News from 2012

KBase Team at Argonne for November Build

Members of the KBase Team from several partnering labs and universities met at Argonne National Laboratory during the last week of November. At the Build, developers worked in teams on deployment, testing, technical documentation, data upload, and user/developer documentation (tutorials). 28 KBase services were tested and successfully deployed during the meeting, and many of those […]

November Build at Argonne

Argonne National Laboratory will be hosting the next KBase build, which corresponds with the project’s first production candidate release. The meeting will bring together the greatest number of team members and collaborators to date, with nearly 50 participants. This larger gathering follows an intense series of smaller mini-builds, and will result in public releases of […]

KBase Ramps Up Efforts with Mini-Builds

In addition to KBase’s quarterly builds, in which every module is tested, documented and deployed, we have started to organize “Mini-Builds” that focus on only a few of the KBase modules. The October Mini-Build was held October 2-5, 2012, at Argonne National Laboratory. Services that were deployed during this build included: Assembly Service Variation Service […]

First Developer’s Bootcamp

Developers from Lawrence Berkeley National Laboratory, Oak Ridge National Laboratory and Yale University attended the first KBase developer’s bootcamp last week at Argonne National Laboratory. The intensive two-day training is intended for those who wish to become core KBase developers. The bootcamp prepares developers to develop services in the KBase environment. Participants learned how to […]

August Build Produced Public Developer’s Beta Release

The KBase team follows a quarterly build process to prepare each public software release, making sure that each module has been tested and documented. The August build produced our first public developer’s beta release. This release is intended  for members of the community ranging from those who are comfortable using command-line interfaces and a few […]

August Build

Next week, August 13-17, KBase will be holding a large science and development team meeting in California. The goal of the weeklong meeting is to produce a developers’ beta release that exposes many underlying data types and analysis functions. These range from interrogating plant variation and phenotypic traits to statistical analysis of metagenomics data to […]

Nomi Harris Joins KBase

Nomi Harris has been appointed Program Manager for KBase, reporting to the team PI Adam Arkin at LBNL. She has been involved in bioinformatics for over 25 years, and has successfully launched a number of tools used widely by the experimental and computational biological communities. She chairs the Bioinformatics Open Source Conference, a Special Interest […]

KBase in June HPC Source

HPC Source published an article describing the need for KBase, and a description of what KBase will offer: Make No Little Plans Enabling an open, evolving framework for integrative modeling and data management

Argonne Holds First KBase API Tutorial

Our first KBase API tutorial was held on the 14th and 15th of June 2012, at Argonne National Laboratory.  The primary goal of the tutorial was to provide a guided tutorial through available KBase tools via the API (application programming interface). On the first day, the class entered an interactive tutorial using IRIS (interactive remote […]

KBase and JGI Talk Collaboration

Members of the DOE Systems Biology KBase team traveled to the DOE Joint Genome Institute (JGI) on Monday, June 4 to discuss opportunities to collaborate. KBase team members briefed JGI on progress in the science domains and crosscutting infrastructure, and in our outreach efforts. Both teams identified areas of interest for collaborating that are expected […]

Tom Brettin at SFAF Annual Meeting

Tom Brettin gave a presentation on KBase at the Sequencing, Finishing and Analysis in the Future (SFAF) Meeting on Tuesday, June 5. SFAF is an annual meeting dedicated to bringing together experts in the field of genomic sequencing, finishing and analysis – including representatives from the industries that serve this specialized scientific community. Tom said […]

Congratulations Dr. Christopher Henry

Dr. Christopher Henry, a researcher at Argonne National Laboratory, and the KBase Microbes Team Co-lead, has been named the recipient of the Jay Bailey Young Investigator Award in Metabolic Engineering. The purpose of the award is to recognize outstanding research accomplishments in the field of metabolic engineering by a young investigator who has advanced the […]

KBase at GLBRC on May 22

KBase will be conducting a workshop at the Great Lakes Bioenergy Research Center retreat May 22nd. http://retreat.glbrc.org We are looking forward to seeing you there!

May 2 and 3 Progress Review in Chicago

The KBase Science Team leads and their staff met in Chicago for an internal progress review and discussion of future plans for the development of KBase scientific software. Several capabilities were demonstrated including the automated generation of FBA models, an interactive remote invocation shell and large scale workflows on the KBase cloud. This meeting generated […]

KBase Network Meeting: Leveraging ESNet

KBase representatives Dan Olson and Tom Brettin met with ORNL Chief Information Security Officer Kevin Kerr and his key policy and networking staff to discuss the first implementation of a KBase computer network. It would span four national labs and leverage the nation’s premier scientific computer network ESNet.

Hackathon at CSHL

A report on the event from the meeting participants: “The hackathon was remarkably successful. It was focused, productive, and fun. We’ll go out on a limb and say that although we made much progress coding, the best achievement of the workshop was the new working relationship that it garnered among geographically distributed developers.” The participants […]

Thanks to our recent workshop participants

Our KBase workshop at the JGI User meeting, Monday, March 19th was a success. The purpose of this workshop was to foster deeper engagement from the science community’s key partners and stakeholders, and to provide information on how the KBase system is being developed, the progress to date, and the targets. This was our second […]

KBase workshop and posters at the 2012 JGI User Meeting

Attend our workshop and visit our posters at the 2012 JGI User Meeting. The KBase Outreach Workshop will begin with an introduction and timeline for the KBase Project. The Plants, Microbes, Communities, and Infrastructure teams will present short introductions to the objectives for prototype demonstrations for March 2013. Subsequently there will be separate breakout sessions […]