News from 2013

New Iris release

We are pleased to announce a new release of Iris (http://iris.kbase.us), the web-based command line interface to KBase. You can type “whatsnew” at the Iris command line to see a complete list of new features. The new KBase Quick-Start guide (http://www.kbase.us/for-users/get-started/) explains the process of obtaining a KBase account, using the Workspace Browser to create […]

KBase Demo @ ACM-BCB

Bob Cottingham represented KBase at the ACM-BCB Conference on September 23-24 in Washington, D.C. ACM (Association for Computing Machinery) is the original computer science professional society (since the 1940s) and BCB is the Conference on Bioinformatics, Computational Biology and Biomedical Informatics sponsored by SIGBio. The conference is usually attended by computer scientists working on biological […]

Folker Meyer to give KBase tutorial at UMass

KBase’s Microbial Communities lead, Folker Meyer of Argonne National Laboratory, will present a tutorial about KBase at the University of Massachusetts, Amherst, on August 15, 2013. The tutorial will focus on how to analyze genomic and systems biology data in KBase using the KBase API.

American Society of Plant Biology 2013 Meeting

KBase members presented a talk, booth, and three posters at the annual American Society of Plant Biology meeting that took place July 20-24, 2013, in Providence, RI. One of the minisymposiums on “Genomic Tools” was chaired by Doreen Ware, KBase Plants Lead. She spoke about KBase resources in “Cyberinfrastructures for Plant Science: iPlant and KBase”.

KBase participation at 2013 BESC Annual Retreat

KBase participated in the BioEnergy Science Center (BESC) [http://bioenergycenter.org/besc/index.cfm] Annual Science Retreat July 22-24, 2013, in Chattanooga, TN. In the plenary session attended by more than 230 BESC members on the first day, KBase Chief Operations Officer Bob Cottingham gave an overview talk describing the founding principles of KBase, why it is needed and how […]

KBase members participate in ISMB and BOSC 2013

The annual international conference on Intelligent Systems for Molecular Biology just took place in Berlin. Several KBase people were involved in ISMB and its spinoff mini-conferences called Special Interest Groups, or SIGs. Elizabeth Glass, KBase’s Outreach lead, presented an “oral poster” (a short talk) at the main ISMB meeting; Microbes lead Paramvir Dehal gave a […]

June 2013 Release

A new release of KBase is available as a downloadable Mac or Ubuntu Linux disk image (kbase.us/developer-zone/downloads) or via the IRIS web-based command interface.

Workshop at Functional Genomics Data Society (FGED) conference

Michael Sneddon of LBNL and Ric Colasanti of ANL presented a 3-hour KBase workshop last week at the Functional Genomics Data Society (FGED) 15th International Conference in Seattle. The hands-on workshop introduced participants to KBase and guided them through the process of building metabolic models from genomic sequence data using IRIS and other KBase Labs […]

Tutorial on KBase Variation Services

Mike Schatz and James Gurtowski will give a tutorial on executing the KBase Variation services for computing genome variations from resequencing reads.

KBase workshop at the 2013 Annual Great Lakes Bioenergy Research Center (GLBRC) Retreat

Chris Henry (Argonne National Laboratory) and Doreen Ware (Cold Spring Harbor Laboratory) recently presented a plenary talk and hands-on workshop at the 2013 Annual Great Lakes Bioenergy Research Center (GLBRC) Retreat in South Bend, Indiana, May 21-23. The workshop demonstrated how to use KBase to do genome annotation, build metabolic models, perform plant GWAS analysis, […]

KBase at ASM 2013

The 113th General Meeting of the American Society for Microbiology (ASM, http://gm.asm.org/) took place May 18-21 in Denver, Colorado, and KBase was there. KBase head of Outreach, Elizabeth Glass, ran the KBase booth, which was visited by hundreds of interested researchers, educators, and students eager to hear more about how KBase can help them with […]

Poster and flash talk at at the Genomic Standards Consortium’s “Standards-enabled Research in Genomics” meeting

Elizabeth Glass, KBase’s Outreach lead, presented a flash talk and poster entitled “KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research”, at the Genomic Standards Consortium’s “Standards-enabled Research in Genomics” (GSC15) meeting at the National Institutes of Health on April 22, 2013.

KBase workshop at the Laboratorio Nacional de Genómica para la Biodiversidad (Langebio) Cinvestav, Mexico

Janaka N Edirisinghe of Argonne National Laboratory conducted a hands-on KBase workshop April 11th and 12th, 2013, at the Laboratorio Nacional de Genómica para la Biodiversidad (Langebio) Cinvestav in Guanajuato, Mexico.

KBase Co-PI Finds Surprising Similarities Between Biological and Software Systems

Computational biologist Sergei Maslov of Brookhaven National Laboratory, a co-principal investigator of KBase, worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components “survive” in two complex systems: bacterial genomes and operating systems on Linux computers. In both cases, the more a component is relied upon by […]

KBase talk at Pittcon 2013

During the session on “New Instrumentation for Biofuels Research – And How to Deal with the Flood of New Data” at Pittcon 2013, Bob Cottingham provided an overview of KBase, how it has been developed and its capabilities. He then described a biomass-to-biofuel research project at the BioEnergy Science Center that is investigating microbial conversion […]

KBase workshop presented at 2013 JGI User Meeting

KBase presented a workshop on March 25th at the 8th Annual JGI DOE User Meeting, which focused on the application of genome sciences and technologies to challenges in bioenergy and environmental issues.

KBase Booth at PAG Reported in JGI Newsletter

The winter 2013 JGI Primer (the JGI’s quarterly newsletter) is out! Check out the highlight on the KBase Booth at PAG XXI. At the both booth at PAG, KBase Outreach provided an introduction to KBase, conducted surveys, and arranged meetings with team members to demo services and find out how KBase can specifically connect with […]

Register for the KBase Workshop at the 2013 JGI User Meeting

KBase Workshop at the JGI User Meeting, March 25th, 2013 Join us at the KBase workshop on March 25th at the JGI! You will hear about the DOE Systems Biology Knowledgebase project, see demos of our current capabilities, and learn how to work with us by contributing data or analysis tools.

KBase demos and talks at DOE Science meeting

Today at the annual Genomic Sciences Contractor-Grantee Meeting in Bethesda, MD, three of the KBase leaders–Adam Arkin, Rick Stevens, and Elizabeth Glass–spoke about KBase’s current capabilities and future plans. These talks were followed by breakout sessions for the three scientific domains encompassed by the KBase project, which included demos and tutorials showing how to use […]

KBase talks at the Genomic Sciences Contractor-Grantee Meeting

The Genomic Sciences Contractor-Grantee Meeting XI, the annual conference for genomic science researchers funded by the Department of Energy, kicked off today in Bethesda, Maryland, with three plenary talks by KBase collaborators.

The First Major KBase Public Release is Now Available!

The initial public KBase release in January 2013 included only a few of the KBase analysis and database access services. Our February 2013 Developer’s Release includes a much more complete set of these services, as well as better user documentation and a wider set of web-based and downloadable products. New services in this release include […]

KBase Developer’s Minor Release

The first KBase public Developer’s Release is now available to download as a Mac disk image (DMG) that contains a partial set of the services scheduled for complete release in late February. This release is intended for developers who want early access to some of the KBase APIs and services.

KBase at International Plant and Animal Genome XXI

Come visit us at PAG XXI (1/12-1/16) in San Diego! Join us at the KBase booth (#122) and learn more about the DOE Systems Biology Knowledgebase project and how to work with us. We look forward to talking one-on-one with you and learning about your research and informatics needs!