APPLICATIONS: Genomics research BACKGROUND: Metabolomics has been used for obtaining direct measures of metabolic activities from diverse biological systems. However, metabolomics can be limited by ambiguous metabolite identifications. Furthermore, interpretation can be limited by incomplete and inaccurate genome-based predictions of enzyme activities (e.g., gene … [Read more...] about Metabolite, Annotation and Gene Integration System (MAGI) and Software 2017-063, 2017-105
Synthetic Biology Tools and Software
Synthetic Promoters Useful for Expression in Plant Cells 2015-049
APPLICATIONS OF TECHNOLOGY: Bioenergy feedstock plants ABSTRACT: Researchers at Berkeley Lab's Joint BioEnergy Institute (JBEI) have invented a genetically modified plant cell or plant, comprising: (a) (i) one or more nucleic acids each encoding one or more transcription factors (or transcription activators) operatively linked to a first tissue-specific or … [Read more...] about Synthetic Promoters Useful for Expression in Plant Cells 2015-049
Spectroscopic Imaging and Analysis of Live Cells 2015-077
ABSTRACT: Researchers at Berkeley Lab led by Hoi-Ying Holman have developed technologies for measurement, visualization, and analysis of chemical dynamics in living cells or tissues for diagnostic pathology. Devices can be open- or closed-channel microfluidic membrane devices for long-term IR spectroscopy of live adherent cells and ultimately for rapidly identifying … [Read more...] about Spectroscopic Imaging and Analysis of Live Cells 2015-077
Arrowland: An Online Multiscale Interactive Tool for -omics Data Visualization 2016-102
APPLICATIONS OF TECHNOLOGY Data visualization for metabolic modeling ADVANTAGES: Convenient data input Flux data visualization Simultaneous visualization of -omics data Embedding in Jupyter notebooks ABSTRACT: Arrowland is a web-based software application primarily for mapping, integrating, and visualizing a variety of metabolism data of living … [Read more...] about Arrowland: An Online Multiscale Interactive Tool for -omics Data Visualization 2016-102
Predicting Metabolic Pathway Dynamics from Time Series Multiomics Data Using Machine Learning Techniques 2017-049
APPLICATIONS OF TECHNOLOGY: Genetic engineering ADVANTAGES: Outperforms kinetic models to predict pathway dynamics in bioengineered systems ABSTRACT: Hector Garcia Martin and Zac Costello of Berkeley Lab’s Joint BioEnergy Institute (JBEI) have determined that the combination of machine learning and abundant multiomics data (proteomics and metabolomics) can be … [Read more...] about Predicting Metabolic Pathway Dynamics from Time Series Multiomics Data Using Machine Learning Techniques 2017-049