Dagmar Waltemath

About Dagmar Waltemath:

I am a computer scientist by training with a specialisation on database and information systems. Since December 2018 I am professor of Medical Informatics at the University Medicine in Greifswald, Germany, at the Institute of Community Medicine. My lab focuses on research data management in biomedicine, data integration across health care providers, and provenance of clinical research data items within clinical information systems. Furthermore, I am actively involved in COMBINE standardisation efforts (http://co.mbine.org). My lab will continue to develop methods and tools for model management in computational biology.

SEEK ID: https://fairdomhub.org/people/600

Location:  Germany

ORCID: https://orcid.org/0000-0002-5886-5563

Joined: 2nd Nov 2015

Expertise: Data Management, Databases, standards, model management, Information Retrieval, Semantic Enrichment, Provenance, Medical informatics, Data Integration

Tools: Computational Systems Biology, Data Management, Databases, Neo4J, SBML, SED-ML, Ontologies

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nfdi4health - German National Research Data Infrastructure for Personal Health Data

nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show ...

Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data

Web page: https://www.nfdi4health.de

German Association for Medical Informatics, Biometry and Epidemiology (GMDS)

The GMDS (Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie) is the German Association for Medical Informatics, Biometry and Epidemiology and is the only scientific organization in this field in Germany. It is the official national member society within the EFMI and IMIA and closely cooperates with related scientific societies.

Projects: GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"

Web page: https://gmds.de

COMBINE (Computational Modeling in Biology Network)

This is the exchange platform of the COMBINE network.

COMBINE is an initiative to coordinate the development of various community standards and formats for computational models: BioPax, CellML, NeuroML, Synthetic Biology Open Language (SBOL), Systems Biology Graphical Notation (SBGN), Systems Biology Markup Language (SBML), Simulation Experiment Description Markup Language (SED-ML).

Projects: COMBINE Multicellular Modelling, ModeleXchange initiative

Web page: http://co.mbine.org

The Digital Salmon

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted ...

Projects: GenoSysFat, DigiSal, SEEK tutorial for DigiSal

Web page: http://tinyurl.com/digisal

de.NBI Systems Biology Service Center (de.NBI-SysBio)

The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...

Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, CEPLAS – Cluster of Excellence on Plant Sciences

Web page: http://www.denbi.de

GenoSysFat

Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?

One option is ...

Programme: The Digital Salmon

Public web page: http://tinyurl.com/genosysfat

COVID-19 related studies and tools in Germany

This project bundles information about COVID-19 related studies and tools in Germany. It intends to provide an information hub for the different initiatives, their aims, their processes, standards and study protocols, as well as their available data and metadata. It is initiated by the German National Research Data Infrastructure for Personal Health Data (nfdi4health), a consortium that plans to establish a concept for a federated research data infrastructure for personal health data in Germany. ...

Programme: nfdi4health - German National Research Data Infrastructure for Personal Health Data

Public web page: https://www.nfdi4health.de/index.php/de/task-force-covid-19/

nfdi4health - German National Research Data Infrastructure for Personal Health Data

nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show ...

Programme: nfdi4health - German National Research Data Infrastructure for Personal Health Data

Public web page: https://www.nfdi4health.de

Start date: 1st Jul 2020

COMBINE Multicellular Modelling
No description specified

Programme: COMBINE (Computational Modeling in Biology Network)

Public web page: https://multicellml.org/

GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"

The GMDS project group bundles activities for health-related FAIR data infrastructures in the fields of biomedical research, clinical data management and medical informatics in Germany. It aims at providing a platform for information exchange about best practice for and implementation of FAIR data management in these fields and constructing a network of FAIR data managements providers in these fields. Through bridging between providers and potential users of such data management platforms within ...

