; doi: http://dx.doi.org/10.1101/096354.
Preprint: http://biorxiv.org/content/early/2016/12/22/096354

How can I find out more about KBase plans and new features?

We regularly post announcements on our news page, as well as via social media (Facebook and Twitter).
You can also sign up for our quarterly newsletter and read past issues.

Who can I contact with further questions?

Please see Contact Us. In our new KBase Help Board, you can engage in a two-way dialog with KBase staff without revealing your email address.