Expertise: Data Management, Python, Programming
Tools: Python
Projects: NL-Bioimaging FAIR Metadata Templates
Institutions: University of Leiden
https://orcid.org/0000-0002-0615-9616Expertise: Data Management, Plant sciences
Tools: MIAPPE
Expertise: Computer Science
Tools: Data Management
Projects: nfdi4health - German National Research Data Infrastructure for Personal Health Data
Institutions: University of Cologne
https://orcid.org/0000-0002-2140-4616Expertise: Public Health
Tools: Data Management
Christin is a project manager at DOCYET. She has a degree in social work, public health and medical ethics. In addition to her full-time professional work, she is a PhD candidate at the University of Bremen. She has training and certificates in data stewardship, project & change & hospital management. The following research and application areas fascinate her mostly: health-related data/infrastructure, FAIRification, robotics in medicine, health standards and digital health solutions.
Projects: FAIRDOM, BioCreative VII, The BeeProject, SDBV/HITS, Semantic Table Interpretation in Chemistry
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-7585-4479Expertise: Data analysis, Computational Systems Biology, Databases, Data Management, Table Curation
Tools: Machine Learning, Python, Java, standards, Data Integration
Expertise: Bioinformatics, Computational Systems Biology, Data Management, Databases, Python, R, Transcriptomics, Image analysis, Genomics, Molecular Biology, Microbiology, Data analysis, Genetics
Tools: qPCR, Isolation purification and separation, Genomics, Data Science, RNA / DNA Techniques, Transcriptomics, Microbiology, Molecular Biology, Databases
I am a biochemist & bio-informatician working in phytobacteriology at the Plant Sciences Unit of ILVO, the Flanders Research Institute for Agricultural, Fisheries and Food Research. The focus is on genomics-based research and diagnostics for Plant Health.
My expertise is 'wet-lab' work (microbiology, sequencing, molecular biology, design & validation of diagnostics assays using qPCR/LAMP, automatisation) and 'dry-lab' work such as bio-informatics/data analysis (e.g. scripting analysis ...
Projects: COVID-19 Disease Map
Institutions: Luxembourg Centre for Systems Biomedicine (LCSB)
https://orcid.org/0000-0003-3951-6680Expertise: Bioinformatics, Data Management, Data Integration
Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map, NMTrypI - New Medicines for Trypanosomatidic Infections, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation
Institutions: Kinetics on the move Workshop at HITS, Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Eastern Finland (UEF)
https://orcid.org/0000-0002-2801-8902Expertise: Data Management
Projects: MPIEvolBio-SciComp
Institutions: Max Planck Institute for Evolutionary Biology
https://orcid.org/0000-0002-2579-5546I'm heading the Scientific Computing Unit at Max Planck Institute for Evolutionary Biology in Plön, Germany. My interest is the application of high performance and high throughput computing in data processing, data analysis, and numerical simulations of dynamical processes. I have a background in Theoretical Physics with a Ph.D. from Rostock University (2008), where I studied analytical models and numerical simulations of extremely dense and hot matter.
After a postdoc at the Lawrence Livermore ...
Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Institutions: University Medicine of Greifswald
https://orcid.org/0000-0001-7838-9050Expertise: Medical informatics, Public Health, Data Management, Data Quality
Expertise: Bioinformatics, Biochemistry, Data Management
Tools: Bioinformatics, Data Management, Biochemistry and protein analysis
Data Steward for the Plant Biology and Breeding Division of INRAe (https://www.inrae.fr/en/divisions/bap)
Projects: COVID-19 Disease Map
Institutions: Golestan University of Medical Sciences
https://orcid.org/0000-0002-0773-1610Expertise: Microbiology, Parameter estimation, Curation, Data Management, Databases
Tools: Microbiology, Data Management
I would like to collaborate on the COVID-19 projects. I am currently a faculty member of the Infectious Diseases research center, at the Golestan University of Medical Sciences, Iran, and studying clinical information of patients with COVID-19. I am a microbiologist and can help other teams to evaluate the data obtained from COVID-19 cases.