Programme: German Association for Medical Informatics, Biometry and Epidemiology (GMDS)

Public web page: https://gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/

Start date: 28th Feb 2019

End date: 27th Feb 2022

de.NBI-SysBio

The Systems Biology Service Center of de.NBI (de.NBI-SysBio) provides bioinformatics support and a standards-based data management for systems biology projects, with focus on the provenance of experimental results and on the reproducibility of modeling experiments, as well as high-quality curated biochemical data to modelers and experimentalists. The node concentrates on two tools for the data management in life sciences research: SEEK, a catalogue for storage, registration and exchange of data ...

Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: Not specified

Example use cases

Public showcase and collection of training material

Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: http://www.denbi.de

Kinetics on the move - Workshop 2016

The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.

Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: http://www.h-its.org/event/kinetics-on-the-move/

Hands-on: Model Management in SEEK
Kinetics on the move - Workshop 2016
No description specified

Submitter: Ron Henkel

Studies: Hands-On: Tyson1991 - Cell Cycle 6 var

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

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Hands-On: Tyson1991 - Cell Cycle 6 var
Kinetics on the move - Workshop 2016
No description specified

Submitter: Ron Henkel

Investigation: Hands-on: Model Management in SEEK

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

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BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var
Kinetics on the move - Workshop 2016
No description specified

Submitter: Ron Henkel

Biological problem addressed: Cell Cycle

Investigation: Hands-on: Model Management in SEEK

Study: Hands-On: Tyson1991 - Cell Cycle 6 var

1 hidden item
SEDML for BIOMD0000000005
No description specified

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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2 hidden items
BIOMD0000000005 from BioModels Database
Kinetics on the move - Workshop 2016

This is BIOMD0000000005.

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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2 hidden items
DNA extraction from intestinal samples
GenoSysFat

Describes how the DNA was isolated from salmon intestinal samples before preparations of 16S rRNA gene amplicons for the Illumina MiSeq system.

Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Gareth Gillard, Arne Gjuvsland, Fabian Grammes, Hanne Hellerud Hansen, Thomas Harvey, Torgeir R. Hvidsten, Vitor Martins dos Santos, Dominic Nanton, Stuart Owen, Jacob Seilø Torgersen, Sandve Simen, Lars Snipen, Natalie Stanford, Kristil Sundsaasen, Kristina Vagonyte-Hallan, Dagmar Waltemath, Jesse van Dam, RAGNHILD ÅNESTAD, Sahar Hassani

Submitter: Inga Leena Angell

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The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

Abstract (Expand)

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together … researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers

Date Published: 29th Jun 2020

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status and developments in 2020
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology. …Not specified

Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 29th Jun 2020

Publication Type: Journal

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

Abstract (Expand)

Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating … datasets and integrating them into models involves a wide range of scientific expertise. As a result these datasets are often collected by one set of researchers, and exchanged with others researchers for constructing the models. For this process to run smoothly the data and models must be FAIR-findable, accessible, interoperable, and reusable. In order for data and models to be FAIR they must be structured in consistent and predictable ways, and described sufficiently for other researchers to understand them. Furthermore, these data and models must be shared with other researchers, with appropriately controlled sharing permissions, before and after publication. In this chapter we explore the different data and model standards that assist with structuring, describing, and sharing. We also highlight the popular standards and sharing databases within computational systems biology.

Authors: N. J. Stanford, M. Scharm, P. D. Dobson, M. Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep

Date Published: 12th Oct 2019

Publication Type: Journal

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational … modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

Authors: Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 13th Jul 2019

Publication Type: Journal

Harmonizing semantic annotations for computational models in biology
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

Abstract (Expand)

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability … and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.

Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

Date Published: 1st Mar 2019

Publication Type: Journal

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), FAIRDOM & LiSyM & de.NBI Data Structuring Training

Abstract

Not specified

Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath

Date Published: 29th Mar 2018

Publication Type: Journal

A brief history of COMBINE
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"

Abstract (Expand)

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and … to reproduce scientific results. Over the past two decades, a range of standards have been developed to facilitate the exchange and reuse of information in the domain of representation and modeling of biological systems. These standards are complementary, so the interactions between their developers increased over time. By the end of the last decade, the community of researchers decided that more interoperability is required between the standards, and that common development is needed to make better use of effort, time, and money devoted to this activity. The COmputational MOdeling in Biology NEtwork (COMBINE) was created to enable the sharing of resources, tools, and other infrastructure. This paper provides a brief history of this endeavor and the challenges that remain.

