Outreach and User Development for the KBase Science Community
Authors:
Benjamin Allen3* ([email protected]), Ellen G. Dow1 ([email protected]), Zachary Crockett3, Elisha Wood-Charlson1; Jason Baumohl1, Kathleen Beilsmith2, Joseph Bezouska2, David Dakota Blair4, John-Marc Chandonia1, Dylan Chivian1, Meghan Drake3, Janaka N. Edirisinghe2, José P. Faria2, Jason Fillman1, Andrew Freiburger2, Tianhao Gu2, Prachi Gupta1, A. J. Ireland1, Marcin P. Joachimiak1, Sean Jungbluth1, Roy Kamimura1, Keith Keller1, Dileep Kishore3, Dan Klos2, Filipe Lui2, David Lyon1, Cody O’Donnell1, Mikaela McDevitt1, Chris Neely1, Erik Pearson1, Gavin Price1, Priya Ranjan3, William Riehl1, Boris Sadkhin2, Samuel Seaver2, Alan Seleman2, Gwyneth Terry1, Pamela Weisenhorn2, Ziming Yang4, Shinjae Yoo4, Sijie Xiang1, Qizhi Zhang2, Shane Canon1, Paramvir S. Dehal1, Robert Cottingham3, Christopher S. Henry2, Adam P. Arkin1 (PI)
Institutions:
1Lawrence Berkeley National Laboratory; 2Argonne National Laboratory; 3Oak Ridge National Laboratory; 4Brookhaven
National Laboratory
URLs:
Goals
The DOE Systems Biology Knowledgebase (KBase) is a knowledge creation and discovery environment designed for biologists and bioinformaticians. KBase integrates a large variety of data and analysis tools, from DOE and other public services, into a user-friendly platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses. KBase is a publicly available and developer extensible platform, enabling scientists to analyze their own data alongside public and collaborator data, then share their findings across the system and ultimately publish reproducible analyses.
References
The KBase user development and outreach team works to accelerate user research, develop skills and knowledge of computational biology across experience levels, and promote advances in research and software development for the betterment of the scientific community. User development activities promote applications of many analytical pathways available, including protocol and tutorial development for the KBase platform, as well as conducting workshops and webinars. Outreach and user engagement helps identify, grow, and support the scientific communities using KBase for research. The KBase Educators program supports professors and teachers integrating hands-on computational biology exercises and analyses through KBase. The variety of programming targets different cross-sections of the BER research community, with the goal to empower the next generation of researchers using KBase.
Outreach and User Development: The KBase team hosts training events to support institutions, research groups, collaborators, and educators advance their research. Training events include workshops and webinars to demonstrate use of the platform and showcase features of interest. Workshops are designed to support specific institutional research needs and facilitate collaboration between research groups utilizing KBase. A recent example is the Long-Reads Isolate Sequencing and Assembly workshop hosted by the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area and KBase to demonstrate new tools for microbial genomics. Webinars are broadcast to a global audience and showcase powerful workflows, new tools and features, and speakers from community developers to subject matter experts. Recorded webinars are shared via the KBase YouTube channel (youtube.com/DOEKBase) as a persistent resource for training materials.
Help Desk: KBase is committed to helping users utilize KBase for their research. The KBase Help Board allows users to report bugs or ask questions to be addressed by KBase staff in a forum that is public so that questions are findable by future users. Users may also submit new feature requests to inform KBase development to better serve their needs.
KBase Educators: The KBase Educators Community (kbase.us/engage/educators/) includes biology and data science instructors teaching students at community colleges, primarily undergraduate, and doctoral research institutions that represent diverse populations, including minority serving and emerging research institutions. Instructors find KBase enables their students to conduct hands-on data science research and analysis without programming skills or additional computational resources. The KBase Educators Org provides free, open-access to instructional workflows—teaching resources, data, analysis tools, and mark-down utility to customize instructions and learning goals, including Spanish versions. Working groups seeking new opportunities for their students have designed and are piloting a modular curriculum based on the open, reproducible scientific process: (1) research question and hypothesis development, (2) experimental design and sample metadata, (3) sample collection and processing, which build upon the existing resources for (4) data analysis, and (5) conclusions and publishing.
Through each of these approaches, KBase empowers researchers and inspires the next generation of biologists and data scientists by providing a platform to investigate systems biology problems with sophisticated tools and share knowledge across the scientific community.
Funding Information
This work is supported as part of the Genomic Science program of BER. The DOE Systems Biology Knowledgebase (KBase) is funded by the DOE Office of Science, BER program under award numbers DE-AC02- 05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886. The Educator Working Groups described is funded by a National Science Foundation RCN-UBE Incubator under award number 2316244.