FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

Other names: SBML

The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations.

Webpage:

http://sbml.org

Publications:

Publications
More detailed information about this field from each metasource.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
PMID: 12611808
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models PubMed citations: 985.

985 articles citing: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. PMID:35729113
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Discrete modeling for integration and analysis of large-scale signaling networks. PMID:35696426
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. PMID:35694833
EDEN: A High-Performance, General-Purpose, NeuroML-Based Neural Simulator. PMID:35669596
A semantics, energy-based approach to automate biomodel composition. PMID:35657966
Combining Pharmacokinetics and Vibrational Spectroscopy: MCR-ALS Hard-and-Soft Modelling of Drug Uptake In Vitro Using Tailored Kinetic Constraints. PMID:35563861
Network Reconstruction and Modelling Made Reproducible with moped. PMID:35448462
BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts. PMID:35442944
From Qualitative to Quantitative AOP: A Case Study of Neurodegeneration. PMID:35434701
Hybrid modelling of biological systems: current progress and future prospects. PMID:35352101
Computational Models on Pathological Redox Signalling Driven by Pregnancy: A Review. PMID:35326235
Multiscale modeling in disease. PMID:35310906
NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories. PMID:35283794
Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. PMID:35243212
Computational models in systems biology: standards, dissemination, and best practices. PMID:35217296
From Petri Plates to Petri Nets, a revolution in yeast biology. PMID:35142857
Agent-based models for detecting the driving forces of biomolecular interactions. PMID:35115584
Mini-batch optimization enables training of ODE models on large-scale datasets. PMID:35013141
Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity. PMID:34968385
Evaluation framework for systems models. PMID:34921743
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations. PMID:34907432
MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. PMID:34877484
Computational Studies of the Intestinal Host-Microbiota Interactome. PMID:34765258
Curating COBRA Models of Microbial Metabolism. PMID:34719001
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
Recent applications of quantitative systems pharmacology and machine learning models across diseases. PMID:34671863
A protocol for dynamic model calibration. PMID:34619769
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. PMID:34600580
Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells. PMID:34599254
Mechanism of actin filament nucleation. PMID:34509503
QSPcc reduces bottlenecks in computational model simulations. PMID:34471226
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways. PMID:34436117
A Spatial Quantitative Systems Pharmacology Platform spQSP-IO for Simulations of Tumor-Immune Interactions and Effects of Checkpoint Inhibitor Immunotherapy. PMID:34359653
Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling. PMID:34354723
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19. PMID:34340125
PolyRound: Polytope rounding for random sampling in metabolic networks. PMID:34329395
Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node. PMID:34280231
Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure. PMID:34230992
The LASER database: Formalizing design rules for metabolic engineering. PMID:34150506
Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. PMID:34129600
An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PMID:34061819
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Hierarchical semantic composition of biosimulation models using bond graphs. PMID:33983945
Ten steps to investigate a cellular system with mathematical modeling. PMID:33983922
A modular computational framework for medical digital twins. PMID:33972437
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling. PMID:33937210
AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models. PMID:33821950
Temporal constrained objects for modelling neuronal dynamics. PMID:33816812
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modeling. PMID:33556763
Benchmarking of numerical integration methods for ODE models of biological systems. PMID:33514831
Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks. PMID:33511367
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. PMID:33507922
PEtab-Interoperable specification of parameter estimation problems in systems biology. PMID:33497393
Towards reproducible computational drug discovery. PMID:33430992
Impact of explicit area scaling on kinetic models involving multiple compartments. PMID:33430767
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. PMID:33372654
Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. PMID:33302373
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. PMID:33247931
Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids. PMID:33240469
Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. PMID:33237849
Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model. PMID:33207684
An Understandable, Extensible, and Reusable Implementation of the Hodgkin-Huxley Equations Using Modelica. PMID:33117198
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. PMID:33097709
A Computational Model of Mitochondria Motility in Axons. PMID:33018464
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. PMID:33015004
Principles of synthetic biology: a MOOC for an emerging field. PMID:32995535
ACRE: Absolute concentration robustness exploration in module-based combinatorial networks. PMID:32995502
Synthetic Biology: fostering the cyber-biological revolution. PMID:32995500
A compiler for biological networks on silicon chips. PMID:32966274
Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. PMID:32954378
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
The Atlas of Inflammation Resolution (AIR). PMID:32893032
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Clustering analysis of tumor metabolic networks. PMID:32838750
Publishing reproducible dynamic kinetic models. PMID:32793969
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation. PMID:32747737
Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis. PMID:32722118
Parameter Estimation and Uncertainty Quantification for Systems Biology Models. PMID:32719822
Editorial Reproducibility of Computational Models. PMID:32636531
Effects of repetitive Iodine thyroid blocking on the foetal brain and thyroid in rats: a systems biology approach. PMID:32616734
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
BioModels Parameters: a treasure trove of parameter values from published systems biology models. PMID:32573648
Iterative community-driven development of a SARS-CoV-2 tissue simulator. PMID:32511322
Automated inference of Boolean models from molecular interaction maps using CaSQ. PMID:32403123
Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants. PMID:32376972
Dealing with bio- and ecological complexity: Challenges and opportunities. PMID:32362769
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. PMID:32348298
libsbmljs-Enabling web-based SBML tools. PMID:32339626
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization. PMID:32155140
Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt. PMID:32126976
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies. PMID:32049957
Bayesian inference using qualitative observations of underlying continuous variables. PMID:32049328
Organizing genome engineering for the gigabase scale. PMID:32019919
TopoFilter: a MATLAB package for mechanistic model identification in systems biology. PMID:31996136
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
Pathogenic Processes Underlying Alzheimer's Disease: Modeling the Effects of Amyloid Beta on Synaptic Transmission. PMID:31946282
Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows. PMID:31941545
Automatic construction of metabolic models with enzyme constraints. PMID:31937255
Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning. PMID:31926940
Integrative analysis of time course metabolic data and biomarker discovery. PMID:31918658
Interactive Multiresolution Visualization of Cellular Network Processes. PMID:31884165
XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images. PMID:31749833
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. PMID:31722383
BioModels-15 years of sharing computational models in life science. PMID:31701150
Key challenges facing data-driven multicellular systems biology. PMID:31648301
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track. PMID:31603193
Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems. PMID:31602619
PathBank: a comprehensive pathway database for model organisms. PMID:31602464
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Multiscale Modelling Tool: Mathematical modelling of collective behaviour without the maths. PMID:31568526
