News from 2015

Printable “Quick Start” guide

Our documentation elves have been busy putting together materials to help our users, new and old, get the most out of KBase. Their latest creation is a new four-page printable Quick Start guide introducing the Narrative Interface. It’s perfect for those who prefer to read documentation on paper, and for use at workshops and tutorial […]

New Narrative Tutorial on Microbial Metabolic Modeling

KBase supports a suite of apps and methods for metabolic model inference, simulation, comparison, editing, and improvement. Much of this functionality is featured in a new “Microbial Metabolic Model Reconstruction and Analysis” tutorial (narrative.kbase.us/narrative/ws.10054.obj.1) available within the Narrative Interface. This tutorial demonstrates how to use KBase to build a draft metabolic model from an annotated […]

Video Tutorial: Introduction to the Narrative Interface

Check out our new video tutorial introducing KBase’s Narrative Interface: https://www.youtube.com/watch?v=6ql7HAUzU7U KBase’s Narrative Interface lets you design and carry out collaborative computational experiments while creating Narratives: interactive, shareable, and reproducible records of your data, computational steps, and thought processes. The video demonstrates how to create a Narrative, find data, use Apps and Method to perform […]

Frequently Asked Questions about KBase’s Metabolic Modeling Tools and Datasets

KBase has a suite of analysis tools and datasets that support the reconstruction, prediction, and design of metabolic networks in microbes and plants. To help our users leverage the metabolic modeling suite, we have put together a set of Frequently Asked Questions (a “FAQ”): http://kbase.us/metabolic-modeling-faq/. […]

KBase at Genome Informatics

As part of the 2015 Genome Informatics conference, KBase scientist Vivek Kumar will discuss KBase capabilities for managing, integrating, and analyzing the ever-increasing wealth of diverse and complex data emanating from systems biology research. Dr. Kumar will present a poster titled “The DOE Systems Biology Knowledgebase—A system for collaborative and reproducible inference and modeling of biological […]

First Narrative Tutorial – Assemble and Annotate Microbial Genome

KBase’s Assemble and Annotate Microbial Genome app is a convenient way to go from sequence reads to an assembled annotated sequence with a single click. Our new interactive Assemble & Annotate Narrative tutorial will introduce you to this useful app in the context of the Narrative Interface. Not only can you read through an example of how […]

Data Upload and Download Guide

In addition to providing access to a wide range of public data, KBase lets users upload their own data for analysis and then download the results in several standard formats (with more to come).  A new Data Upload and Download Guide (http://kbase.us/data-upload-download-guide/) describes the different data types currently available in KBase, including contigs, genomes, short reads, plant […]

Minor release

Yesterday’s scheduled maintenance included a minor release of the Narrative Interface software. For notes about some of the bug fixes and improvements, see https://github.com/kbase/narrative/blob/develop/RELEASE_NOTES.md We are still debugging a few of the new changes, so if you notice anything not working right, please contact us. We appreciate your patience as we work to improve KBase!

KBase at ASPB 2015

The 2015 Plant Biology conference (ASPB, http://plantbiology.aspb.org/) will be held in Minneapolis July 26-30, 2015. ASPB attendees will have several opportunities to learn more about KBase: Booth 401: The DOE Systems Biology Knowledgebase (KBase) (with KBase representatives Meghan Drake, Bob Cottingham, Priya Ranjan and Sam Seaver) Sunday, July 26 – Tuesday, July 28 (Exhibit Hall) Sunday: 6:15-7:30pm […]

Jupyter/IPython awarded $6M in new funding

The Jupyter/IPython project (co-led by Fernando Perez) has just been awarded $6M in additional funding. Jupyter is an open-source software project that supports scientific computing and data science across a wide range of programming languages via a large, open community. The grant will enable the expansion of the capabilities of the Jupyter Notebook, a web-based platform that […]

KBase at ASM 2015

At last week’s American Society of Microbiology (ASM) 2015 Annual Meeting, 52 people attended the all-day hands-on KBase workshop. Entitled “Genome-Scale Modeling of Microbial Metabolism and Regulation using the DOE Systems Biology Knowledgebase (KBase),” the workshop included speakers Paramvir Dehal, Chris Henry, Bill Riehl, and Andreas Wilke. We also had an exhibit booth, which about 120 […]

