Fall 2018 Newsletter

The U.S. Department of Energy (DOE) Systems Biology Knowledgebase (KBase) is a knowledge creation and discovery environment designed for both biologists and bioinformaticians.
New Tutorial: Genome Extraction from Metagenomic Data
This new Narrative Tutorial guides users through the process of obtaining high-quality genomes from a metagenome assembly and placing them into phylogenetic context. In the tutorial, you will learn how to clean raw metagenomic shotgun sequencing reads, assemble these reads, perform genome binning on these assemblies, and generate annotated genomes and species predictions from these bins. You can also generate taxonomic abundance based on protein similarity from the raw reads using Kaiju app or using annotated genomes to analyze similarity to reference genomes through the creation of phylogenetic species trees. Genome extraction and species prediction are just the beginning of how metagenomic samples can be analyzed within KBase, as these extracted genomes can be used as input for downstream analysis with our powerful tools for metabolic modeling and comparative phylogenomics. 

View this Narrative Tutorial on KBase
DOE Funded Collaborations to Grow KBase
The Department of Energy recently funded five Science Focus Area (SFA) awards that will provide valuable tools and data directly to our research community through the KBase platform. Awards were made to LBNL, LLNL, LANL, and ORNL, in collaborations with MIT, Ohio State University, and University of California Berkeley. The two-year funded projects range from developing tools that will improve the quality of genomes inferred from metagenomic data (MAGs – Metagenome Assembled Genomes), to allowing users to do protein structure-bases analyses on the KBase platform. Keep watching this newsletter and follow us on social media to stay informed as new data sets and tools come online!
KBase at AGU Fall 2018 Workshop
KBase scientist Chris Henry will be among many researchers presenting at the  Modeling Microbial Dynamic and Processes from Cells to Ecosystems workshop at the American Geophysical Union Fall Meeting 2018, on December 9 from 8 a.m. to 4 p.m.  The workshop focuses on tools for understanding the incorporation of microbial processes in mechanistic models at various levels of complexity using a variety of methods including genome-informed, trait-based, enzyme-based reaction networks, and flux balance analysis. The workshop will start with research presentations from leading pioneers in this field, followed by tutorials and hands-on demonstrations. Bring laptops!
Recent Publications Using KBase
Several new publications have been released that showcase the diversity of applications for KBase in genomics research. Check out how scientists are using KBase to explore data, run analyses, and discover new findings.
KBase SDK Documentation Upgrades
The KBase Software Development Kit (SDK) is a set of tools for developing KBase apps that can be dynamically registered and run on the KBase. Feedback from external developers about the content of previous SDK trainings led us to overhaul the documentation to address common issues and improve it overall. Check out the new SDK documentation on Github: 
Newsletter #9 November 28, 2018

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