Spring 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 KBase Search Feature Online
The beta version of KBase Search is now online and available for all users! KBase Search allows you to search for reference data, Narratives, and data within shared Narratives. Type what you are looking for into the search box and KBase will search and list all the data and Narratives that match your search terms. Once you have found the data you are looking for, you can make copies to add to your own Narratives for analysis. You can also search for reads and assemblies contained in the Joint Genome Institute (JGI) Genomes Online Database and add them directly to your Narratives from the Search feature. Access KBase Search via your Dashboard. You can help us develop the Search feature by reporting bugs and making feature requests to our Help Board.

Publication Highlight: Using KBase RNA-seq Tools to Analyze Transcriptomics Data of Salmonella Typhi
A new publication used tools in KBase to investigate gene expression changes in human intestinal and bacterial cells to elucidate mechanistic strategies used by Salmonella Typhi to successfully invade the intestinal epithelial cells. Researchers used KBase to run the Tuxedo suite of RNA-seq tools to analyze transcriptomics data obtained from Salmonella Typhi to explore differential expression changes in these bacteria on host cells. They also used KBase to identify patterns of gene expression using clustering Apps. Read more about their research in the following publication:

Nickerson KP, Senger S, Zhang Y, Lima R, Patel S, Ingano L, et al. Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue. EBioMedicine. 2018; doi:10.1016/j.ebiom.2018.04.005

 
Two New JGI Communities Analysis Apps in KBase
KBase and JGI staff continue to collaborate on bringing tools and data online for public use with two new Apps designed to enable analysis of microbial communities! MetaBAT2 is used to group large genomic fragments assembled from shotgun metagenomic sequences into contig "bins" that can be analyzed to decipher the constituencies within microbial communities. The JGI Metagenome Annotation Pipeline App allows users to annotate these bins in metagenome assemblies with both protein family and non-coding RNA content contained within each bin. Both the MetaBAT2 and the Metagenome Annotation Pipeline Apps are available in the App Catalog and can be added to Narratives to use for analyzing your microbial communities sequencing data.
 
New Narrative: Protein family discovery in Arabidopsis
A new addition to our Narrative Library shows how to use KBase to discover and characterize families of proteins in a genome. In plants, members of the Ethylene-Response Factor (ERF) gene family encode transcription factors that are involved in various important developmental and physiological processes. This Narrative uses KBase tools to identify and characterize ERF gene family members in Arabidopsis thaliana.

Have a Narrative that you would like to add to the library? Contact us!

 
KBase and JGI at ASM Microbe and Plant Biology
KBase and JGI staff will be present at biology conferences this summer to provide information and give demonstrations about using our systems. Come visit us June 8-10 in Atlanta at booth #1311 during  ASM Microbe 2018. We will also be at ASPB's Plant Biology 2018 meeting in Montreal from July 14-17 at booth #1200. Visit us to learn more about leveraging JGI and KBase resources in your research. 
 
Profile of KBase Engineer Arfath Pasha
KBase staff member Arfath Pasha, an advanced applications engineer at Brookhaven National Lab (BNL), is part of the team working to improve the infrastructure and search capabilities of the knowledgebase. BNL featured Arfath’s work in a recent article published on their website. Arfath brings his engineering expertise to the project and highlights how KBase facilitates collaboration between those who use the system and help develop it. He and his team’s work aim to make navigating the vast amount of data available to scientists in KBase easier, faster, and more meaningful.
 
Newsletter #7 May 30, 2018
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