Cargando…

StrainDesign: a comprehensive Python package for computational design of metabolic networks

SUMMARY: Various constraint-based optimization approaches have been developed for the computational analysis and design of metabolic networks. Herein, we present StrainDesign, a comprehensive Python package that builds upon the COBRApy toolbox and integrates the most popular metabolic design algorit...

Descripción completa

Detalles Bibliográficos
Autores principales:	Schneider, Philipp, Bekiaris, Pavlos Stephanos, von Kamp, Axel, Klamt, Steffen
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2022
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9620819/ https://www.ncbi.nlm.nih.gov/pubmed/36111857 http://dx.doi.org/10.1093/bioinformatics/btac632

Ejemplares similares

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks
por: Thiele, Sven, et al.
Publicado: (2021)

Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals
por: Bekiaris, Pavlos Stephanos, et al.
Publicado: (2021)

GIL: a python package for designing custom indexing primers
por: Mateyko, Nicholas, et al.
Publicado: (2023)

GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
por: Fang, Zhuoqing, et al.
Publicado: (2022)

Automatic construction of metabolic models with enzyme constraints
por: Bekiaris, Pavlos Stephanos, et al.
Publicado: (2020)

Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions
por: Bekiaris, Pavlos Stephanos, et al.
Publicado: (2023)

graphkernels: R and Python packages for graph comparison
por: Sugiyama, Mahito, et al.
Publicado: (2018)

pyrpipe: a Python package for RNA-Seq workflows
por: Singh, Urminder, et al.
Publicado: (2021)

localpdb—a Python package to manage protein structures and their annotations
por: Ludwiczak, Jan, et al.
Publicado: (2022)

Knot_pull—python package for biopolymer smoothing and knot detection
por: Jarmolinska, Aleksandra I, et al.
Publicado: (2019)

dipwmsearch: a Python package for searching di-PWM motifs
por: Mille, Marie, et al.
Publicado: (2023)

MEWpy: a computational strain optimization workbench in Python
por: Pereira, Vítor, et al.
Publicado: (2021)

PyPanda: a Python package for gene regulatory network reconstruction
por: van IJzendoorn, David G.P., et al.
Publicado: (2016)

MEANS: python package for Moment Expansion Approximation, iNference and Simulation
por: Fan, Sisi, et al.
Publicado: (2016)

COSIFER: a Python package for the consensus inference of molecular interaction networks
por: Manica, Matteo, et al.
Publicado: (2020)

SBMLDiagrams: a python package to process and visualize SBML layout and render
por: Xu, Jin, et al.
Publicado: (2022)

PyOncoPrint: a python package for plotting OncoPrints
por: Park, Jeongbin, et al.
Publicado: (2023)

tableone: An open source Python package for producing summary statistics for research papers
por: Pollard, Tom J, et al.
Publicado: (2018)

MolClustPy: a Python package to characterize multivalent biomolecular clusters
por: Chattaraj, Aniruddha, et al.
Publicado: (2023)

BioServices: a common Python package to access biological Web Services programmatically
por: Cokelaer, Thomas, et al.
Publicado: (2013)

ProtPOS: a python package for the prediction of protein preferred orientation on a surface
por: Ngai, Jimmy C. F., et al.
Publicado: (2016)

multiTFA: a Python package for multi-variate thermodynamics-based flux analysis
por: Mahamkali, Vishnuvardhan, et al.
Publicado: (2021)

MSPypeline: a python package for streamlined data analysis of mass spectrometry-based proteomics
por: Heming, Simon, et al.
Publicado: (2022)

The DynaSig-ML Python package: automated learning of biomolecular dynamics–function relationships
por: Mailhot, Olivier, et al.
Publicado: (2023)

PyWGCNA: a Python package for weighted gene co-expression network analysis
por: Rezaie, Narges, et al.
Publicado: (2023)

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
por: Hart, Reece K., et al.
Publicado: (2015)

WSIC: a Python package and command-line interface for fast whole slide image conversion
por: Pocock, Johnathan, et al.
Publicado: (2023)

PyDESeq2: a python package for bulk RNA-seq differential expression analysis
por: Muzellec, Boris, et al.
Publicado: (2023)

Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping
por: Ren, Xiaoliang, et al.
Publicado: (2023)

pyBedGraph: a python package for fast operations on 1D genomic signal tracks
por: Zhang, Henry B, et al.
Publicado: (2020)

AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge
por: Voytik, Eugenia, et al.
Publicado: (2021)

AlphaPulldown—a python package for protein–protein interaction screens using AlphaFold-Multimer
por: Yu, Dingquan, et al.
Publicado: (2022)

GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions
por: Abraham, Abin, et al.
Publicado: (2023)

PyGenePlexus: a Python package for gene discovery using network-based machine learning
por: Mancuso, Christopher A, et al.
Publicado: (2023)

Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
por: Wang, Linhua, et al.
Publicado: (2023)

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
por: Salvy, Pierre, et al.
Publicado: (2019)

scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data
por: Faure, Louis, et al.
Publicado: (2022)

vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA
por: Vogt, Frank, et al.
Publicado: (2021)

FRED 2: an immunoinformatics framework for Python
por: Schubert, Benjamin, et al.
Publicado: (2016)

AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics
por: Krismer, Elena, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_bejagduis7r6g6vlilbpjaq70j