Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
出版年份 2022 全文链接
标题
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
作者
关键词
-
出版物
BRIEFINGS IN BIOINFORMATICS
Volume 23, Issue 4, Pages -
出版商
Oxford University Press (OUP)
发表日期
2022-06-08
DOI
10.1093/bib/bbac212
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- BioSimulators: a central registry of simulation engines and services for recommending specific tools
- (2022) Bilal Shaikh et al. NUCLEIC ACIDS RESEARCH
- Reproducibility in systems biology modelling
- (2021) Krishna Tiwari et al. Molecular Systems Biology
- SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
- (2021) Andreas Dräger et al. BIOINFORMATICS
- libOmexMeta: enabling semantic annotation of models to support FAIR principles
- (2021) Ciaran Welsh et al. BIOINFORMATICS
- The SPARC DRC: Building a Resource for the Autonomic Nervous System Community
- (2021) Mahyar Osanlouy et al. Frontiers in Physiology
- COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
- (2021) Marek Ostaszewski et al. Molecular Systems Biology
- The reactome pathway knowledgebase 2022
- (2021) Marc Gillespie et al. NUCLEIC ACIDS RESEARCH
- WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
- (2021) Vincent Noël et al. Frontiers in Molecular Biosciences
- Automated inference of Boolean models from molecular interaction maps using CaSQ
- (2020) Sara Sadat Aghamiri et al. BIOINFORMATICS
- Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors
- (2020) Gianluca Selvaggio et al. CANCER RESEARCH
- COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
- (2020) Marek Ostaszewski et al. Scientific Data
- From Raw Data to FAIR Data: The FAIRification Workflow for Health Research
- (2020) A. Anil Sinaci et al. METHODS OF INFORMATION IN MEDICINE
- Identifiers.org - Compact Identifier Services in the Cloud
- (2020) Manuel Bernal Llinares et al. BIOINFORMATICS
- Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective
- (2020) Ahmet Erdemir et al. Journal of Translational Medicine
- SBML Level 3: an extensible format for the exchange and reuse of biological models
- (2020) Sarah M Keating et al. Molecular Systems Biology
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
- (2020) Vasundra Touré et al. BRIEFINGS IN BIOINFORMATICS
- Model annotation and discovery with the Physiome Model Repository
- (2019) Dewan M. Sarwar et al. BMC BIOINFORMATICS
- Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health
- (2018) Petr Holub et al. BIOPRESERVATION AND BIOBANKING
- Community-driven roadmap for integrated disease maps
- (2018) Marek Ostaszewski et al. BRIEFINGS IN BIOINFORMATICS
- Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health
- (2018) Petr Holub et al. Biopreservation and Biobanking
- Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
- (2018) Méziane Aite et al. PLoS Computational Biology
- PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
- (2018) Ahmadreza Ghaffarizadeh et al. PLoS Computational Biology
- The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
- (2018) Aurélien Naldi et al. Frontiers in Physiology
- SemGen: a tool for semantics-based annotation and composition of biosimulation models
- (2018) Maxwell L Neal et al. BIOINFORMATICS
- FAIRDOMHub: a repository and collaboration environment for sharing systems biology research
- (2016) Katherine Wolstencroft et al. NUCLEIC ACIDS RESEARCH
- The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable
- (2016) David Nickerson et al. Interface Focus
- The FAIR Guiding Principles for scientific data management and stewardship
- (2016) Mark D. Wilkinson et al. Scientific Data
- Cooperative development of logical modelling standards and tools with CoLoMoTo
- (2015) A. Naldi et al. BIOINFORMATICS
- FactoMineR: AnRPackage for Multivariate Analysis
- (2015) Sébastien Lê et al. Journal of Statistical Software
- The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
- (2014) James P. Sluka et al. BIOINFORMATICS
- COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
- (2014) Frank T Bergmann et al. BMC BIOINFORMATICS
- Multistate Model Builder (MSMB): a flexible editor for compact biochemical models
- (2014) Alida Palmisano et al. BMC Systems Biology
- Conversion of KEGG metabolic pathways to SBGN maps including automatic layout
- (2013) Tobias Czauderna et al. BMC BIOINFORMATICS
- SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
- (2013) Claudine Chaouiya et al. BMC Systems Biology
- Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks
- (2013) Regina Samaga et al. Cell Communication and Signaling
- Chaste: An Open Source C++ Library for Computational Physiology and Biology
- (2013) Gary R. Mirams et al. PLoS Computational Biology
- The Cell Collective: Toward an open and collaborative approach to systems biology
- (2012) Tomáš Helikar et al. BMC Systems Biology
- Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
- (2011) Dagmar Waltemath et al. BMC Systems Biology
- Modeling formalisms in Systems Biology
- (2011) Daniel Machado et al. AMB Express
- Editing, validating and translating of SBGN maps
- (2010) T. Czauderna et al. BIOINFORMATICS
- A cell-based simulation software for multi-cellular systems
- (2010) Stefan Hoehme et al. BIOINFORMATICS
- BoolNet—an R package for generation, reconstruction and analysis of Boolean networks
- (2010) Christoph Müssel et al. BIOINFORMATICS
- A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
- (2010) N Tenazinha et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- A generic algorithm for layout of biological networks
- (2009) Falk Schreiber et al. BMC BIOINFORMATICS
- A Comparison of User-Generated and Automatic Graph Layouts
- (2009) T. Dwyer et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- The Systems Biology Graphical Notation
- (2009) Nicolas Le Novère et al. NATURE BIOTECHNOLOGY
- Synchronous versus asynchronous modeling of gene regulatory networks
- (2008) A. Garg et al. BIOINFORMATICS
- Using Physiome standards to couple cellular functions for rat cardiac excitation-contraction
- (2008) Jonna R. Terkildsen et al. EXPERIMENTAL PHYSIOLOGY
- Exploration of Networks using overview+detail with Constraint-based cooperative layout
- (2008) T. Dwyer et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
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