Projects: COVID-19 Disease Map
Institutions: BIOASTER
Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Institutions: ZB MED - Information Centre for Life Sciences
https://orcid.org/0000-0001-5246-9351Expertise: Data Management, Databases, Dynamic modelling, Ontology
Tools: Data Management, Java, semantic web, linux, sparql, Jena
Projects: COVID-19 Disease Map
Institutions: Hospital del Mar Research Institute (IMIM)
https://orcid.org/0000-0002-9383-528XExpertise: Data Integration
Tools: DisGeNET, Data Management, Data Integration, Text Mining
Projects: COVID-19 Disease Map
Institutions: Biomax Informatics AG
Projects: GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"
Institutions: University Medical Center Göttingen
https://orcid.org/0000-0002-6307-3253Expertise: Data Management, Databases, Health Informatics, Data Integration
Tools: R, Docker, linux, Data Management
Researcher at the University Medical Center Göttingen, Department of Medical Informatics
Projects: EnzymeML, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling
Institutions: Beilstein Institut
https://orcid.org/0000-0002-8697-6842Expertise: Biochemistry, Project Management, electrophysiology
Tools: Data Management, standards, Databases
Project manager of STRENDA and MIRAGE @Beilstein-Institut
Projects: de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, MIX-UP, COVID-19 Disease Map, ERNEST Mapping Group Pilot Study, NMTrypI - New Medicines for Trypanosomatidic Infections, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling, ModeleXchange initiative, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation, Mass spectrometry proteomics for biomarker discovery, Thymidylate synthase dimer dissociation, WG1 - Compound libraries coordination and integration of compound design, WG2 - Integration of early phase studies and low environmental impact actions, WG3 - Coordination of in vitro-to-in vivo translation of OneHealth leads and candidates, WG4 - Integration of R&D process-environmental studies and translation in informed whitepaper, WG5 - Promote dissemination, WG6 - Promote the transfer of knowledge, SABIO-VIS, SDBV/HITS
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-9077-5664Expertise: Biochemistry, Databases, Data Management, Curation
Projects: pISA-tree, HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, tst, tst2
Institutions: National Institute of Biology, tst
https://orcid.org/0000-0002-1669-6482Expertise: Molecular Biology, Statistics, Bioinformatics, Mathematical and statistical modeling, Programming, Data analysisMathematical modellingBioinformaticsSystems biology, Data Management, Data analysis, Visualization, Data Integration, Computational Biology
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Molecular Biology, Python, R, Systems Biology, Data Integration
Computational Biologist and Biostatistician at Department of Biotechnology and Systems Biology, National Institute of Biology (NIB)
Projects: WG Infrastructure for Translational Research, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Translational Bioinformatics, Medical Biometry, Epidemiology, Medical Informatics
Institutions: University Medical Center Göttingen, University of Tübingen, University of Saarland
https://orcid.org/0000-0002-1505-594XExpertise: Programming, Bioinformatics, Data Management, Databases, Java, Python, R, standards, Data Integration
Tools: Python, Bioinformatics, Data Management, Databases, R, Java, Data Integration
Expertise: Data Management
Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato
Institutions: National Institute of Biology
https://orcid.org/0000-0003-4776-7164Projects: EmPowerPutida
Institutions: LifeGlimmer GmbH
Expertise: Data Management, Databases, Bioinformatics, Python, Java, Molecular Biology, Data Integration
Tools: Data Management
Computational Biologist
Projects: FAIRDOM user meeting
Institutions: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)
Expertise: Bioinformatics, Data Management, Python, R, Databases, RNA-Seq, secondary metabolites, gene clusters, Perl
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburgh
https://orcid.org/0000-0003-1756-3654Projects: FAIRDOM & LiSyM & de.NBI Data Structuring Training
Institutions: University of Rostock
Expertise: Data Management, Data Integration
Tools: COBRA toolbox
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomington
https://orcid.org/0000-0002-7440-2905Expertise: Mathematical modelling, Data Management, Software Engineering, Python, standards, c++
Research Associate in the Macklin Lab, School of Informatics, Computing, and Engineering. Indiana University, Bloomington, IN USA.
