Cargando…

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

BACKGROUND: Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optimal experimental design are p...

Descripción completa

Detalles Bibliográficos
Autores principales:	Villaverde, Alejandro F, Henriques, David, Smallbone, Kieran, Bongard, Sophia, Schmid, Joachim, Cicin-Sain, Damjan, Crombach, Anton, Saez-Rodriguez, Julio, Mauch, Klaus, Balsa-Canto, Eva, Mendes, Pedro, Jaeger, Johannes, Banga, Julio R
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2015
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342829/ https://www.ncbi.nlm.nih.gov/pubmed/25880925 http://dx.doi.org/10.1186/s12918-015-0144-4

Ejemplares similares

Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster
por: Becker, Kolja, et al.
Publicado: (2013)

Medium-Throughput Processing of Whole Mount In Situ Hybridisation Experiments into Gene Expression Domains
por: Crombach, Anton, et al.
Publicado: (2012)

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network
por: Crombach, Anton, et al.
Publicado: (2012)

High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita
por: Wotton, Karl R, et al.
Publicado: (2015)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
por: Egea, Jose A, et al.
Publicado: (2014)

AMIGO, a toolbox for advanced model identification in systems biology using global optimization
por: Balsa-Canto, Eva, et al.
Publicado: (2011)

Lack of tailless leads to an increase in expression variability in Drosophila embryos()
por: Janssens, Hilde, et al.
Publicado: (2013)

SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos
por: Cicin-Sain, Damjan, et al.
Publicado: (2014)

Benchmarking optimization methods for parameter estimation in large kinetic models
por: Villaverde, Alejandro F, et al.
Publicado: (2019)

GenSSI: a software toolbox for structural identifiability analysis of biological models
por: Chiş, Oana, et al.
Publicado: (2011)

DOTcvpSB, a software toolbox for dynamic optimization in systems biology
por: Hirmajer, Tomáš, et al.
Publicado: (2009)

Benchmark suite #1
por: Programmable electronics performance. Los Gatos
Publicado: (1993)

An iterative identification procedure for dynamic modeling of biochemical networks
por: Balsa-Canto, Eva, et al.
Publicado: (2010)

Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods
por: Chis, Oana-Teodora, et al.
Publicado: (2011)

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology
por: Balsa-Canto, Eva, et al.
Publicado: (2016)

HEP Analysis workloads for the benchmarking suite
por: Kankowska, Dominika
Publicado: (2020)

Hybrid optimization method with general switching strategy for parameter estimation
por: Balsa-Canto, Eva, et al.
Publicado: (2008)

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
por: Henriques, David, et al.
Publicado: (2017)

Global dynamic optimization approach to predict activation in metabolic pathways
por: de Hijas-Liste, Gundián M, et al.
Publicado: (2014)

A quantitative atlas of Even-skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos
por: Janssens, Hilde, et al.
Publicado: (2014)

ESBM: An Entity Summarization BenchMark
por: Liu, Qingxia, et al.
Publicado: (2020)

DynOmics: dynamics of structural proteome and beyond
por: Li, Hongchun, et al.
Publicado: (2017)

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models
por: Ligon, Thomas S, et al.
Publicado: (2018)

Suite mexicana
por: Oliva, Julio César
Publicado: (2005)

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques
por: Vilas, Carlos, et al.
Publicado: (2012)

Unraveling membrane properties at the organelle-level with LipidDyn
por: Scrima, Simone, et al.
Publicado: (2022)

Reverse engineering and identification in systems biology: strategies, perspectives and challenges
por: Villaverde, Alejandro F., et al.
Publicado: (2014)

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation
por: Villaverde, Alejandro F., et al.
Publicado: (2017)

Suite Montebello : una flor en la laguna
por: Oliva, Julio César
Publicado: (1991)

TreeDyn: towards dynamic graphics and annotations for analyses of trees
por: Chevenet, François, et al.
Publicado: (2006)

6DYN : 6TiSCH with Heterogeneous Slot Durations
por: Rady, Mina, et al.
Publicado: (2021)

Reverse Engineering Cellular Networks with Information Theoretic Methods
por: Villaverde, Alejandro F., et al.
Publicado: (2013)

Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models
por: Villaverde, Alejandro F., et al.
Publicado: (2019)

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems
por: Gábor, Attila, et al.
Publicado: (2017)

Structural identifiability and observability of compartmental models of the COVID-19 pandemic()
por: Massonis, Gemma, et al.
Publicado: (2021)

Improving dynamic predictions with ensembles of observable models
por: Massonis, Gemma, et al.
Publicado: (2022)

Distilling identifiable and interpretable dynamic models from biological data
por: Massonis, Gemma, et al.
Publicado: (2023)

Melatonin activates FIS1, DYN1, and DYN2 Plasmodium falciparum related‐genes for mitochondria fission: Mitoemerald‐GFP as a tool to visualize mitochondria structure
por: Scarpelli, Pedro H., et al.
Publicado: (2018)

CavBench: A benchmark for protein cavity detection methods
por: Dias, Sérgio, et al.
Publicado: (2019)

From laboratory bench to benchmark: technology transfer in laboratory medicine
por: Cariati, Federica, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_9i4eq538hoib3b72mrl5meu8g6