PyBioNetFit and the Biological Property Specification Language. PMID:31522114
Model annotation and discovery with the Physiome Model Repository. PMID:31492098
Systems Biology of Cancer Metastasis. PMID:31465728
JigCell Model Connector: building large molecular network models from components. PMID:31303682
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. PMID:31293525
iMet: A graphical user interface software tool to merge metabolic networks. PMID:31286073
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. PMID:31216234
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. PMID:31201122
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
A multidimensional perspective on microbial interactions. PMID:31187139
The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis. PMID:31178829
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Quantitative Systems Pharmacology: An Exemplar Model-Building Workflow With Applications in Cardiovascular, Metabolic, and Oncology Drug Development. PMID:31087533
Cell studio: A platform for interactive, 3D graphical simulation of immunological processes. PMID:31069304
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer. PMID:30999849
Metabopolis: scalable network layout for biological pathway diagrams in urban map style. PMID:30991966
The 2019 mathematical oncology roadmap. PMID:30991381
Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis. PMID:30971939
Multiscale computing for science and engineering in the era of exascale performance. PMID:30967040
Hierarchical sequence labeling for extracting BEL statements from biomedical literature. PMID:30961584
Scalable nonlinear programming framework for parameter estimation in dynamic biological system models. PMID:30908479
Recent advances in biomedical simulations: a manifesto for model engineering. PMID:30881691
Integrative and theoretical research on the architecture of a biological system and its disorder. PMID:30868372
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
Gsmodutils: a python based framework for test-driven genome scale metabolic model development. PMID:30759197
Quantitative systems pharmacology of interferon alpha administration: A multi-scale approach. PMID:30759154
Length-independent telomere damage drives post-mitotic cardiomyocyte senescence. PMID:30737259
Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities. PMID:30697975
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions. PMID:30691403
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PMID:30677026
Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network. PMID:30667172
Combining relation extraction with function detection for BEL statement extraction. PMID:30624649
Benchmark problems for dynamic modeling of intracellular processes. PMID:30624608
A computational model to understand mouse iron physiology and disease. PMID:30608934
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. PMID:30577742
Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology. PMID:30568914
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. PMID:30564458
Scaling up genetic circuit design for cellular computing: advances and prospects. PMID:30524216
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. PMID:30488036
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma. PMID:30456354
Code Generation in Computational Neuroscience: A Review of Tools and Techniques. PMID:30455637
"Essentially, all models are wrong, but some are useful"-a cross-disciplinary agenda for building useful models in cell biology and biophysics. PMID:30421276
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Using Systems Biology and Mathematical Modeling Approaches in the Discovery of Therapeutic Targets for Spinal Muscular Atrophy. PMID:30334226
A community-driven reconstruction of the Aspergillus niger metabolic network. PMID:30275963
SemGen: a tool for semantics-based annotation and composition of biosimulation models. PMID:30256901
Using both qualitative and quantitative data in parameter identification for systems biology models. PMID:30254246
"Reproducible" Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach. PMID:30232583
httk: R Package for High-Throughput Toxicokinetics. PMID:30220889
Synthetic negative feedback circuits using engineered small RNAs. PMID:30212900
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans. PMID:30201842
Reproducible Research Using Biomodels. PMID:30191472
Comprehensive network map of interferon gamma signaling. PMID:30191398
Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. PMID:30175326
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
Using quantitative systems pharmacology to evaluate the drug efficacy of COX-2 and 5-LOX inhibitors in therapeutic situations. PMID:30083389
The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression. PMID:30077635
An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. PMID:30047562
The 5-Hydroxytryptamine signaling map: an overview of serotonin-serotonin receptor mediated signaling network. PMID:30043327
A network map of thrombopoietin signaling. PMID:30039510
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
Identifying frequent patterns in biochemical reaction networks: a workflow. PMID:29992320
Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges. PMID:29989102
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. PMID:29982278
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. PMID:29971009
BEL2ABM: agent-based simulation of static models in Biological Expression Language. PMID:29949955
An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. PMID:29938118
RACIPE: a computational tool for modeling gene regulatory circuits using randomization. PMID:29914482
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. PMID:29914475
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. PMID:29872544
A portable structural analysis library for reaction networks. PMID:29857031
Reproducible model development in the cardiac electrophysiology Web Lab. PMID:29842853
A blueprint for human whole-cell modeling. PMID:29806041
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PMID:29791443
A logic-based method to build signaling networks and propose experimental plans. PMID:29777117
Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. PMID:29771304
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. PMID:29713272
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. PMID:29688451
Community-driven roadmap for integrated disease maps. PMID:29688273
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation. PMID:29599715
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
A Digitally Programmable Cytomorphic Chip for Simulation of Arbitrary Biochemical Reaction Networks. PMID:29570063
Arkheia: Data Management and Communication for Open Computational Neuroscience. PMID:29556187
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
A graphical and computational modeling platform for biological pathways. PMID:29543794
Quantifying complexity in metabolic engineering using the LASER database. PMID:29468127
Formalizing Knowledge in Multi-Scale Agent-Based Simulations. PMID:29338063
Agents and networks to model the dynamic interactions of intracellular transport. PMID:29296512
Emerging whole-cell modeling principles and methods. PMID:29275251
Data Sharing: Convert Challenges into Opportunities. PMID:29270401
Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research. PMID:29247253
MAGPIE: Simplifying access and execution of computational models in the life sciences. PMID:29244826
pSSAlib: The partial-propensity stochastic chemical network simulator. PMID:29206229
MitoCore: a curated constraint-based model for simulating human central metabolism. PMID:29178872
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. PMID:29123162
Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PMID:29095952
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
ndexr-an R package to interface with the network data exchange. PMID:29087446
PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K. PMID:29056325
PyBEL: a computational framework for Biological Expression Language. PMID:29048466
Towards dynamic genome-scale models. PMID:29040409
Recent Advances in the Systems Biology of Aging. PMID:29020802
Compartmental and Spatial Rule-Based Modeling with Virtual Cell. PMID:28978431
Using computer simulation models to investigate the most promising microRNAs to improve muscle regeneration during ageing. PMID:28951568
Disease Progression Modeling: Key Concepts and Recent Developments. PMID:28936389
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
SBMLPkgSpec: a LaTeX style file for SBML package specification documents. PMID:28877760
Multi-level and hybrid modelling approaches for systems biology. PMID:28855977
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. PMID:28804499
Qualitative causal analyses of biosimulation models. PMID:28804276
Network design and analysis for multi-enzyme biocatalysis. PMID:28797226
Modeling and simulation of biological systems using SPICE language. PMID:28787027
