Video Tip of the Week: KBase, DOE’s Systems Biology Knowledgebase

kbase_genomesI’ve been following the development of KBase for a long time. A couple of times I started draft blog posts to highlight them. But it always seemed like they were just about ready to launch some new features–so I figured I’d wait–or they had a beta interface in testing and about to change a lot of things. So I back-burnered my posts.

But I was notified of a new video on their YouTube channel recently, so I decided to have another look. It appears that there is a new drive to show folks what they have, and there is now a lot of mature documentation and outreach. So it seemed to be time to have another look. Their new intro is this week’s Video Tip of the Week.

As they describe themselves on their homepage:

KBase is an open platform for comparative functional genomics and systems biology for microbes, plants and their communities, and for sharing results and methods with other scientists.

KBase’s ultimate goal is to enable systems biology researchers to predict and even design biological function.

They have a framework that offers a large number of data sources, but they stress that they aren’t just a database. Their landing page notes that at this time they have “23,000 plant and microbial genomes and over 15,000 metagenomic datasets”.

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.

It also includes analysis and workflow tools, and ways to use apps to work with and share data with colleagues in a range of ways. They are doing specific work on metabolic modeling, which they note will include specific guidance on using these complicated tools.

But in one of the most definitive warnings I’ve seen ever on genomics software, there’s this part of the terms and conditions:


I was worried what would happen if I ran an analysis on a human protein by accident. A lot of my go-to examples are things I know well, and that have lots of annotation around them because they are medically relevant human examples. But this scares me off a bit. Jes’ sayin’.

Anyway, have a look at the KBase setup. And if you have non-human analyses to do, try out some of those tools. Look for more help on their metabolic modeling tools if that’s something else you might find useful, there’s a video specifically on that feature as well.

Quick link:

KBase: http://kbase.us


Benedict, M., Mundy, M., Henry, C., Chia, N., & Price, N. (2014). Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models PLoS Computational Biology, 10 (10) DOI: 10.1371/journal.pcbi.1003882

Wilke, A., Bischof, J., Harrison, T., Brettin, T., D’Souza, M., Gerlach, W., Matthews, H., Paczian, T., Wilkening, J., Glass, E., Desai, N., & Meyer, F. (2015). A RESTful API for Accessing Microbial Community Data for MG-RAST PLoS Computational Biology, 11 (1) DOI: 10.1371/journal.pcbi.1004008