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DuctApe specifications

Information


Unique identifier OMICS_25743
Name DuctApe
Software type Toolkit/Suite
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.17.12
Stability Stable
Requirements
biopython, numpy, scipy, matplotlib, scikits.learn, networkx, pyyaml, blast+
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Marco Galardini

Additional information


http://combogenomics.github.io/DuctApe/howto.html

Publication for DuctApe

DuctApe citations

 (9)
library_books

Integrated phenotypic genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

2018
PLoS One
PMCID: 5784923
PMID: 29370210
DOI: 10.1371/journal.pone.0191053

[…] plate consists of an od reading for each well, recorded at 15 min intervals over the 48 h incubation period. the data output for the control and ultrasound treated l. sakei cells were analysed using ductape software []. negative controls (wells containing the inoculated omnilog™ growth medium, but without any substrate for each pm plate was used to normalise differences in inoculums and redox […]

library_books

Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences

2017
PLoS One
PMCID: 5302386
PMID: 28187198
DOI: 10.1371/journal.pone.0171363

[…] different statistical methods were used to analyze the data: the biolog phenotype microarraytm analysis software; the opm and pipeline packages based on r language, as described previously [–]; the ductape suite []; and a two-way anova model using data normalized to positive control scores, as implemented in sas® system's proc genmod procedure. the results of these analyses were in general […]

library_books

Phenotypic Profiling Reveals that Candida albicans Opaque Cells Represent a Metabolically Specialized Cell State Compared to Default White Cells

2016
MBio
PMCID: 5120136
PMID: 27879329
DOI: 10.1128/mBio.01269-16

[…] plates (biolog) coated with different nutrients and chemical substrates. growth of white and opaque cells was monitored at 25°c and 37°c for a period of 24 to 48 h. growth data were analyzed using ductape, which weighs cell fitness by combining multiple growth parameters (length of the lag phase, slope of the growth curve, average height of the curve, maximum cell respiration, and area […]

library_books

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

2016
Nat Commun
PMCID: 4961836
PMID: 27447951
DOI: 10.1038/ncomms12219

[…] type, and the lack of growth in wells with l-histidine or d-glucosamine may simply reflect cobalt chelation., in addition to model refinement, integrating the mutant phenotype data with igd1575, the ductape software, the s. meliloti genome annotation and an abc transporter induction study allowed for the prediction of novel carbon catabolic loci. one example compound is the monosaccharide […]

library_books

Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL

2016
Stand Genomic Sci
PMCID: 4785650
PMID: 26966509
DOI: 10.1186/s40793-016-0145-y

[…] of r. palustris (data not shown). exclusive reactions were then mapped on kegg with respect to other r. palustris strains sequenced so far (bisa53, bisb18, bisb5, cga009, haa2, tie1) by using ductape v 0.17.2 software []. data obtained are reported in table . the proteome size ranged between 4392 and 5242 protein coding genes, corresponding respectively to strains bisb5 and tie1. […]

library_books

Genomic and phenotypic characterization of the species Acinetobacter venetianus

2016
Sci Rep
PMCID: 4763211
PMID: 26902269
DOI: 10.1038/srep21985

[…] general feature, we analysed in more detail their global metabolic landscape. phenotype microarray (pm) data previous experiments were more comprehensively analysed exploiting the recently developed ductape suite. additionally, pm data were de novo generated for one of the a. venetianus strains, i.e. luh 13518, that had been excluded from previous experiments. all pm raw data are available as […]


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DuctApe institution(s)
Department of Biology, University of Florence, Florence, Italy; Interdisciplinary Research Institute USR3078, CNRS-Université Lille Nord de France, Villeneuve d'Ascq, France; Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per lo studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Rome, Italy; Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per l’Agrobiologia e la Pedologia (CRA-ABP), Florence, Italy
DuctApe funding source(s)
Supported by the Italian Ministry of Research (PRIN 2008 research grant contract No. TCKNJL, “Il pangenoma di Sinorhizobium meliloti: L’uso della genomica per il miglioramento agronomico dell’erba medica”) and by the project MARKERINBIO (DM 8348, 5/27/2010).

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