MUFINS: multi-formalism interaction network simulator. PMID:28725480
Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways. PMID:28725465
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Systems modelling ageing: from single senescent cells to simple multi-cellular models. PMID:28698310
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
GPU-powered model analysis with PySB/cupSODA. PMID:28666314
COPASI and its applications in biotechnology. PMID:28655634
HD Physiology Project-Japanese efforts to promote multilevel integrative systems biology and physiome research. PMID:28649429
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. PMID:28646877
PharmML in Action: an Interoperable Language for Modeling and Simulation. PMID:28575551
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. PMID:28555150
Quantitative computational models of molecular self-assembly in systems biology. PMID:28535149
Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. PMID:28521769
Modeling oxygen requirements in ischemic cardiomyocytes. PMID:28487363
Graphical Modeling Meets Systems Pharmacology. PMID:28469411
A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. PMID:28455349
In SilicoModel-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. PMID:28449558
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. PMID:28444480
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. PMID:28297646
A Web Tool for Generating High Quality Machine-readable Biological Pathways. PMID:28287524
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
A taxonomy of visualization tasks for the analysis of biological pathway data. PMID:28251869
Design Automation in Synthetic Biology. PMID:28246188
MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME. PMID:28190948
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PMID:28187134
Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. PMID:28167777
ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour. PMID:28158307
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function. PMID:28133437
Modelling the molecular mechanisms of aging. PMID:28096317
Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. PMID:28083530
SED-ML web tools: generate, modify and export standard-compliant simulation studies. PMID:28049131
Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. PMID:27993779
A Dormant Microbial Component in the Development of Preeclampsia. PMID:27965958
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. PMID:27930676
A computational method for the investigation of multistable systems and its application to genetic switches. PMID:27927198
Agent-based modelling in synthetic biology. PMID:27903820
A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120. PMID:27899536
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PMID:27870845
Advances on plant-pathogen interactions from molecular toward systems biology perspectives. PMID:27870294
A systems study reveals concurrent activation of AMPK and mTOR by amino acids. PMID:27869123
Analysis of the enzyme network involved in cattle milk production using graph theory. PMID:27844001
Mathematical modeling and synthetic biology. PMID:27840651
Semi-Automated Curation Allows Causal Network Model Building for the Quantification of Age-Dependent Plaque Progression in ApoE-/- Mouse. PMID:27840576
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. PMID:27830063
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. PMID:27774871
The promises of quantitative systems pharmacology modelling for drug development. PMID:27761201
Multi-level regulation of cellular glycosylation: from genes to transcript to enzyme to structure. PMID:27744149
Notions of similarity for systems biology models. PMID:27742665
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. PMID:27736793
Process-based design of dynamical biological systems. PMID:27686219
A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PMID:27636091
SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models. PMID:27628934
VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. PMID:27619687
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data. PMID:27595107
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
Quantitative Systems Pharmacology: A Framework for Context. PMID:27570730
Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development. PMID:27570648
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PMID:27563720
A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. PMID:27522000
Databases and tools for constructing signal transduction networks in cancer. PMID:27502015
Handling Metadata in a Neurophysiology Laboratory. PMID:27486397
Revealing disease-associated pathways by network integration of untargeted metabolomics. PMID:27479327
Signaling network map of the aryl hydrocarbon receptor. PMID:27465749
Guidelines for Reproducibly Building and Simulating Systems Biology Models. PMID:27429432
Where next for the reproducibility agenda in computational biology? PMID:27422148
Short relaxation times but long transient times in both simple and complex reaction networks. PMID:27411726
BioNetGen 2.2: advances in rule-based modeling. PMID:27402907
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language. PMID:27402677
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution. PMID:27380265
Simulated Interventions to Ameliorate Age-Related Bone Loss Indicate the Importance of Timing. PMID:27379013
Coreference resolution improves extraction of Biological Expression Language statements from texts. PMID:27374122
Modular modelling with Physiome standards. PMID:27353233
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. PMID:27307645
Qualitative dynamics semantics for SBGN process description. PMID:27306057
Toward Community Standards and Software for Whole-Cell Modeling. PMID:27305665
Logical Modeling and Dynamical Analysis of Cellular Networks. PMID:27303434
A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT. PMID:27302920
Vesicles-on-a-chip: A universal microfluidic platform for the assembly of liposomes and polymersomes. PMID:27286954
OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems. PMID:27270918
Challenges in structural approaches to cell modeling. PMID:27255863
GESDB: a platform of simulation resources for genetic epidemiology studies. PMID:27242038
Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing. PMID:27239440
A Caenorhabditis elegans Genome-Scale Metabolic Network Model. PMID:27211857
Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. PMID:27185383
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling. PMID:27178561
BELTracker: evidence sentence retrieval for BEL statements. PMID:27173525
SBtab: a flexible table format for data exchange in systems biology. PMID:27153616
An integrated signal transduction network of macrophage migration inhibitory factor. PMID:27139435
eSTGt: a programming and simulation environment for population dynamics. PMID:27117841
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PMID:27081850
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
A physiome interoperability roadmap for personalized drug development. PMID:27051513
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
The systems biology format converter. PMID:27044654
Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth. PMID:27044046
Learning stochastic process-based models of dynamical systems from knowledge and data. PMID:27005698
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves. PMID:26990967
Challenges in horizontal model integration. PMID:26968798
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. PMID:26932523
KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments. PMID:26925206
Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data. PMID:26918190
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. PMID:26909353
Modeling-Enabled Systems Nutritional Immunology. PMID:26909350
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
The Electron Microscopy eXchange (EMX) initiative. PMID:26873784
MOCCASIN: converting MATLAB ODE models to SBML. PMID:26861819
Piecewise parameter estimation for stochastic models in COPASI. PMID:26787664
Pathway Analysis: State of the Art. PMID:26733877
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PMID:26716837
FlexFlux: combining metabolic flux and regulatory network analyses. PMID:26666757
Antiviral innate immunity through the lens of systems biology. PMID:26657882
Tracing regulatory routes in metabolism using generalised supply-demand analysis. PMID:26635009
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PMID:26629901
Representation and inference of cellular architecture for metabolic reconstruction and modeling. PMID:26628588
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks. PMID:26566394
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. PMID:26556387
Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. PMID:26538313
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. PMID:26528569
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. PMID:26528564