Projects: DigiSal, GenoSysFat, SAFE-Aqua, Unlock
Institutions: Wageningen University & Research
https://orcid.org/0000-0001-8172-8981Expertise: semantics, Software Engineering, R, Python, Java, Data Management, Databases, Genetics, Genomics, Microbiology
Projects: Not specified
Institutions: Not specified
Expertise: Data Management, Databases
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, INDIE - Biotechnological production of sustainable indole, _p_stRT, Public project, Playground, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Institutions: National Institute of Biology, NewHorizon
https://orcid.org/0000-0001-7484-6031Postdoctoral researcher at Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg
Projects: HUMET Startup, COVID-19 Disease Map
Institutions: Centro de Investigación Príncipe Felipe, Fundación Progreso y Salud
https://orcid.org/0000-0003-3318-120XExpertise: Bioinformatics, Data Management, Mathematical modelling, Genomics, Genetics, Transcriptomics, Systems Biology, Microarray analysis, Data Integration
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Genetics, Genomics, R, Systems Biology, Transcriptomics, Java
My scientific interests revolve around functional genomics, systems biology and the development of algorithms and software for the analysis of high-throughput data (mainly, but not restricted to, Next Generation Sequencing) and its application to the relationship between genotype and phenotype, mainly oriented to personalized and precision medicine. I am especially interested in the study of disease mechanisms and drug action mechanisms, drug repositioning and the definition of mechanism-based ...
Projects: FAIRDOM user meeting
Institutions: SYSBIO - Centre of Systems Biology
https://orcid.org/0000-0002-6566-2844Expertise: Bioinformatics, Data Management, Databases, Microarray analysis, Systems Biology
Projects: SulfoSys - Biotec
Institutions: University Bielefeld
Expertise: Bioinformatics, Data Management, Transcriptomics, Proteomics, Metabolomics, Databases, Data Integration
Tools: Bioinformatics, Data Management, Databases, R, Java
Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map
Institutions: Kinetics on the move Workshop at HITS, Luxembourg Centre for Systems Biomedicine (LCSB)
https://orcid.org/0000-0003-1473-370XExpertise: Data Management, Molecular Biology, Systems Biology, Curation
Tools: SBGN, CellDesigner, MIRIAM, SBML, Data Science
Scientific Project Manager at Luxembourg Centre for Systems Biomedicine, University of Luxembourg http://lcsb.uni.lu
Projects: Kinetics on the move - Workshop 2016
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: computational structural biology
Tools: Molecular Dynamics, Data Management, Databases, Data Science, web development, Ruby on Rails, Python
Research associate at HITS, software developer
Systems biology for salmon farming is what I do. I lead the DigiSal project (http://tinyurl.com/digisal), whose full title is "Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture". DigiSal is part of Digital Life, the first call dedicated to systems biology by the Research Council of Norway. I'm also one of the lead modellers in GenoSysFat (http://tinyurl.com/genosysfat), working to improve the omega-3 content of salmon farmed on sustainable feeds by ...
Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, MS_DILI, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, ModeleXchange initiative, SDBV/HITS, EDITH (Ecosystem Digital Twins in Health) test project
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-8683-7084Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team. Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and ...
Projects: SysMO-LAB, de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: Biochemistry, Biology
Tools: Databases, Data Management
I'm a biologist working in the field of scientific datases as a biocurator.
Projects: de.NBI-SysBio, GenoSysFat, Kinetics on the move - Workshop 2016, Example use cases, COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Institutions: University of Rostock, University of Greifswald, University Medicine of Greifswald
https://orcid.org/0000-0002-5886-5563I 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 ...
Projects: FAIRDOM
Institutions: University of Manchester - Department of Computer Science
https://orcid.org/0000-0003-1604-1512Expertise: Molecular Biology, Bioinformatics, Genomics, metagenomics, standards, Ontology
Tools: Bioinformatics, Data Management
FAIRDOM Project Wrangler
Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-4958-0184Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Institute of Cytology and Genetics
I am a biomodeler, PhD student. Actually, I've graduated from Novosibirsk State University on two specialities: my bachelor diploma is done in computer science and the master thesis is defended in information biology. So, I'm kind of drifting towards biology. I am a part of the Haploid Evolutionary Constructor project. Our research group studies are dedicated to the simulation of prokaryotic communities. Personally, I am involved into the simulation of spatially distributed bacterial communities ...
