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Title: Metabolites Annotations and Genes Integrated (MAGI) v1.0

Abstract

With the benefit of hindsight, it is easy to see that the readout of the human genome, spectacular milestone that it was, represents only the beginning of the "omics" information explosion. The technical side of the 'omics explosion--enabling researchers to efficiently readout terabytes of information spelling out whole genomes, transcriptomes, proteomes and metabolomes, does not per se provide a clear picture of how life works. Nor does it show us how we can engineer biology to solve the grand challenges of the 21st century: feeding 10 billion people with declining per capita supplies of arable land and clean water, sustaining biological diversity and slowing the increase in greenhouse gas formation, primarily carbon dioxide and methane. The 2017-063 invention--Metabolites and Genes Integration Technology--proposes an integrated approach to correcting and connecting the dots of the 'omics explosion: linking genes to proteins, proteins to pathways, pathways to biochemical reactions and metabolites. The '063 invention is potentially transformational in that it can generate testable hypotheses across thousands of genes to predict their chemical and metabolic products. It can also do the reverse; i.e., starting from chemical and metabolic products it can generate testable hypotheses about which genes and pathways those molecules are linked to.more » Since we know that genomic, transcriptomic, proteomic and metabolomic databases are chock full or erroneous information, MAGI also has the unique benefit of correcting these errors through its own independent pathway of bidirectional hypothesis generation (genes=>proteins=>metabolites + metabolites=>proteins=>genes). Perfectly amenable to high-throughput hypothesis generation and experimentation, MAGI can transform our understanding of human, animal, plant and microbial biology over several decades, laying the essential knowledge foundation to addressing the grand scientific challenges of the 21st century.« less

Developers:
 [1];  [1];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Release Date:
Project Type:
Open Source, Publicly Available Repository
Software Type:
Scientific
Licenses:
BSD 3-clause "New" or "Revised" License
Sponsoring Org.:
USDOE

Primary Award/Contract Number:
AC02-05CH11231
Code ID:
23353
Site Accession Number:
2017-105
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Country of Origin:
United States

Citation Formats

Bowen, Benjamin, Erbilgin, Onur, Ruebel, Oliver, and USDOE. Metabolites Annotations and Genes Integrated (MAGI) v1.0. Computer software. https://www.osti.gov//servlets/purl/1494987. USDOE. 14 Aug. 2017. Web. doi:10.11578/dc.20190215.2.
Bowen, Benjamin, Erbilgin, Onur, Ruebel, Oliver, & USDOE. (2017, August 14). Metabolites Annotations and Genes Integrated (MAGI) v1.0 [Computer software]. https://www.osti.gov//servlets/purl/1494987. doi:10.11578/dc.20190215.2.
Bowen, Benjamin, Erbilgin, Onur, Ruebel, Oliver, and USDOE. Metabolites Annotations and Genes Integrated (MAGI) v1.0. Computer software. August 14, 2017. https://www.osti.gov//servlets/purl/1494987. doi:10.11578/dc.20190215.2.
@misc{osti_1494987,
title = {Metabolites Annotations and Genes Integrated (MAGI) v1.0},
author = {Bowen, Benjamin and Erbilgin, Onur and Ruebel, Oliver and USDOE},
abstractNote = {With the benefit of hindsight, it is easy to see that the readout of the human genome, spectacular milestone that it was, represents only the beginning of the "omics" information explosion. The technical side of the 'omics explosion--enabling researchers to efficiently readout terabytes of information spelling out whole genomes, transcriptomes, proteomes and metabolomes, does not per se provide a clear picture of how life works. Nor does it show us how we can engineer biology to solve the grand challenges of the 21st century: feeding 10 billion people with declining per capita supplies of arable land and clean water, sustaining biological diversity and slowing the increase in greenhouse gas formation, primarily carbon dioxide and methane. The 2017-063 invention--Metabolites and Genes Integration Technology--proposes an integrated approach to correcting and connecting the dots of the 'omics explosion: linking genes to proteins, proteins to pathways, pathways to biochemical reactions and metabolites. The '063 invention is potentially transformational in that it can generate testable hypotheses across thousands of genes to predict their chemical and metabolic products. It can also do the reverse; i.e., starting from chemical and metabolic products it can generate testable hypotheses about which genes and pathways those molecules are linked to. Since we know that genomic, transcriptomic, proteomic and metabolomic databases are chock full or erroneous information, MAGI also has the unique benefit of correcting these errors through its own independent pathway of bidirectional hypothesis generation (genes=>proteins=>metabolites + metabolites=>proteins=>genes). Perfectly amenable to high-throughput hypothesis generation and experimentation, MAGI can transform our understanding of human, animal, plant and microbial biology over several decades, laying the essential knowledge foundation to addressing the grand scientific challenges of the 21st century.},
url = {https://www.osti.gov//servlets/purl/1494987},
doi = {10.11578/dc.20190215.2},
year = {2017},
month = {8},
note =
}

Software:
Publicly Accessible Repository
https://github.com/biorack/magi

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