Wolfgang Müller

The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.

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. ...

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 ...

We will contribute to the LiSyM Research Network an open source, freely available and reproducible multiscale model of the human liver from single cell metabolism to whole liver function. The model will be available in existing standards of systems biology, provide standardized interfaces for data integration and be fully annotated to available biological, medical and computational ontologies. All data, models and source code will be shared within the LiSyM Research Network and made available to ...

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.

Multi-level mathematical modeling of erythropoiesis for optimized expansion of erythroid progenitor cells and improved treatment regimes

Systems Biology studies the properties and phenotypes that emerge from the interaction of biomolecules where such properties are not obvious from those of the individual molecules. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex ...

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 ...

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 ...

Here we share resources and best practices to develop a disease map for COVID-19. The project is progressing as a broad community-driven effort. We aim to establish a knowledge repository on virus-host interaction mechanisms specific to the SARS-CoV-2. The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence.

FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.

The Integrated Platform for Endocrine Disruptor Risk Assessment (SNAPPER) project will propose solutions based around three core philosophies: Integrated Science: Integration of knowledge from a complete pipeline of systems biology into a holistic yet mechanistic framework that enhances the understanding both of endocrine biology and of adverse effects due to externally induced disruption of the body’s endocrine system. The pipeline includes in vivo, in vitro, and in silico data resulting both ...

The purpose of this project is to exchange public and private research data that is not attached to "normal" projects together with SDBV via the FAIRDOMHub.

One example of a ReStoRunT sheet.

This file is part of a tutorial for the Gesellschaft für Ökologie and the NFDI4Biodiversity.

The purpose of this is using it in ModelXChange.

This table validation code is about simplifying validation of templates for end users. The main use case is an experimental scientist Elie sharing data with a Bioinformatician Bob. Elie and Bob agree to use a common template. This code enables Bob to provide Elie with a validator that checks if Elie's data conforms to the template. Making such a template check should be simple, using the checker should be simple, too. We seek to fill both requirements.

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling. The publication for the introduction and analysis of the benchmark problem collection is available at https://academic.oup.com/bioinformatics/article/35/17/3073/5280731.

Report of the Data Management Foundry Workshop, 19th-20th of March, 2012, Vienna, Austria

a test file

Participants of 2nd FAIRDOM PALs meeting in Munich

FAIRDOM User Meeting Introduction

SEEK functionalities presented by Olga Krebs

Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016

Written and presented by Wolfgang Müller (HITS) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

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.

Presentation of data management concepts for ERASysAPP projects at IMOMESIC kick off meeting on 8 th of May 2015 in Heidelberg. Part I presented by Olga Krebs

Carole Goble's talk at ERASysAPP - EXCHANGE Networking and Info Day for research projects of the first ERASysAPP call (a day before PALs meeting)

Poster presented at SWAT4LS - Semantic web applications and tools for life science- in Berlin at 10 of december 2014 by Olga Krebs

Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.

The talk presented by Carole Goble and Wolfgang Mueller at the SysMO evaluation conference 2013 in Berlin.

SEEK at ICSB 2012 (presented by Olga Krebs)