Specifications of Standards in Systems and Synthetic Biology. PMID:26528556
Pycellerator: an arrow-based reaction-like modelling language for biological simulations. PMID:26504142
Differential ligand-signaling network of CCL19/CCL21-CCR7 system. PMID:26504105
An algorithm to detect and communicate the differences in computational models describing biological systems. PMID:26490504
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. PMID:26468131
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Databases for multilevel biophysiology research available at Physiome.jp. PMID:26441671
Dynamical modeling of uncertain interaction-based genomic networks. PMID:26423606
Program Code Generator for Cardiac Electrophysiology Simulation with Automatic PDE Boundary Condition Handling. PMID:26356082
Supervised learning methods in modeling of CD4+ T cell heterogeneity. PMID:26339293
Multiscale modeling of mucosal immune responses. PMID:26329787
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PMID:26313928
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
A network map of Interleukin-10 signaling pathway. PMID:26253919
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. PMID:26249223
Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. PMID:26225259
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Regulation of ERK-MAPK signaling in human epidermis. PMID:26209520
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Construction of biological networks from unstructured information based on a semi-automated curation workflow. PMID:26200752
Modeling for (physical) biologists: an introduction to the rule-based approach. PMID:26178138
Fasting cycles potentiate the efficacy of gemcitabine treatment in in vitro and in vivo pancreatic cancer models. PMID:26176887
SEEK: a systems biology data and model management platform. PMID:26160520
Evolutionary trends and functional anatomy of the human expanded autophagy network. PMID:26103419
libRoadRunner: a high performance SBML simulation and analysis library. PMID:26085503
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. PMID:26079347
A knowledgebase resource for interleukin-17 family mediated signaling. PMID:26077014
CONNJUR Workflow Builder: a software integration environment for spectral reconstruction. PMID:26066803
HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual. PMID:26053019
Automatising the analysis of stochastic biochemical time-series. PMID:26051821
GFVO: the Genomic Feature and Variation Ontology. PMID:26019997
Next generation distributed computing for cancer research. PMID:25983539
Implementation of a model of bodily fluids regulation. PMID:25935135
Pathways with PathWhiz. PMID:25934797
Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer. PMID:25910075
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PMID:25905717
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. PMID:25887162
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. PMID:25880925
Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data. PMID:25871730
A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems. PMID:25859426
A systematic simulation of the effect of salicylic acid on sphingolipid metabolism. PMID:25859253
RobOKoD: microbial strain design for (over)production of target compounds. PMID:25853130
Reconstructing genome-scale metabolic models with merlin. PMID:25845595
Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain. PMID:25806817
MetaNET--a web-accessible interactive platform for biological metabolic network analysis. PMID:25779921
Acceleration of discrete stochastic biochemical simulation using GPGPU. PMID:25762936
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Computational modeling of drug response with applications to neuroscience. PMID:25733952
PathVisio 3: an extendable pathway analysis toolbox. PMID:25706687
OpenCOR: a modular and interoperable approach to computational biology. PMID:25705192
Current state of genome-scale modeling in filamentous fungi. PMID:25700817
A novel mathematical model describing adaptive cellular drug metabolism and toxicity in the chemoimmune system. PMID:25699998
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model. PMID:25629405
Systems approach for the selection of micro-RNAs as therapeutic biomarkers of anti-EGFR monoclonal antibody treatment in colorectal cancer. PMID:25622824
Using argument notation to engineer biological simulations with increased confidence. PMID:25589574
Genome-scale modeling for metabolic engineering. PMID:25578304
Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. PMID:25566296
Transparency in metabolic network reconstruction enables scalable biological discovery. PMID:25562137
An integrated network visualization framework towards metabolic engineering applications. PMID:25547011
Mathematical and computational modeling in biology at multiple scales. PMID:25542608
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits. PMID:25506588
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. PMID:25475114
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. PMID:25471253
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. PMID:25466481
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. PMID:25414366
BioModels: ten-year anniversary. PMID:25414348
Estimating relative changes of metabolic fluxes. PMID:25412287
Integrated network analysis and effective tools in plant systems biology. PMID:25408696
Energy-based analysis of biochemical cycles using bond graphs. PMID:25383030
Diagnostics for stochastic genome-scale modeling via model slicing and debugging. PMID:25368989
Computational modeling of heterogeneity and function of CD4+ T cells. PMID:25364738
Human cardiac systems electrophysiology and arrhythmogenesis: iteration of experiment and computation. PMID:25362174
Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. PMID:25344492
Parts & pools: a framework for modular design of synthetic gene circuits. PMID:25340051
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. PMID:25315994
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. PMID:25309419
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. PMID:25295490
Multi-state modeling of biomolecules. PMID:25254957
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. PMID:25253680
Dynamic modelling of pathways to cellular senescence reveals strategies for targeted interventions. PMID:25166345
Effects of small particle numbers on long-term behaviour in discrete biochemical systems. PMID:25161236
Modeling biology spanning different scales: an open challenge. PMID:25143952
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack. PMID:25074435
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Lineage grammars: describing, simulating and analyzing population dynamics. PMID:25047682
A computational framework for the automated construction of glycosylation reaction networks. PMID:24978019
e!DAL--a framework to store, share and publish research data. PMID:24958009
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. PMID:24911500
Event-based text mining for biology and functional genomics. PMID:24907365
SensA: web-based sensitivity analysis of SBML models. PMID:24903418
Signaling hypergraphs. PMID:24857424
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
Genome scale modeling in systems biology: algorithms and resources. PMID:24822031
libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. PMID:24795618
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data. PMID:24792167
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
Python-based geometry preparation and simulation visualization toolkits for STEPS. PMID:24782754
Principles of genetic circuit design. PMID:24781324
A computer simulation approach to assessing therapeutic intervention points for the prevention of cytokine-induced cartilage breakdown. PMID:24757149
Bridging the gaps in systems biology. PMID:24728588
Plant systems biology: insights, advances and challenges. PMID:24671625
Modelling hormonal response and development. PMID:24630843
A network map of the gastrin signaling pathway. PMID:24584707
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. PMID:24573880
GraTeLPy: graph-theoretic linear stability analysis. PMID:24572152
JSim, an open-source modeling system for data analysis. PMID:24555116
BiNA: a visual analytics tool for biological network data. PMID:24551056
Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium. PMID:24516572
ModeLang: a new approach for experts-friendly viral infections modeling. PMID:24454531
Computer-assisted design for scaling up systems based on DNA reaction networks. PMID:24451393
Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations. PMID:24427530
Multi-scale computational models of the airways to unravel the pathophysiological mechanisms in asthma and chronic obstructive pulmonary disease (AirPROM). PMID:24427517
Characterization of negative feedback network motifs in the TGF-β signaling pathway. PMID:24386222
A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. PMID:24354351