Projects: IMOMESIC
Institutions: German Cancer Research Center (DKFZ)
Projects: FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, FAIRDOM user meeting
Institutions: University of Zürich, ETH Zurich, Manchester Centre for Integrative Systems Biology, University of Manchester
Expertise: Bioinformatics, Proteomics, Genomics
Tools: Matlab, Microarray analysis, Data Management, Computational Systems Biology, Perl, Python
I hold a Medical Doctor Diploma (Lviv, Ukraine) with the specialization in General Medicine. After the graduation from the Post Graduate Program in Bioinformatics at the Seneca College/York University (Toronto, Canada), I successfully participated in the number of scientific projects conducted at the University of Toronto (Canada) and the Toronto East General Hospital (Canada).
I obtained the PhD in Bioinformatics at the Swiss Institute of Bioinformatics (Geneva, Switzerland). As a PhD student, ...
Projects: de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Rostock
Expertise: Data Management, Databases
Tools: MySQL, Java, graphdatabase, Neo4J
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, Kinetics on the move - Workshop 2016
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: Software Engineering, Data Management, Databases
Tools: Ruby on Rails, MySQL, HTML, Ruby, Java, Javascript
Software developer for FAIRDOM
Projects: KOSMOBAC
Institutions: University of Aberdeen
I am a research technician at the Institute of Medical Science in Aberdeen, working for Prof. Ian Booth. The topic of our workpackage deals with K+ homostasis in Escherichia coli. I am working with the protein KefF, a regulatory subunit of the potassium channel KefC.
Institutions: University of Tuebingen, University of Tübingen
Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
https://orcid.org/0000-0001-6096-1354Expertise: Mathematical modelling, Data Management, coupling metabolome and environome, rapid sampling experiments, dynamics of biological networks, bioreactor models, Optimal experimental design, Dynamic optimization., Nonlinear Dynamics, Data Integration, Parameter estimation
Tools: SBML, Matlab, Fermentation, Material balance based modeling, stimulus response experiments, evaluation of process dynamics, continuous cultivation, Dynamic modelling
Process engineer, modeling biological systems since 1985.
Projects: STREAM
Institutions: University of Warwick
Research fellow in Bioinformatics at the Warwick Systems Biology Centre, University of Warwick.
Working on high throughput data analysis (microarray data, next generation sequencing) and data integration (database management, text-mining, gene annotation via public databases)...
Projects: SUMO
Institutions: University of Stuttgart
Expertise: Mathematical modelling, Data Management, Systems Biology, Parameter estimation
Tools: SBML, ODE, Matlab, Mathematica
Former: PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMO-DB pals for SUMO. Now: Industrial affiliation
Projects: SulfoSys, PSYSMO, SulfoSys - Biotec, EbN1 Systems Biology
Institutions: University of Braunschweig
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting, FAIRDOM Community Workers
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-2130-0865Expertise: Software Engineering, Data Management, Software Architecture, REST, Cloud computing, Agile development, Docker
Tools: Databases, Java, Workflows, Web services, Taverna, Ruby, Ruby on Rails, linux, J2EE, semantic web, AWS, Research Objects, Docker
Senior Research Software Engineer and Architect working at the University of Manchester within the FAIRDOM team.
Leads the development of FAIRDOM SEEK and RightField.
Projects: TRANSLUCENT
Institutions: Humboldt-Universität zu Berlin
Expertise: Bioinformatics, Data Management
I created this for all SysMo Modellers
http://www.semanticsbml.org/aym Annotate Your Model
There you can annotate your non SBML models with biological terms (MIRIAM annotations). As a cool extra you can view you model source code with inserted biological infomation.