Join us at ASM 2015

KBase will lead a full-day workshop at the American Society of Microbiology (ASM) 2015 Annual Meeting. Entitled “Genome-Scale Modeling of Microbial Metabolism and Regulation using the DOE Systems Biology Knowledgebase (KBase)”, the workshop will take place on Saturday, May 30 from 8:30am-4:30pm in meeting room 243 (session number WS17). The workshop will include a combination […]

Chris Henry leads KBase workshop for DOE GLBRC

KBase’s Chris Henry led a workshop on “Annotation, Modeling, and Comparison of Plant and Microbial Genomes” at the invitation-only 2015 U.S. Department of Energy’s Great Lakes Bioenergy Research Center’s (GLBRC) annual science retreat last week. Over 25 GLBRC researchers attended. Henry covered (1) how to get a KBase account, (2) creating a Narrative, (3) building […]

Glossary of KBase terms

What *is* a Narrative? An App? A cell? You may be familiar with those words in other contexts, but what do they mean in KBase? Our new Glossary explains our usage of […]

IRIS will be retired May 18, 2015

IRIS, KBase’s web-based command-line interface, will be decommissioned on May 18, 2015.  KBase has transitioned to a new user interface, the Narrative Interface.  You are encouraged to transfer any work you have been doing in IRIS to the Narrative Interface before May 18. However, depending on which features of IRIS you use, there may not be […]

First Annual KBase User Meeting: Tuesday, March, 24, 2015

The first annual KBase User Meeting will include talks, discussions, and opportunities for hands-on experience. The meeting will be held Tuesday, March, 24, from 9:30 am–5:00 pm, in conjunction with the DOE Joint Genome Institute’s 10th Annual User Meeting (March 23-26), in Walnut Creek, CA.

Schatz wins Sloan Foundation Fellowship

Quantitative biologist Michael Schatz, a member of KBase’s plant science team, was just awarded an Alfred P. Sloan Foundation Research Fellowship in Computational & Evolutionary Molecular Biology. He was recognized for his innovative research in cloud computing and analysis of large biomedical data sets. Schatz is a faculty member at Cold Spring Harbor Laboratory (CSHL). […]

KBase at the 2015 DOE Genomic Science Annual Contractors Meeting

KBase will present in two formats at the invitation-only 2015 DOE Genomic Science Annual Contractors Meeting. On Monday and Tuesday, February 23-24, 2015, from 1:00pm – 7:00pm each day, the KBase Experience Room (Wolf Trap Room) will be available for all attendees to try KBase hands-on. In addition, Prof. Adam Arkin will present a short talk entitled “DOE Systems Biology Knowledgebase (KBase)” during the Wednesday, February 25, 2015 Plenary Session at 10:30am.

Analyze JGI sequencing data in KBase

With the click of a button, KBase users can now transfer microbial genome reads from the DOE Joint Genome Institute (JGI) to KBase’s Narrative Interface for assembly, annotation, metabolic modeling, and more! The Push to KBase feature lets users select raw or quality-controlled read data from sequencing projects available on JGI’s website and add them to a Narrative of their choice, all in a few simple steps.

What’s new at KBase?

On February 13, 2015, KBase released a new version of our website and a new and improved Narrative Interface. You may be wondering what’s changed.

Big changes to the user interface

We are excited to announce the launch of a new version of the KBase Narrative Interface, as well as a redesigned website. The kbase.us and narrative.kbase.us websites will be unavailable on February 13 from 10am (Pacific Time) until some time that afternoon as we switch over. We suggest that you return to kbase.us on Monday to check […]

Beta Testing

January 9, 2015: Would you like to be among the first KBase Beta Testers? In preparation for the next release KBase is conducting beta testing of its new apps. Testers do not need computational biology experience, and will be given guidance, instruction and support during the testing process. Can you spend a few hours per […]

KBase at PAG 2015

If you’re attending the International Plant & Animal Genome conference (PAG XXIII, http://www.intlpag.org/2015/) next week, you will have several opportunities to learn more about KBase. PAG, which brings together about 3000 researchers each year, will take place in San Diego, California from January 10-14, 2015. Join us on Tuesday, January 13, from 4:00-6:10pm in the San […]

Coming Soon

The KBase team is working hard to improve the KBase user experience. There will be new, preconfigured methods we call KBase Apps that simplify the process of performing complex analyses on your data. We are also redesigning our website. Stay tuned for our next release at the end of February 2015.