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KBase Narrative - SOMATA - Motivating Example

Dataset ·
 [1];  [2];  [3];  [2]
  1. Oak Ridge National Laboratory ORNL; Oak Ridge National Laboratory
  2. Iowa State University
  3. Oak Ridge National Laboratory ORNL
+ Show Author Affiliations
A systems view in the biological context is a useful approach to study complex and potentially interacting systems. In this narrative (accompanying an associated manuscript), we take a systems view of software tools themselves. Instead of using software as a single tool, we demonstrate how users can approach software with the same mindset as the organisms they study; as a complex system that can be optimized based on one’s environment and goals. We demonstrate this idea with an example KBase narrative showing how application parameters in KBase tools can change how a researcher perceives and interacts with bioinformatics tools while conducting a common experimental scenario. In this scenario we are trying to understand how different chemical compounds in a growth media change the metabolic pathways utilized in Escherichia coli.
Research Organization:
U.S. Department of Energy Systems Biology Knowledgebase
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
DOE Contract Number:
AC05-00OR22725; AC05-00OR22725
OSTI ID:
1960315
Country of Publication:
United States
Language:
English

References (19)

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
Identifying bacterial genes and endosymbiont DNA with Glimmer journal January 2007
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations journal January 2009
What is flux balance analysis? journal March 2010
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013
Efficiently gap-filling reaction networks journal June 2014
Identification, variation and transcription of pneumococcal repeat sequences journal February 2011
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies journal May 2012
BLAT---The BLAST-Like Alignment Tool journal March 2002
Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism journal February 2006
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal February 2015
High-throughput generation, optimization and analysis of genome-scale metabolic models journal August 2010
Dissecting Complexity: The Hidden Impact of Application Parameters on Bioinformatics Research posted_content March 2013
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM journal July 2013
Translational recoding in archaea journal September 2012
FIGfams: yet another set of protein families journal September 2009
Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks journal August 2008

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