Analytical solution of steady-state equations for chemical reaction networks with bilinear rate laws. PMID:24334389
Systematic construction of kinetic models from genome-scale metabolic networks. PMID:24324546
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. PMID:24321545
Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. PMID:24307567
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. PMID:24307566
Reaction-diffusion in the NEURON simulator. PMID:24298253
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. PMID:24295137
Pathway Commons at virtual cell: use of pathway data for mathematical modeling. PMID:24273241
How reliable is the linear noise approximation of gene regulatory networks? PMID:24266939
MC3: a steady-state model and constraint consistency checker for biochemical networks. PMID:24261865
StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PMID:24260203
A Signaling Network of Thyroid-Stimulating Hormone. PMID:24255551
What can we learn from global sensitivity analysis of biochemical systems? PMID:24244458
Sybil--efficient constraint-based modelling in R. PMID:24224957
SBML and CellML translation in antimony and JSim. PMID:24215024
Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. PMID:24195591
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures. PMID:24167490
Toward an integrated software platform for systems pharmacology. PMID:24150748
Root systems biology: integrative modeling across scales, from gene regulatory networks to the rhizosphere. PMID:24143806
Using cellzilla for plant growth simulations at the cellular level. PMID:24137172
HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. PMID:24137008
Community structure and multi-modal oscillations in complex networks. PMID:24130720
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. PMID:24123887
Function of dynamic models in systems biology: linking structure to behaviour. PMID:24103739
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
Investigating interventions in Alzheimer's disease with computer simulation models. PMID:24098635
Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. PMID:24098096
A comprehensive map of the influenza A virus replication cycle. PMID:24088197
Modeling of rifampicin-induced CYP3A4 activation dynamics for the prediction of clinical drug-drug interactions from in vitro data. PMID:24086247
yApoptosis: yeast apoptosis database. PMID:24082050
A C library for retrieving specific reactions from the BioModels database. PMID:24078714
Computational models of the JAK1/2-STAT1 signaling. PMID:24069559
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. PMID:24064420
Simulating an infection growth model in certain healthy metabolic pathways of Homo sapiens for highlighting their role in Type I Diabetes mellitus using fire-spread strategy, feedbacks and sensitivities. PMID:24039701
A proposal for augmenting biological model construction with a semi-intelligent computational modeling assistant. PMID:23990750
Simulating physiological interactions in a hybrid system of mathematical models. PMID:23990270
Modelling the efficacy of hyperthermia treatment. PMID:23985732
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
HSC-explorer: a curated database for hematopoietic stem cells. PMID:23936191
Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PMID:23935467
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. PMID:23935056
FieldML, a proposed open standard for the Physiome project for mathematical model representation. PMID:23900627
Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. PMID:23892182
An analysis of a 'community-driven' reconstruction of the human metabolic network. PMID:23888127
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. PMID:23873954
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach. PMID:23847397
Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803. PMID:23843751
Individualised proteome profiling of human endometrial tumours improves detection of new prognostic markers. PMID:23839494
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. PMID:23831062
The systems biology simulation core algorithm. PMID:23826941
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. PMID:23813008
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. PMID:23800136
On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. PMID:23730363
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology. PMID:23708369
Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. PMID:23705868
Mathematical modeling of folate metabolism. PMID:23703958
MIMO: an efficient tool for molecular interaction maps overlap. PMID:23672344
Large-scale event extraction from literature with multi-level gene normalization. PMID:23613707
A network map of BDNF/TRKB and BDNF/p75NTR signaling system. PMID:23606317
A metabolite-centric view on flux distributions in genome-scale metabolic models. PMID:23587327
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PMID:23555215
Chaste: an open source C++ library for computational physiology and biology. PMID:23516352
A stochastic simulator of birth-death master equations with application to phylodynamics. PMID:23505043
An integrated map of corticotropin-releasing hormone signaling pathway. PMID:23504413
Hierarchical approaches for systems modeling in cardiac development. PMID:23463736
A community-driven global reconstruction of human metabolism. PMID:23455439
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. PMID:23453054
Programming biological models in Python using PySB. PMID:23423320
Linking genome-scale metabolic modeling and genome annotation. PMID:23417799
Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways. PMID:23409788
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
A method for comparing multivariate time series with different dimensions. PMID:23393554
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Random parameter sampling of a generic three-tier MAPK cascade model reveals major factors affecting its versatile dynamics. PMID:23365667
D-Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae. PMID:23361949
Visual data mining of biological networks: one size does not fit all. PMID:23341759
From desk to bed: computational simulations provide indication for rheumatoid arthritis clinical trials. PMID:23339423
SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology. PMID:23329415
BioCause: Annotating and analysing causality in the biomedical domain. PMID:23323613
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. PMID:23311978
Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo. PMID:23284653
Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations. PMID:23233838
Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology. PMID:23230149
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
Accelerating cancer systems biology research through Semantic Web technology. PMID:23188758
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. PMID:23175748
Logic modeling and the ridiculome under the rug. PMID:23171629
Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation. PMID:23166792
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
A multicellular signal transduction network of AGE/RAGE signaling. PMID:23161412
Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast. PMID:23149687
VANTED v2: a framework for systems biology applications. PMID:23140568
A travel guide to Cytoscape plugins. PMID:23132118
Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales. PMID:23110897
Modeling regulatory networks to understand plant development: small is beautiful. PMID:23110896
Addressing human variability in next-generation human health risk assessments of environmental chemicals. PMID:23086705
A CellML simulation compiler and code generator using ODE solving schemes. PMID:23083065
Bio-logic builder: a non-technical tool for building dynamical, qualitative models. PMID:23082121
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. PMID:23072312
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. PMID:23046614
Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation. PMID:23007888
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
Kinetic modelling of GlmU reactions - prioritization of reaction for therapeutic application. PMID:22952829
Qualitative translation of relations from BioPAX to SBML qual. PMID:22923304
Hybrid models and biological model reduction with PyDSTool. PMID:22912566
The Cell Collective: toward an open and collaborative approach to systems biology. PMID:22871178
The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. PMID:22855577
Condor-COPASI: high-throughput computing for biochemical networks. PMID:22834945
Reduction of dynamical biochemical reactions networks in computational biology. PMID:22833754
CIDeR: multifactorial interaction networks in human diseases. PMID:22809392
Multiscale modeling and data integration in the virtual physiological rat project. PMID:22805979
Biochemical fluctuations, optimisation and the linear noise approximation. PMID:22805626
Declarative representation of uncertainty in mathematical models. PMID:22802941