Together with this http://www.semanticsbml.org/semanticSBML you can serach for similar BioModels. The similarity search is based on MIRIAM annotations that are attached to you model. AYM also allows you to create annotations without ...
Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems. I am a PAL and I am looking forward to communication with other SYSMO members.
Projects: SysMO DB, HUMET Startup, FAIRDOM, Consensus Hallmark Annotation, NL-Bioimaging FAIR Metadata Templates, FAIR Functional Enrichment, Benefit for All FAIR Data
Institutions: University of Leiden, LIACS
https://orcid.org/0000-0002-1279-5133Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies, semantic web
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, OLCIR: Optimization of Lung Cancer Therapy with Ionizing Radiation, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, CC-TOP, BioCreative VII, MESI-STRAT Review, SDBV/HITS, MESI-Review 2024
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology, University of Rostock, University of Innsbruck
https://orcid.org/0000-0003-3540-0402Expertise: Genetics, Molecular Biology, Bioinformatics, Data Management, Transcriptomics, semantics, Curation, Ontology, Data Modelling
Tools: Cell and tissue culture, Databases, Chip-chip, BioMart, Protege, RightField, SEEK
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In **[SySMO-DB ...
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, BioCreative VII, SDBV ephemeral data exchanges, The BeeProject, SDBV/HITS, MESI-STRAT Review, MESI-Review 2024, DeepCurate
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-4980-3512I am group leader of the SDBV (Scientific Databases and Visualisation) group at the HITS gGmbH, the Heidelberg Institute for Theoretical Studies.
I am interested in finding data. Starting with my master's thesis I have always worked on how to store data in a way that you can find it, and how to make sense out of data that has been stored.
Within FAIRDOM I find interesting to help people to store their data in a way that they make sense even after years.
Projects: MOSES
Institutions: Medical University Vienna
Expertise: Bioinformatics
Tools: Data Management, Computational and theoretical biology, Transcriptomics, Perl, Microarray analysis, R, PHP, SQL
General Bioinformatics
Projects: SysMO DB, FAIRDOM, FAIRDOM user meeting, COVID-19 Disease Map
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-1219-2137Expertise: Software Engineering, semantics, VREs, standards, Distributed Systems
Tools: Data Management, Workflows, semantic web, Web services, Ontologies, web development
Professor of Computer Science University of Manchester Co-Director of the FAIRDOM Initiative and co-leader of the SEEK4Science Platform Development Deputy Head of Node ELIXIR-UK Co-lead ELIXIR Interoperability Backbone Platform Lead ISBE WP Data and Model Management Data lead SynBioChem Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals
The NFDI4Health Task Force COVID-19 Metadata Schema Mapping (Metadata Schema Mapping) contains a list of properties describing a resource being registered in the Study Hub of the NFDI4Health Task Force COVID-19 (Study Hub) and how those properties align with other standards (FHIRE, CDISK, DRKS, ITRCP)
Creators: None
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The NFDI4Health Task Force COVID-19 Metadata Schema (Metadata Schema) contains a list of properties describing a resource being registered in the Study Hub of the NFDI4Health Task Force COVID-19 (Study Hub).
Creators: Aliaksandra Shutsko, Carsten Oliver Schmidt, Johannes Darms, Martin Golebiewski, Moritz Lehne, Matthias Löbe, Sophie Klopfenstein, Carina Nina Vorisek
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT pipeline
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Supplementary Table S2 - Detailed de novo assemblies information table. Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation. Layer _p_stRT/_I_STRT/_S_02_denovo/reports/
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies. Raw and processed reads summary. Layer _p_stRT/_I_STRT/ _S_01_sequences/reports
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
How to connect to the FAIRDOM SEEK with the collection of their APIs.
Creators: None
Submitter: Andrej Blejec
Creator: Martin Golebiewski
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Metabolic networks with gene expression are researched under very different banners with different techniques. For example, there are the dynamic enzyme-cost Flux Balance Analysis (deFBA) [1], conditional Flux Balance Analysis [2], Metabolism and Expression models (ME models) [3], Resource Balance Analysis [4], etc. At their core, these methods can all understood as Resource Allocation Models (RAM) and while investigating their potential and their results, we encountered the problem of sharing ...
