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List of works by Dagmar Waltemath

A brief history of COMBINE

A call for virtual experiments: accelerating the scientific process

scientific article

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

scientific article

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

scientific article published in 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

scientific article published on 21 October 2015

Annotation-based feature extraction from sets of SBML models

scientific article published in 2015

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

scientific article

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

scientific article published on 11 July 2016

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

scientific article

Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)

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

scientific article published on 01 January 2019

Democratizing knowledge representation with BioCypher

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

scientific article published on 12 April 2018

Exploring the evolution of biochemical models at the network level

scientific article published on 21 March 2022

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

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

scientific article published on 02 June 2016

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.

scientific article published on 3 July 2018

Improving the reuse of computational models through version control

scientific article published on 18 January 2013

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

scientific article published in 2021

Kinetic Simulation Algorithm Ontology

scholarly article

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

scientific article published on 9 August 2018

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)

scientific article

Notions of similarity for computational biology models

Notions of similarity for systems biology models

scientific article published on 14 October 2016

Notions of similarity for systems biology models.

scientific article published in September 2017

OMEX metadata specification (version 1.2)

scientific article published in 2021

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

scientific article published in 2010

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

scientific article published on 25 June 2020

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

scientific article published on 11 May 2022

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

scientific article (publication date: 2015)

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

scientific article published on 15 February 2018

Ranked retrieval of Computational Biology models

scientific article

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

scientific article

SBML Level 3 Package Proposal: Annotation

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

scientific article published on 01 August 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

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

scientific article published on 2 January 2017

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

scientific article

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

scientific article published on 04 September 2015

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

scientific article published in June 2015

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

scientific article published on 19 March 2018

Specifications of Standards in Systems and Synthetic Biology

scientific article published on 04 September 2015

Specifications of Standards in Systems and Synthetic Biology

scientific article published in June 2015

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

scientific article published on 18 December 2016

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

scientific article published in September 2016

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

scientific article published on 29 March 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

scientific article published on 29 June 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

scientific article published in March 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

scientific article

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

scientific article published on 28 April 2023

The JWS online simulation database

scientific article published on 27 January 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

scientific article published on 20 June 2019

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

scientific article published on 9 March 2018

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

scientific article published on 29 June 2020

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

scientific article published in 2021

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

scientific article published in March 2024

Toward Community Standards and Software for Whole-Cell Modeling

scientific article

Towards standardization guidelines for in silico approaches in personalized medicine

scientific article published on 24 July 2020

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