Lista de obras - Dagmar Waltemath - Dominio Público Uruguay

A brief history of COMBINE

A call for virtual experiments: accelerating the scientific process

artículo científico publicado en 2014

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

artículo científico publicado en 2016

A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools

artículo científico publicado en 2022

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>

An algorithm to detect and communicate the differences in computational models describing biological systems

artículo científico publicado en 2015

Annotation-based feature extraction from sets of SBML models

artículo científico publicado en 2015

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

artículo científico publicado en 2014

COMODI: an ontology to characterise differences in versions of computational models in biology

artículo científico publicado en 2016

Combining computational models, semantic annotations and simulation experiments in a graph database

artículo científico publicado en 2015

Controlled vocabularies and semantics in systems biology

artículo científico publicado en 2011

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

artículo científico publicado en 2019

Democratizing knowledge representation with BioCypher

Evolution of computational models in BioModels Database and the Physiome Model Repository.

artículo científico publicado en 2018

Exploring the evolution of biochemical models at the network level

artículo científico publicado en 2022

Harmonizing semantic annotations for computational models in biology

artículo científico publicado en 2019

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

artículo científico publicado en 2016

Identifying frequent patterns in biochemical reaction networks - a workflow

Identifying frequent patterns in biochemical reaction networks: a workflow.

artículo científico publicado en 2018

Improving the reuse of computational models through version control

artículo científico

Information Retrieval in Life Sciences: A Programmatic Survey

Initiatives, Concepts, and Implementation Practices of FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles in Health Data Stewardship Practice: Protocol for a Scoping Review

artículo científico publicado en 2021

Kinetic Simulation Algorithm Ontology

scholarly article

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

artículo científico publicado en 2014

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

article by Dagmar Waltemath et al published 15 March 2014 in Standards in genomic sciences

Minimum Information About a Simulation Experiment (MIASE)

artículo científico publicado en 2011

Notions of similarity for computational biology models

Notions of similarity for systems biology models

artículo científico publicado en 2016

Notions of similarity for systems biology models.

artículo científico publicado en 2017

OMEX metadata specification (version 1.2)

artículo científico publicado en 2021

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY

artículo científico publicado en 2010

Open modeling and exchange (OMEX) metadata specification version 1.0.

artículo científico publicado en 2020

Opportunities of Digital Infrastructures for Disease Management-Exemplified on COVID-19-Related Change in Diagnosis Counts for Diabetes-Related Eye Diseases

artículo científico publicado en 2022

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

artículo científico publicado en 2015

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.

artículo científico publicado en 2018

Ranked retrieval of Computational Biology models

artículo científico publicado en 2010

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

artículo científico publicado en 2011

SBML Level 3 Package Proposal: Annotation

SBML Level 3: an extensible format for the exchange and reuse of biological models

artículo científico publicado en 2020

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

artículo científico publicado en 2017

STON: exploring biological pathways using the SBGN standard and graph databases

artículo científico publicado en 2016

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

artículo científico

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

artículo científico publicado en 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). ⬇️

artículo científico publicado en 2018

Specifications of Standards in Systems and Synthetic Biology

artículo científico

Specifications of Standards in Systems and Synthetic Biology

artículo científico publicado en 2015

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

artículo científico publicado en 2016

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

artículo científico publicado en 2016

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

artículo científico publicado en 2018

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

scientific article published on 13 July 2019

Specifications of standards in systems and synthetic biology: status and developments in 2020

artículo científico publicado en 2020

Specifications of standards in systems and synthetic biology: status and developments in 2021

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022

artículo científico publicado en 2023

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024

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

artículo científico publicado en 2015

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

TAPP: Defining standard provenance information for clinical research data and workflows - Obstacles and opportunities

artículo científico publicado en 2023

The JWS online simulation database

artículo científico publicado en 2017

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

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

artículo científico publicado en 2019

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

artículo científico publicado en 2018

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

artículo científico publicado en 2020

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

artículo científico publicado en 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

artículo científico publicado en 2024

Toward Community Standards and Software for Whole-Cell Modeling

artículo científico publicado en 2016

Towards standardization guidelines for in silico approaches in personalized medicine

scientific article published on 24 July 2020

Lista de obras de Dagmar Waltemath

A brief history of COMBINE

A call for virtual experiments: accelerating the scientific process

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>

An algorithm to detect and communicate the differences in computational models describing biological systems

Annotation-based feature extraction from sets of SBML models

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

COMODI: an ontology to characterise differences in versions of computational models in biology

Combining computational models, semantic annotations and simulation experiments in a graph database

Controlled vocabularies and semantics in systems biology

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Democratizing knowledge representation with BioCypher

Evolution of computational models in BioModels Database and the Physiome Model Repository.

Exploring the evolution of biochemical models at the network level

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

Identifying frequent patterns in biochemical reaction networks - a workflow

Identifying frequent patterns in biochemical reaction networks - a workflow

Identifying frequent patterns in biochemical reaction networks - a workflow

Identifying frequent patterns in biochemical reaction networks: a workflow.

Improving the reuse of computational models through version control

Information Retrieval in Life Sciences: A Programmatic Survey

Initiatives, Concepts, and Implementation Practices of FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles in Health Data Stewardship Practice: Protocol for a Scoping Review

Kinetic Simulation Algorithm Ontology

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Minimum Information About a Simulation Experiment (MIASE)

Notions of similarity for computational biology models

Notions of similarity for systems biology models

Notions of similarity for systems biology models.

OMEX metadata specification (version 1.2)

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY

Open modeling and exchange (OMEX) metadata specification version 1.0.

Opportunities of Digital Infrastructures for Disease Management-Exemplified on COVID-19-Related Change in Diagnosis Counts for Diabetes-Related Eye Diseases

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.

Ranked retrieval of Computational Biology models

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

SBML Level 3 Package Proposal: Annotation

SBML Level 3: an extensible format for the exchange and reuse of biological models

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

STON: exploring biological pathways using the SBGN standard and graph databases

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). ⬇️

Specifications of Standards in Systems and Synthetic Biology

Specifications of Standards in Systems and Synthetic Biology

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Specifications of standards in systems and synthetic biology: status and developments in 2020

Specifications of standards in systems and synthetic biology: status and developments in 2021

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024

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

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

TAPP: Defining standard provenance information for clinical research data and workflows - Obstacles and opportunities

The JWS online simulation database

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

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

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

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Toward Community Standards and Software for Whole-Cell Modeling

Towards standardization guidelines for in silico approaches in personalized medicine