Authors: Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novere, David P. Nickerson, Falk Schreiber, Dagmar Waltemath

Date Published: 1st Dec 2017

Publication Type: InProceedings

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COVID-19 Disease Map

Abstract (Expand)

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special … issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.

Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath

Date Published: 12th Feb 2017

Publication Type: Not specified

An allosteric model of calmodulin explains differential activation of PP2B and CaMKII
Kinetics on the move - Workshop 2016

Abstract (Expand)

Calmodulin plays a vital role in mediating bidirectional synaptic plasticity by activating either calcium/calmodulin-dependent protein kinase II (CaMKII) or protein phosphatase 2B (PP2B) at different … calcium concentrations. We propose an allosteric model for calmodulin activation, in which binding to calcium facilitates the transition between a low-affinity [tense (T)] and a high-affinity [relaxed (R)] state. The four calcium-binding sites are assumed to be nonidentical. The model is consistent with previously reported experimental data for calcium binding to calmodulin. It also accounts for known properties of calmodulin that have been difficult to model so far, including the activity of nonsaturated forms of calmodulin (we predict the existence of open conformations in the absence of calcium), an increase in calcium affinity once calmodulin is bound to a target, and the differential activation of CaMKII and PP2B depending on calcium concentration.

Authors: M. I. Stefan, S. J. Edelstein, N. Le Novere

Date Published: 31st Jul 2008

Publication Type: Not specified

Positive cooperative binding of calcium to bovine brain calmodulin
Kinetics on the move - Workshop 2016

Abstract

Not specified

Authors: Thomas H. Crouch, Claude B. Klee

Date Published: 1st Aug 1980

Publication Type: Not specified

Hands-on Model Management in SEEK: Hint Task 4

Hint Task 4. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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Hands-on Model Management in SEEK: Hint Task 5

Hint Task 5. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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Hands-on Model Management in SEEK: Hint Task 9A

Hint Task 9A. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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Hands-on Model Management in SEEK: Hint Task 9B

Hint Task 9. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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Hands-on Model Management in SEEK: Example Paper

The paper by Tyson for the Hands-on Model Management in SEEK. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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Data and model Management in Systems Biology
de.NBI-SysBio, Kinetics on the move - Workshop 2016

Presentation at the 10th anniversary of SABIO-RK, Heidelberg 2016

Creator: Dagmar Waltemath

Submitter: Dagmar Waltemath

External Link
Hands-on Model Management in SEEK - Task sheet

Here you find the Tasks for todays Hands-on Model Management in SEEK session

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

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Improving the management of computational models.
FAIRDOM

Written by Martin Scharm (University of Rostock), Ron Henkel (University of Rostock), Dagmar Waltemath (University of Rostock), Olaf Wolkenhauer (University of Rostock, Stellenbosch University), and presented by Martin Scharm (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel, Martin Scharm (University of Rostock)

Submitter: Natalie Stanford

External Link
Reproducibility of model-based results: standards, infrastructure, and recognition.
FAIRDOM

Written and presented by Dagmar Waltemath (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Dagmar Waltemath

Submitter: Natalie Stanford

External Link
Reproducible and citable data and models: an introduction.
FAIRDOM

Prepared and presented by Carole Goble (University of Manchester), Wolfgang Mueller (HITS), Dagmar Waltermath (University of Rostock), at the Reproducible and Citable Data and Models Workshop, Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Wolfgang Müller, Carole Goble, Dagmar Waltemath

Submitter: Natalie Stanford

External Link
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