Form Submission: Session, Poster, Demo Submission

Demo/Poster Number

Steel
73

Contact Information
First Name: 
Dan
Last Name: 
Gunter
Session Information
Session Submissions: 
Yes
Presentation Title: 
The DOE Systems Biology Knowledgebase (KBase): A System for Collaborative and Reproducible Inference and Modeling of Biological Function
Description: 
The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) aims to provide a computational environment to meet the key challenges of systems biology: predicting and ultimately designing biological function. Experience from the KBase project provides a perspective from the “front lines” of an effort to revolutionize scholarship in bioinformatics. In KBase, computational experiments are captured in dynamic, interactive documents called Narratives that promote collaboration and reproducibility of scientific results. In addition to data and analysis steps, Narratives can include images, links, and commentary. They can be kept private, shared with colleagues and collaborators, or made public for the benefit of the research community. A key design principle of KBase is that all the data and analysis steps, including their provenance, are stored in a unified data model and the full chain of provenance for every result is searchable and can be reproduced within the system. This unified model creates challenges for integration with the existing, large, bioinformatics ecosystem of multiple file formats and command-line tools. While there is no silver bullet, KBase has gained experience with these challenges, which are echoed in many scientific domains, and which we believe are key to the reproducibility revolution in scientific scholarship. This work is supported by the Office of Science, Office of Biological and Environmental Research, of the US Department of Energy under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886, as part of the DOE Systems Biology Knowledgebase.
Presenter Information
Same As Contact: 
Yes
Organization/Affiliation: 
Lawrence Berkeley National Laboratory
ORCID ID: 
orcid.org/0000-0002-2779-2744
Contributors
First Name: 
Fernando
Last Name: 
Perez
Organization/Affiliation: 
Lawrence Berkeley National Laboratory
Project Role: 
Laboratory Resource Manager
First Name: 
Adam
Last Name: 
Arkin
Organization/Affiliation: 
Lawrence Berkeley National Laboratory
Project Role: 
Lead Principal Investigator
First Name: 
Rick
Last Name: 
Stevens
Organization/Affiliation: 
Argonne National Laboratory
Project Role: 
Principal Investigator
First Name: 
Robert
Last Name: 
Cottingham
Organization/Affiliation: 
Oak Ridge National Laboratory
Project Role: 
Principal Investigator
First Name: 
KBase
Last Name: 
Team
Organization/Affiliation: 
Multiple laboratories