Creators: Henning Lindhorst, Alexandra-M. Reimers
Submitter: Henning Lindhorst
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll, Špela Baebler, Kristina Gruden
Date Published: 21st Nov 2021
Publication Type: Journal
DOI: 10.1101/2021.11.18.468977
Citation: biorxiv;2021.11.18.468977v2,[Preprint]
Abstract (Expand)
Author: Martin Golebiewski
Date Published: 2019
Publication Type: InBook
DOI: 10.1016/B978-0-12-809633-8.20471-8
Citation: Encyclopedia of Bioinformatics and Computational Biology,pp.884-893,Elsevier
Abstract (Expand)
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
PubMed ID: 31602618
Citation: Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17.
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/845818
Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Abstract
Editor:
Date Published: 24th Oct 2017
Publication Type: Not specified
Citation: Knopp C. Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung [Bachelorarbeit]. Göttingen: Georg-August-Universität; 2017.
Abstract
Authors: Wolfgang Müller, Meik Bittkowski, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig
Date Published: 1st Mar 2017
Publication Type: Journal
DOI: 10.1007/s13222-016-0243-4
Citation: Datenbank Spektrum 17(1):21-28
Abstract (Expand)
Authors: D. Nickerson, K. Atalag, B. de Bono, J. Geiger, C. Goble, S. Hollmann, J. Lonien, W. Muller, B. Regierer, N. J. Stanford, M. Golebiewski, P. Hunter
Date Published: 7th Apr 2016
Publication Type: Not specified
PubMed ID: 27051515
Citation: Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103.
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Keynote presented at the workshop FAIRe Data Infrastructures, 15 October 2020 https://www.gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/workshop-2020/
Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility ...
Creator: Carole Goble
Submitter: Carole Goble
Introductory talk given by Olga Krebs in the Department of Chemical Engineering at the University of Rovira i Virgili on 19th of July 2017
Creator: Olga Krebs
Submitter: Olga Krebs
Introductory talk given by Olga Krebs in the Department of Chemical Engineering at the University of Rovira i Virgili on 19th of July 2017
Creator: Olga Krebs
Submitter: Olga Krebs
Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016
Creators: Olga Krebs, Carole Goble, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford
Submitter: Olga Krebs
Talk given by Sergey Lashin from Institute of Cytology and Genetics, Novosibirsk, Russia
Creators: Sergey Lashin, Alexandra Klimenko
Submitter: Olga Krebs
Introduction to RightField and Demo were presented at the Virtual Liver Network PALs meeting on 31st of October in Hünfeld, Germany
Creators: Olga Krebs, Stuart Owen, Katy Wolstencroft
Submitter: Olga Krebs
Issues and considerations for data management as SysMO projects approach the end of their funding
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
The Research Data Alliance (RDA) is a volunteer community of over 10,500 professionals from 145 countries across the globe. In less than two months, the community responded to an urgent call for action and defined much needed, comprehensive recommendations and guidelines for data sharing under the present COVID-19 circumstances.
Creators: Martin Golebiewski, see full list of members of the RDA COVID-19 working group: https://www.rd-alliance.org/node/68704/members
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This is the fifth and final draft of the Recommendations and Guidelines from the RDA COVID-19 working group, and is open for public comment until 8th of June 2020. Following the open period, feedback will be considered and then the WG will seek endorsement of the document from the RDA governance bodies prior to final publication.
Creators: Martin Golebiewski, see full list of members of the RDA COVID-19 working group: https://www.rd-alliance.org/node/68704/members
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Data Management Plan (v.1.0) of the project CEPOPA.
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
pISA-tree: Standard project directory tree (ISA-tab compliant) - NIB-SI/pISA https://github.com/NIB-SI/pISA/
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_04_stPanTr
Creators: Maja Zagorscak, Ziva Ramsak
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_03_stCuSTr
Creators: Maja Zagorscak, Ziva Ramsak
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Kristina Gruden, Marko Petek, Ziva Ramsak, Anna Coll Rius
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Andrej Blejec
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays