Literature DB >> 16986321

ScrumPy: metabolic modelling with Python.

M G Poolman1.   

Abstract

ScrumPy is a software package used for the definition and analysis of metabolic models. It is written using the Python programming language that is also used as a user interface. ScrumPy has features for both kinetic and structural modelling, but the emphasis is on structural modelling and those features of most relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy's functionality to readers with some knowledge of metabolic modelling, but implementation, programming and other computational details are omitted. ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ ScrumPy.

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Year:  2006        PMID： 16986321     DOI： 10.1049/ip-syb:20060010

Source DB:  PubMed          Journal:  Syst Biol (Stevenage)        ISSN： 1741-2471


  30 in total

1.  Simulating plant metabolic pathways with enzyme-kinetic models.

Authors:  Kai Schallau; Björn H Junker
Journal:  Plant Physiol       Date:  2010-01-29       Impact factor: 8.340

2.  Antimony: a modular model definition language.

Authors:  Lucian P Smith; Frank T Bergmann; Deepak Chandran; Herbert M Sauro
Journal:  Bioinformatics       Date:  2009-07-03       Impact factor: 6.937

Review 3.  Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

Authors:  Kambiz Baghalian; Mohammad-Reza Hajirezaei; Falk Schreiber
Journal:  Plant Cell       Date:  2014-10-24       Impact factor: 11.277

4.  Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism.

Authors:  A Pentjuss; E Stalidzans; J Liepins; A Kokina; J Martynova; P Zikmanis; I Mozga; R Scherbaka; H Hartman; M G Poolman; D A Fell; A Vigants
Journal:  J Ind Microbiol Biotechnol       Date:  2017-04-25       Impact factor: 3.346

5.  Phenotypic characterization of Corynebacterium glutamicum using elementary modes towards synthesis of amino acids.

Authors:  Devesh Radhakrishnan; Meghna Rajvanshi; K V Venkatesh
Journal:  Syst Synth Biol       Date:  2011-02-22

6.  Phenotypic characterization of Corynebacterium glutamicum under osmotic stress conditions using elementary mode analysis.

Authors:  Meghna Rajvanshi; K V Venkatesh
Journal:  J Ind Microbiol Biotechnol       Date:  2010-12-05       Impact factor: 3.346

7.  Contribution of NADH increases to ethanol's inhibition of retinol oxidation by human ADH isoforms.

Authors:  Jennifer R Chase; Mark G Poolman; David A Fell
Journal:  Alcohol Clin Exp Res       Date:  2009-01-16       Impact factor: 3.455

8.  A genome-scale metabolic model of Arabidopsis and some of its properties.

Authors:  Mark G Poolman; Laurent Miguet; Lee J Sweetlove; David A Fell
Journal:  Plant Physiol       Date:  2009-09-15       Impact factor: 8.340

9.  A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf.

Authors:  C Y Maurice Cheung; R George Ratcliffe; Lee J Sweetlove
Journal:  Plant Physiol       Date:  2015-08-11       Impact factor: 8.340

Review 10.  Genome-scale models of bacterial metabolism: reconstruction and applications.

Authors:  Maxime Durot; Pierre-Yves Bourguignon; Vincent Schachter
Journal:  FEMS Microbiol Rev       Date:  2008-12-03       Impact factor: 16.408
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