The systems biology simulation core algorithm (Q34798508)

4 August 2017

title

The systems biology simulation core algorithm (English)

1 reference

4 August 2017

1 reference

8

1 reference

4 August 2017

Nicolas Rodriguez

7

0 references

Andreas Dräger

object named as

Andreas Dräger

12

0 references

Akira Funahashi

object named as

Akira Funahashi

4

0 references

Andreas Zell

11

object named as

Andreas Zell

1 reference

4 August 2017

Roland Keller

1

1 reference

4 August 2017

Alexander Dörr

2

1 reference

4 August 2017

Akito Tabira

3

1 reference

4 August 2017

Michael J Ziller

5

1 reference

4 August 2017

Richard Adams

6

1 reference

4 August 2017

Noriko Hiroi

9

1 reference

4 August 2017

Hannes Planatscher

10

1 reference

4 August 2017

language of work or name

1 reference

5 July 2013

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4 August 2017

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4 August 2017

volume

7

1 reference

4 August 2017

page(s)

55

1 reference

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

4 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

LibSBMLSim: a reference implementation of fully functional SBML simulator

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Virtual Cell: computational tools for modeling in cell biology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Controlled vocabularies and semantics in systems biology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

A quantitative comparison of Calvin-Benson cycle models.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Analyzing the functional properties of the creatine kinase system with multiscale 'sloppy' modeling

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

JSBML: a flexible Java library for working with SBML.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Minimum Information About a Simulation Experiment (MIASE)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

An overview of the CellML API and its implementation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

A comprehensive model for the humoral coagulation network in humans.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Virtual Cell modelling and simulation software environment.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Comparing simulation results of SBML capable simulators

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

LibSBML: an API library for SBML.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

SBMLmerge, a system for combining biochemical network models.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

COPASI--a COmplex PAthway SImulator

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

A model diagram layout extension for SBML

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

CellML: its future, present and past

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

The virtual liver: a multidisciplinary, multilevel challenge for systems biology.

8 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-55

The CellML Model Repository

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-55

iBioSim: a tool for the analysis and design of genetic circuits.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-55

A pharmacodynamic model for the time course of tumor shrinkage by gemcitabine + carboplatin in non-small cell lung cancer patients.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-55

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3707837

Systems biology standards—the community speaks

26 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-55

Systems biology: evolving into the mainstream

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23826941

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23826941

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-7-55

1 reference

journals/bmcsb/KellerDTFZARNHPZD13

4 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

4 August 2017

1 reference