pathwaytools.blogspot.com

Pathway Tools Blog

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, April 24, 2015. A New Curated BioCyc Database for Clostridium difficile. Commonly nicknamed “Cdiff”) is a spore-forming bacterium that causes serious healthcare-associated infections. In the United States alone, it is estimated that Cdiff infections were responsible for more than 29,000 deaths in 2011. Antibiotic resistance and recurrent infections are common problems in treating Cdiff infections. One o...

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News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, April 24, 2015. A New Curated BioCyc Database for Clostridium difficile. Commonly nicknamed “Cdiff”) is a spore-forming bacterium that causes serious healthcare-associated infections. In the United States alone, it is estimated that Cdiff infections were responsible for more than 29,000 deaths in 2011. Antibiotic resistance and recurrent infections are common problems in treating Cdiff infections. One o...

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Pathway Tools Blog | pathwaytools.blogspot.com Reviews

https://pathwaytools.blogspot.com

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, April 24, 2015. A New Curated BioCyc Database for Clostridium difficile. Commonly nicknamed “Cdiff”) is a spore-forming bacterium that causes serious healthcare-associated infections. In the United States alone, it is estimated that Cdiff infections were responsible for more than 29,000 deaths in 2011. Antibiotic resistance and recurrent infections are common problems in treating Cdiff infections. One o...

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pathwaytools.blogspot.com

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Pathway Tools Blog: March 2015

http://www.pathwaytools.blogspot.com/2015_03_01_archive.html

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, March 6, 2015. Procedure for Creating Metabolic Models from Sequenced Genomes. In the past, construction of quantitative metabolic flux models has been an extremely time-consuming process, requiring 12-18 months to create a bacterial model. . We can now create metabolic models using MetaFlux in approximately 1 month. Links to this post. Subscribe to: Posts (Atom). Overview of the Pathway Tools Software.

2

Pathway Tools Blog: December 2014

http://www.pathwaytools.blogspot.com/2014_12_01_archive.html

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, December 5, 2014. Propagating Updates from MetaCyc - Nearly Effortless Improvements to your PGDB! New compounds, reactions, enzymes and pathways. Addition of compound structures to existing compounds that previously lacked them. Fixes to errors and other improvements to existing compound structures. Updates to reaction equations to fix errors and so that they balance and are correctly protonated. It wil...

3

Pathway Tools Blog: November 2012

http://www.pathwaytools.blogspot.com/2012_11_01_archive.html

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, November 30, 2012. Atom Mappings for Reactions. The atom mappings were computed using the technique described in Latendresse et al., "Accurate atom-mapping computation for biochemical reactions", J. Chem. Inf. Model., September 2012. Users of Pathway Tools can fix this problem in the following way for a given PGDB. Select the menu command Tools- Propagate MetaCyc Data Updates. Links to this post. Pathwa...

4

Pathway Tools Blog: Querying Databases by Organism Properties

http://www.pathwaytools.blogspot.com/2015/04/querying-databases-by-organism.html

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Wednesday, April 15, 2015. Querying Databases by Organism Properties. A standard for encoding this kind of "metadata" about an organism sample was proposed by the Genomic Standards Consortium. GSC) in a 2008 paper. In Nature Biotechnology. The resulting MIGS. The Genomes OnLine Database) and NCBI BioSample. 1616): The geographical origin of the sample, defined by country or sea name, and/or specific region name.

5

Pathway Tools Blog: A Sequence Data File for Associating Enzymes with MetaCyc Reactions

http://www.pathwaytools.blogspot.com/2013/04/a-sequence-data-file-for-associating.html

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Tuesday, April 30, 2013. A Sequence Data File for Associating Enzymes with MetaCyc Reactions. Metabolic reconstruction typically proceeds in two steps: (1) analyze the proteome of a sequenced organism to infer the set of reactions catalyzed by the organism (the organism's reactome), and (2) infer the metabolic pathways present in the organism from the reactome. The file contains a Lisp list of the form:. Pathwa...

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Pathway Tools Blog

News, tips and tricks from the developers of the Pathway Tools bioinformatics software system. Friday, April 24, 2015. A New Curated BioCyc Database for Clostridium difficile. Commonly nicknamed “Cdiff”) is a spore-forming bacterium that causes serious healthcare-associated infections. In the United States alone, it is estimated that Cdiff infections were responsible for more than 29,000 deaths in 2011. Antibiotic resistance and recurrent infections are common problems in treating Cdiff infections. One o...

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