Aggregation, impaired degradation and immunization targeting of amyloid-beta dimers in Alzheimer's disease: a stochastic modelling approach. PMID:22748062
URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. PMID:22727185
Improving metabolic flux predictions using absolute gene expression data. PMID:22713172
A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. PMID:22711887
A pathway map of prolactin signaling. PMID:22684822
Workflow for generating competing hypothesis from models with parameter uncertainty. PMID:22670212
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. PMID:22663945
A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway. PMID:22649723
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. PMID:22647208
Invariants and other structural properties of biochemical models as a constraint satisfaction problem. PMID:22642806
Computational tools for metabolic engineering. PMID:22629572
Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PMID:22615553
A specialized ODE integrator for the efficient computation of parameter sensitivities. PMID:22607742
A network perspective on metabolic inconsistency. PMID:22583819
Software support for SBGN maps: SBGN-ML and LibSBGN. PMID:22581176
STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. PMID:22574658
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. PMID:22558935
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Systems immunology: a survey of modeling formalisms, applications and simulation tools. PMID:22528121
Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how. PMID:22527402
Systems biology of fungal infection. PMID:22485108
Multi-scale modeling of tissues using CompuCell3D. PMID:22482955
A unifying hypothesis for familial and sporadic Alzheimer's disease. PMID:22482080
Tav4SB: integrating tools for analysis of kinetic models of biological systems. PMID:22480273
What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform. PMID:22419971
Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PMID:22379410
Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches. PMID:22376077
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
graphite - a Bioconductor package to convert pathway topology to gene network. PMID:22292714
Propagating semantic information in biochemical network models. PMID:22289386
FAME, the Flux Analysis and Modeling Environment. PMID:22289213
At the heart of computational modelling. PMID:22271869
Modeling of miRNA and drug action in the EGFR signaling pathway. PMID:22253908
Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments? PMID:22252984
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. PMID:22233419
Design and analysis of DNA strand displacement devices using probabilistic model checking. PMID:22219398
Stable isotope-resolved metabolomics and applications for drug development. PMID:22212615
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. PMID:22199389
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. PMID:22172142
Leveraging modeling approaches: reaction networks and rules. PMID:22161349
Modeling formalisms in Systems Biology. PMID:22141422
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
Programming languages for synthetic biology. PMID:22132053
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
SABIO-RK--database for biochemical reaction kinetics. PMID:22102587
Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks. PMID:22090146
MetaCrop 2.0: managing and exploring information about crop plant metabolism. PMID:22086948
Software for systems biology: from tools to integrated platforms. PMID:22048662
Controlled vocabularies and semantics in systems biology. PMID:22027554
BioPAX support in CellDesigner. PMID:22021903
The Reactome BioMart. PMID:22012987
Toward a comprehensive language for biological systems. PMID:22005092
OBML - Ontologies in Biomedicine and Life Sciences. PMID:21996496
A comprehensive curated resource for follicle stimulating hormone signaling. PMID:21996254
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. PMID:21994219
Visual DSD: a design and analysis tool for DNA strand displacement systems. PMID:21984756
Medusa: A tool for exploring and clustering biological networks. PMID:21978489
Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. PMID:21969679
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
Dupuytren's: a systems biology disease. PMID:21943049
Bioinformatics and systems biology of the lipidome. PMID:21939287
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. PMID:21886097
OnionTree XML: a format to exchange gene-related probabilities. PMID:21875159
Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. PMID:21865275
A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants. PMID:21849042
A mechanistic modeling framework for predicting metabolic interactions in complex mixtures. PMID:21835728
Integrating systems biology models and biomedical ontologies. PMID:21835028
Modelling the role of the Hsp70/Hsp90 system in the maintenance of protein homeostasis. PMID:21779370
A framework for the study of multiple realizations: the importance of levels of analysis. PMID:21772823
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. PMID:21745496
Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. PMID:21745496
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. PMID:21742767
StochKit2: software for discrete stochastic simulation of biochemical systems with events. PMID:21727139
Construction of a computable cell proliferation network focused on non-diseased lung cells. PMID:21722388
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. PMID:21714867
JSBML: a flexible Java library for working with SBML. PMID:21697129
Mining metabolites: extracting the yeast metabolome from the literature. PMID:21687783
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation. PMID:21682905
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. PMID:21653523
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. PMID:21609434
Social engineering for virtual 'big science' in systems biology. PMID:21587248
Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PMID:21559524
Using graph theory to analyze biological networks. PMID:21527005
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
Signaling gateway molecule pages--a data model perspective. PMID:21505029
A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks. PMID:21483730
Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PMID:21483474
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes. PMID:21464833
Module-based multiscale simulation of angiogenesis in skeletal muscle. PMID:21463529
Error detection and unit conversion. PMID:21462417
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PMID:21455299
Systems glycobiology: biochemical reaction networks regulating glycan structure and function. PMID:21436236
Grand challenges in systems physiology. PMID:21423346
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models. PMID:21423324
AllerML: markup language for allergens. PMID:21420460
Mathematical descriptions of biochemical networks: stability, stochasticity, evolution. PMID:21419158
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Analog regulation of metabolic demand. PMID:21406074
Automatic design of digital synthetic gene circuits. PMID:21399700
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
Computer-aided design of biological circuits using TinkerCell. PMID:21327060
Synthetic biology: a foundation for multi-scale molecular biology. PMID:21326830
A PXR-mediated negative feedback loop attenuates the expression of CYP3A in response to the PXR agonist pregnenalone-16α-carbonitrile. PMID:21311750
A simple DNA gate motif for synthesizing large-scale circuits. PMID:21296792
Model annotation for synthetic biology: automating model to nucleotide sequence conversion. PMID:21296753
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
FASIMU: flexible software for flux-balance computation series in large metabolic networks. PMID:21255455
Revision history aware repositories of computational models of biological systems. PMID:21235804
A unique transformation from ordinary differential equations to reaction networks. PMID:21203560
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
A comprehensive map of the mTOR signaling network. PMID:21179025
Computational biology for ageing. PMID:21115530
Software that goes with the flow in systems biology. PMID:21114874
Systematic integration of experimental data and models in systems biology. PMID:21114840
Confidence from uncertainty--a multi-target drug screening method from robust control theory. PMID:21106087
DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells. PMID:21092113
Scalable rule-based modelling of allosteric proteins and biochemical networks. PMID:21079669
Grand challenge commentary: Transforming biosynthesis into an information science. PMID:21079588
BRENDA, the enzyme information system in 2011. PMID:21062828
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
Parameter balancing in kinetic models of cell metabolism. PMID:21038890
Further developments towards a genome-scale metabolic model of yeast. PMID:21029416
Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. PMID:20967426
Modelling the role of UCH-L1 on protein aggregation in age-related neurodegeneration. PMID:20949132
Experimental and computational analysis of polyglutamine-mediated cytotoxicity. PMID:20885783
A comprehensive molecular interaction map of the budding yeast cell cycle. PMID:20865008
Kinetic Modeling using BioPAX ontology. PMID:20862270
Code generation: a strategy for neural network simulators. PMID:20857234
In silico models of cancer. PMID:20836040
Computational modeling of mammalian signaling networks. PMID:20836022
The BioPAX community standard for pathway data sharing. PMID:20829833
SBML2TikZ: supporting the SBML render extension in LaTeX. PMID:20829443
A graphical method for reducing and relating models in systems biology. PMID:20823324
BioXSD: the common data-exchange format for everyday bioinformatics web services. PMID:20823319
Using views of Systems Biology Cloud: application for model building. PMID:20730508
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. PMID:20727200
DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. PMID:20698988
PathwayAccess: CellDesigner plugins for pathway databases. PMID:20647521
SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. PMID:20639523
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. PMID:20628073
Annotation of SBML models through rule-based semantic integration. PMID:20626923
A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment. PMID:20625505
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
A decade of systems biology. PMID:20604711
Mathematical modeling: bridging the gap between concept and realization in synthetic biology. PMID:20589069
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PMID:20585541
Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PMID:20567500
PINT: Pathways INtegration Tool. PMID:20538652
Measurement of single-cell dynamics. PMID:20535203
PathText: a text mining integrator for biological pathway visualizations. PMID:20529930
A multilevel data integration resource for breast cancer study. PMID:20525248
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
BioMet Toolbox: genome-wide analysis of metabolism. PMID:20483918
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. PMID:20470404
VISIBIOweb: visualization and layout services for BioPAX pathway models. PMID:20460470
Arcadia: a visualization tool for metabolic pathways. PMID:20453003
Multiscale modeling for biologists. PMID:20448808
Model composition for macromolecular regulatory networks. PMID:20431147
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
OptFlux: an open-source software platform for in silico metabolic engineering. PMID:20403172
An overview of the CellML API and its implementation. PMID:20377909
Payao: a community platform for SBML pathway model curation. PMID:20371497
What is flux balance analysis? PMID:20212490
A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. PMID:20209100
Trends in programming languages for neuroscience simulations. PMID:20198154
Visualization of omics data for systems biology. PMID:20195258
Modeling auxin-regulated development. PMID:20182620
GSK3 and p53 - is there a link in Alzheimer's disease? PMID:20181016
Simulating plant metabolic pathways with enzyme-kinetic models. PMID:20118273
Towards a genome-scale kinetic model of cellular metabolism. PMID:20109182
NetPath: a public resource of curated signal transduction pathways. PMID:20067622
Snazer: the simulations and networks analyzer. PMID:20056001
Systems biology of embryogenesis. PMID:20003850
Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: an analysis of ATP-induced ribonucleotide reductase R1 hexamerization data. PMID:20003203
Current progress in patient-specific modeling. PMID:19955236
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. PMID:19939940
Computational systems biology in cancer: modeling methods and applications. PMID:19936081
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
phiSITE: database of gene regulation in bacteriophages. PMID:19900969
Model aggregation: a building-block approach to creating large macromolecular regulatory networks. PMID:19880372
TinkerCell: modular CAD tool for synthetic biology. PMID:19874625
The NCBI BioSystems database. PMID:19854944
TIde: a software for the systematic scanning of drug targets in kinetic network models. PMID:19840374
Molecular machines or pleiomorphic ensembles: signaling complexes revisited. PMID:19835637
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
Protopia: a protein-protein interaction tool. PMID:19828077
Trends in modeling Biomedical Complex Systems. PMID:19828068
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. PMID:19814801
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. PMID:19804630
An editor for pathway drawing and data visualization in the Biopathways Workbench. PMID:19799790
Genomic analysis of the function of the transcription factor gata3 during development of the mammalian inner ear. PMID:19774072
Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. PMID:19754933
Saint: a lightweight integration environment for model annotation. PMID:19734151
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. PMID:19732427
Computational reasoning across multiple models. PMID:19717801
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. PMID:19698148
The Systems Biology Graphical Notation. PMID:19668183
Systems biology and the virtual physiological human. PMID:19638973
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. PMID:19623245
Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. PMID:19607691
PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. PMID:19597783
Modeling of the bacterial mechanism of methicillin-resistance by a systems biology approach. PMID:19593454
Systems pathology--taking molecular pathology into a new dimension. PMID:19581910
Antimony: a modular model definition language. PMID:19578039
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
DOTcvpSB, a software toolbox for dynamic optimization in systems biology. PMID:19558728
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. PMID:19541909
Stochastic simulation and analysis of biomolecular reaction networks. PMID:19534796
A systems biology network model for genetic association studies of nicotine addiction and treatment. PMID:19525886
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. PMID:19500393
Consistent design schematics for biological systems: standardization of representation in biological engineering. PMID:19493898
Using chemical organization theory for model checking. PMID:19468053
Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. PMID:19455135
Writing DNA with GenoCAD. PMID:19429897
Modeling molecular regulatory networks with JigCell and PET. PMID:19399431
A general map of iron metabolism and tissue-specific subnetworks. PMID:19381358
CellML metadata standards, associated tools and repositories. PMID:19380315
Towards programming languages for genetic engineering of living cells. PMID:19369220
Intelligently deciphering unintelligible designs: algorithmic algebraic model checking in systems biology. PMID:19364723
Designing and encoding models for synthetic biology. PMID:19364720
Multiscale models of angiogenesis. PMID:19349248
Systems medicine: the future of medical genomics and healthcare. PMID:19348689
GetBonNie for building, analyzing and sharing rule-based models. PMID:19321734
A mathematical model of aging-related and cortisol induced hippocampal dysfunction. PMID:19320982
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. PMID:19307240
Navigating the network: signaling cross-talk in hematopoietic cells. PMID:19295628
Version control of pathway models using XML patches. PMID:19292901
The role of predictive modelling in rationally re-engineering biological systems. PMID:19252506
Toward a systems biology framework for understanding aging and health span. PMID:19223604
PyNEST: A Convenient Interface to the NEST Simulator. PMID:19198667
Model-based redesign of global transcription regulation. PMID:19188257
Benchmarking regulatory network reconstruction with GRENDEL. PMID:19188190
PROMOT: modular modeling for systems biology. PMID:19147665
Stochastic modelling for quantitative description of heterogeneous biological systems. PMID:19139763
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. PMID:19133145
PyMOOSE: Interoperable Scripting in Python for MOOSE. PMID:19129924
Reconstruction of biochemical networks in microorganisms. PMID:19116616
Genome-scale models of bacterial metabolism: reconstruction and applications. PMID:19067749
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. PMID:19045831
Virtual Cell modelling and simulation software environment. PMID:19045830
Domain-oriented reduction of rule-based network models. PMID:19045829
The Alpha Project: a model system for systems biology research. PMID:19045818
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
A survey of visualization tools for biological network analysis. PMID:19040716
Arena3D: visualization of biological networks in 3D. PMID:19040715
Dynamical modeling of the cholesterol regulatory pathway with Boolean networks. PMID:19025648
In silico and in vitro modeling of hepatocyte drug transport processes: importance of ABCC2 expression levels in the disposition of carboxydichlorofluroscein. PMID:19022944
Computational design of digital and memory biological devices. PMID:19003443
Asmparts: assembly of biological model parts. PMID:19003441
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. PMID:18987214
Reactome knowledgebase of human biological pathways and processes. PMID:18981052
ALC: automated reduction of rule-based models. PMID:18973705
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. PMID:18971255
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
Robust simplifications of multiscale biochemical networks. PMID:18854041
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. PMID:18846089
Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. PMID:18835283
The challenges for molecular nutrition research 4: the "nutritional systems biology level". PMID:18825427
Web-based applications for building, managing and analysing kinetic models of biological systems. PMID:18805901
Standards and ontologies in computational systems biology. PMID:18793134
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. PMID:18757046
FERN - a Java framework for stochastic simulation and evaluation of reaction networks. PMID:18755046
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. PMID:18713463
Explaining oscillations and variability in the p53-Mdm2 system. PMID:18706112
WikiPathways: pathway editing for the people. PMID:18651794
Programming with models: modularity and abstraction provide powerful capabilities for systems biology. PMID:18647734
A new strategy for assessing sensitivities in biochemical models. PMID:18632455
A new strategy for assessing sensitivities in biochemical models. PMID:18632455
MicroCore: mapping genome expression to cell pathways and networks. PMID:18629046
Comparing simulation results of SBML capable simulators. PMID:18579569
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. PMID:18541053
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. PMID:18536691
SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. PMID:18447902
A logic-based diagram of signalling pathways central to macrophage activation. PMID:18433497
A comprehensive modular map of molecular interactions in RB/E2F pathway. PMID:18319725
LibSBML: an API library for SBML. PMID:18252737
The cell cycle DB: a systems biology approach to cell cycle analysis. PMID:18160409
Computational prediction of protein-protein interactions. PMID:18095187
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. PMID:18078503
Incremental and unifying modelling formalism for biological interaction networks. PMID:17996051
Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. PMID:17940089
MetaCrop: a detailed database of crop plant metabolism. PMID:17933764
Universally sloppy parameter sensitivities in systems biology models. PMID:17922568
A computational approach to the functional screening of genomes. PMID:17907794
Current approaches to gene regulatory network modelling. PMID:17903290
Algorithms and software for stochastic simulation of biochemical reacting systems. PMID:17894470
Interoperability of neuroscience modeling software: current status and future directions. PMID:17873374
MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. PMID:17873371
Conceptual modeling in systems biology fosters empirical findings: the mRNA lifecycle. PMID:17849002
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Onto-Tools: new additions and improvements in 2006. PMID:17584796
Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach. PMID:17559886
Homeostasis: beyond Curt Richter. PMID:17524521
RMBNToolbox: random models for biochemical networks. PMID:17524136
BioPP: a tool for web-publication of biological networks. PMID:17519033
A minimal and self-consistent in silico cell model based on macromolecular interactions. PMID:17510017
E-photosynthesis: a comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light. PMID:17492490
neuroConstruct: a tool for modeling networks of neurons in 3D space. PMID:17442244
Formal TCA cycle description based on elementary actions. PMID:17426387
An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline. PMID:17408507
Reactome: a knowledge base of biologic pathways and processes. PMID:17367534
SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). PMID:17341299
Global reconstruction of the human metabolic network based on genomic and bibliomic data. PMID:17267599
Biology by design: reduction and synthesis of cellular components and behaviour. PMID:17251159
Ontology-based representation of simulation models of physiology. PMID:17238424
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170
Mathematical modeling as a tool for investigating cell cycle control networks. PMID:17189866
CellCircuits: a database of protein network models. PMID:17135207
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. PMID:17130144
Model storage, exchange and integration. PMID:17118155
Mathematical modeling of intracellular signaling pathways. PMID:17118154
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
XML schemas for common bioinformatic data types and their application in workflow systems. PMID:17087823
GeneTools--application for functional annotation and statistical hypothesis testing. PMID:17062145
Meta-All: a system for managing metabolic pathway information. PMID:17059592
Depicting combinatorial complexity with the molecular interaction map notation. PMID:17016517
Modelling the checkpoint response to telomere uncapping in budding yeast. PMID:17015293
The ion channel inverse problem: neuroinformatics meets biophysics. PMID:16933979
Noise-induced Min phenotypes in E. coli. PMID:16846247
metaSHARK: a WWW platform for interactive exploration of metabolic networks. PMID:16845107
BiologicalNetworks: visualization and analysis tool for systems biology. PMID:16845051
The cognitive phenotype of Down syndrome: insights from intracellular network analysis. PMID:16815222
A comprehensive map of the toll-like receptor signaling network. PMID:16738560
Standardizing the standards. PMID:16738556
Circuit diagrams for biological networks. PMID:16738549
Escalating model sizes and complexities call for standardized forms of representation. PMID:16729046
A comprehensive pathway map of epidermal growth factor receptor signaling. PMID:16729045
On systems and control approaches to therapeutic gain. PMID:16638124
A computational framework for the topological analysis and targeted disruption of signal transduction networks. PMID:16617070
The Gaggle: an open-source software system for integrating bioinformatics software and data sources. PMID:16569235
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. PMID:16553966
Deciphering cellular states of innate tumor drug responses. PMID:16542501
From genomes to systems: the path with yeast. PMID:16524836
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. PMID:16381960
Pathguide: a pathway resource list. PMID:16381921
Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. PMID:16293107
In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. PMID:16269766
A new dynamical layout algorithm for complex biochemical reaction networks. PMID:16124872
Folate system correlations in DNA microarray data. PMID:16080796
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. PMID:15980551
VisANT: data-integrating visual framework for biological networks and modules. PMID:15980487
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. PMID:15929789
Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. PMID:15895265
Integration of the Gene Ontology into an object-oriented architecture. PMID:15885145
Rational polynomial representation of ribonucleotide reductase activity. PMID:15876357
Toward predictive models of mammalian cells. PMID:15869393
Object-oriented biological system integration: a SARS coronavirus example. PMID:15731211
Analyzing the biology on the system level. PMID:15629038
The PANTHER database of protein families, subfamilies, functions and pathways. PMID:15608197
A two-way interface between limited Systems Biology Markup Language and R. PMID:15585059
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). PMID:15518589
Modeling of cell signaling pathways in macrophages by semantic networks. PMID:15494071
MathSBML: a package for manipulating SBML-based biological models. PMID:15087311

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enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

molecular entity
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

network model
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

pathway model
metasource: Fairsharing.org
version: FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

enzymatic reaction mathematical model modeling and simulation molecular entity network model pathway model

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Experimental data repository for KInetic MOdels of biological SYStems