News from 2014

Plant functional genomics article sees need for KBase-like systems

A recent review article by Seung Yon Rhee and Marek Mutwil in Trends in Plant Science identifies a need for a system such as KBase to integrate the large number of networks, inference tools, gold standard datasets, and protocols that are available today.

KBase enables model driven annotation hypothesis generation

Genome-scale metabolic modeling is a key focus of KBase, providing a powerful approach for increasing our understanding of biological systems.

KBase demo at ACM BCB 2014

Robert Cottingham of Oak Ridge National Laboratory, the COO of KBase, will present a KBase demo at the upcoming ACM BCB conference

KBase in the news (September 2014)

The recent press release about KBase from Brookhaven National Laboratory (http://www.bnl.gov/els/news/news.php?a=24961), which we reported last week (http://kbase.us/blog/brookhaven-national-laboratory-press-release/) has triggered a number of other articles in online publications that cover topics including energy, biology, and US government technology news. These articles include: “New Energy Department computing platform paves way for better biological research” (http://www.fiercegovernmentit.com/story/new-energy-department-computing-platform-paves-way-better-biological-resear/2014-09-04). By Stephanie […]

KBase talk and poster at Plant Genomics Congress

The Plant Genomics Congress (http://www.giiconference.com/gel296280-2014/) will take place next week, September 11-12, 2014, in St. Louis, MO. The conference covers a wide range of topics relevant to bioinformatics and genomics of plants. KBase Plants team lead Doreen Ware will give a talk on “Translating Plant Genomes” and KBase Plants team member Sunita Kumari will present […]

Brookhaven National Laboratory press release

In a press release about KBase from Brookhaven National Laboratory, writer Rebecca Harrington describes how KBase enables biologists who aren’t programmers to tackle big questions in computational biology (for example, determining the way in which a particular gene variant might increase a plant’s yield for producing biofuels). The press release is available at http://www.bnl.gov/newsroom/news.php?a=24961.

SciPy: The KBase Narrative Interface – Bioinformatics for the 99%

William Riehl gave a presentation on the Narrative interface at the Scientific Computing with Python Conference (SciPy 2014) Wednesday afternoon in Austin, Texas. Bill reviewed how the KBase Narrative provides cluster computation, analysis and modeling pipelines, large public datasets and a “pluggable” architecture for future services.

ASPB 2014 and Software Carpentry workshop

The Annual Scientific Meeting of the American Society of Plant Biologists (ASPB), which will take place in Portland, OR from July 12-16, 2014, will include a talk by KBase member Sunita Kumari. Entitled “The DOE Systems Biology Knowledgebase: An integrated knowledgebase for biofuel research,” her talk will be part of the Special Minisymposium on Bioinformatic […]

KBase talk and posters at ISMB 2014

ISMB 2014 will include a KBase talk and three posters about KBase. On Monday, July 14, at 11:30am, KBase’s Chief Operating Officer, Robert Cottingham, will present a technology track talk entitled “The DOE Systems Biology Knowledgebase (KBase): Progress towards a system for collaborative and reproducible inference and modeling of biological function.” There will be three […]

Matt DeJongh speaks at COBRA 2014

Matt DeJongh, an associate professor at Hope College and a member of the KBase project, will present a talk this week at COBRA 2014, the Third Conference on Constraint-Based Reconstruction and Analysis, in Charlottesville, VA. Matt’s talk is entitled “Metabolic and Regulatory Modeling of Bacteria in the Department of Energy’s Systems Biology Knowledgebase.”

KBase Symposium at the 2014 ASM General Meeting

On Sunday, May 18th at 6:30pm, William Riehl and Folker Meyer will present two talks on how KBase can help researchers collaborate and perform complex analyses. Their talks will focus on the steps in building and reconciling microbial metabolic models and analyzing a large set of community samples extracting microbial species and functions that vary […]

KBase Hands-on Workshop at the GLBRC Retreat

Chris Henry, a KBase scientist at Argonne National Laboratory, will be conducting a hands-on interactive KBase workshop at the 2014 GLBRC retreat (May 20-22) entitled, “Driving Metabolic Engineering, ‘Omics Data Analysis, and Ecology for Plants, Microbes, and Microbial Communities in the DOE Systems Biology KBase.” Chris will be joined by Sunita Kumari who will be […]

Arkin wins DOE’s Ernest Orlando Lawrence Award

Adam Arkin, KBase’s Principal Investigator and the director of Berkeley Lab’s Physical Biosciences Division (PBD), has been awarded the 2013 Ernest Orlando Lawrence Award, the Department of Energy (DOE)’s highest scientific honor, in recognition “for his work advancing biological and environmental sciences.”

Scheduled maintenance on March 25, 2014

KBase will be undergoing maintenance on Tuesday, March 25, 2014, from 8am-12pm PDT. There may be intermittent disruptions in services during this time.

Adam Arkin to speak about KBase at DOE JGI User Meeting

The annual DOE JGI User Meeting, “Genomics of Energy & Environment” is underway right now in Walnut Creek, CA. KBase’s lead PI, Adam Arkin, will speak at the meeting tomorrow (March 20) at 1:45pm. Dr. Arkin will describe KBase’s open-source, open-architecture framework for reproducible and collaborative computational systems biology, including the new Narrative user interface, […]

New Workspace Service and Workspace Browser

KBase Workspaces provide a way for users to store, share, and manage data objects that they have uploaded or generated by running KBase analyses. We recently redesigned workspaces to provide more functionality and reliability. The new version of the workspace server adds many features, including uploading of data provenance, typechecking, object to object references (which […]

The new Narrative User Interface

The Narrative Interface, which is now operational as an alpha release, provides a novel, more user-friendly way to access KBase’s suite of tools and datasets to tackle problems in systems biology, while recording every step of the workflow and thereby capturing a researcher’s thought process. When complete, the Narrative interface will enable users to easily […]

2014 DOE Genomic Science Contractors-Grantees Meeting: KBase talk, workshop, and posters

The Department of Energy’s annual Genomic Science Contractors-Grantees Meeting will be held in Arlington, VA, February 9-12, 2014. KBase PIs Adam Arkin and Rick Stevens will give a plenary talk at 10:30 on February 11. That afternoon, a three-hour KBase workshop will describe some of the scientific analysis capabilities of KBase and introduce how to […]

KBase @ PAG XXII

We have some rapidly approaching events at PAG this year and we hope you will join us! The Plant & Animal Genome XXII Conference, which brings together roughly 3,000 researchers each year, is designed to provide a forum on recent developments and future plans for plant & animal genome projects. PAG provides an excellent opportunity […]