Projects: C19DM - Macrophage logical model
Institutions: Norwegian University of Science and Technology

Expertise: Systems Biology, Bioinformatics, Immunology, Molecular Biology
Tools: GINsim, Cytoscape, Computational and theoretical biology, Databases, data modeling
Projects: COVID-19 Disease Map
Institutions: University of Surrey

Reader (Professor) of Systems Biology; Executive Director for the International Society of Systems Biology (ISSB); Editor-in-Chief of Current Opinion in Systems Biology (Elsevier).
Projects: COVID-19 Disease Map
Institutions: Fundación Progreso y Salud

Projects: COVID-19 Disease Map
Institutions: MRC-University of Glasgow Centre for Virus Research

Expertise: Modeling, Bioinformatics, Systems Biology
Tools: R
Bioinformatician / Computational Biologist
Projects: CoolWine
Institutions: Norwegian University of Science and Technology
Expertise: Systems Biology
Tools: network theory, FBA, R, Python, Statistics
PhD candidate working on the CoolWine project
Projects: COVID-19 Disease Map
Institutions: Biomax Informatics AG
Projects: COVID-19 Disease Map
Institutions: University of Tübingen

Expertise: Curation, Computational Systems Biology, Constraint-based Modelling, Systems Biology
Tools: SBML, Python, cobrapy toolbox, CellDesigner, libSBML, jupyter notebooks
Projects: COVID-19 Disease Map
Institutions: University of Tübingen

Expertise: Systems Biology, Computational Systems Biology, Databases, Dynamic modelling, Java, Mathematical modelling, Metabolic Engineering, Disease Maps, Curation, Modeling, Data Integration, Constraint-based Modelling, Parameter estimation
Tools: SBML, SBGN, SBGNML, JSBML, Jupyter, Python, cobrapy toolbox, SBSCL, InSilico, Kinetic Modeling
Andreas Dräger is the assistant professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens at the University of Tübingen in Germany. His group aims to combat the spreading antibiotics resistances by using mathematical modeling and computer simulation of bacterial systems up to entire microbiomes and host-pathogen interactions. In doing so, his group actively contributes to the advancement of various COMBINE standards.
Expertise: Systems Biology, SBML, Java, Python, Machine Learning, Mathematical modelling, SBGN, Curation
Tools: CellDesigner, SBML, SBGN
Projects: HUMET Startup, COVID-19 Disease Map, C19DM-Neo4j
Institutions: European Institute for Systems Biology and Medicine, Luxembourg Centre for Systems Biomedicine (LCSB)

Expertise: Systems Biology, Systems Medicine, Disease Maps, Systems Biology Graphical Notation
Tools: SBGN, CellDesigner, SBGN-ED, Newt Editor
Projects: COVID-19 Disease Map
Institutions: Monash University

Expertise: standards, Systems Biology, Bioinformatics, Computational Systems Biology, Java, Python, SBGN
Tools: SBGN-ED
Projects: COVID-19 Disease Map
Institutions: Yenepoya University
Expertise: Biochemistry, Data analysis, Systems Biology, Data Integration
Tools: Proteomics, Systems Biology, Molecular Biology, Bioinformatics, Data Integration
Projects: COVID-19 Disease Map
Institutions: Universität Konstanz
Projects: COVID-19 Disease Map
Institutions: Barcelona Supercomputing Center

I completed my BSc in Biology and MSc in Cell Biology by the University of Valencia. During my last undergrad year I participated in synthetic biology’s iGEM competition where I dove in the use of models in Biology, which pushed me to pursue a PhD in the Department of Applied Mathematics in the Technical University of Valencia.
My research on Metabolic Engineering of hydrogen in cyanobacteria led me to be visiting researcher at Uppsala University, Denmark Technical University and EMBL Heidelberg.
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Expertise: Biochemistry, Cell biology, Data analysis, Dynamic modelling, Systems Biology, Image analysis, Genetics, Molecular Biology, R, SBML, Curation, Quantitative Biology, Physical Chemistry
Tools: Biochemistry and protein analysis, Bioinformatics, Systems Biology, SBML, R, ODE, Molecular biology techniques (RNA/DNA/Protein), Genetics, Dynamic modelling, Computational and theoretical biology, CellDesigner, Parameter estimation
Projects: COVID-19 Disease Map
Institutions: Luxembourg Centre for Systems Biomedicine (LCSB)

Expertise: Biological knowledge managament, Systems Biology, Biocuration
Tools: CellDesigner, Cytoscape, Python, Shell scripting, NetworkX, Protein2GO
Projects: CEPLAS – Cluster of Excellence on Plant Sciences
Institutions: Heinrich Heine University of Düsseldorf

Roles: Postdoc
Expertise: R, Data Management, Data analysis, Metabolomics, Transcriptomics, Systems Biology, Computational Systems Biology, Bioinformatics
Tools: Data Management, Systems Biology, R, Transcriptomics, Bioinformatics
Tools: Systems Biology, R
Projects: ComPASs - Common Pathways in Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA), miRiAD - exploring the role of microRNAs in T cell function and anti-viral defence, LungCARD - Blood test for clinical therapy guidance of non-small cell lung cancer patients
Institutions: RNA Systems Biology Lab - BioISI/FCUL
Expertise: Bioinformatics, Systems Biology
Expertise: biocatalysis, Molecular Biology, Systems Biology
Tools: screening assays, enzymatic synthesis, enzyme engineering
Professor- University Clermont Auyvergne (UCA) - Institute of Chemistry of Clermont-Ferrand (ICCF)
Projects: PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University of Groningen
I work as a project manager for the Innovative Training Network PoLiMeR - Polymers in the LIver: Metabolism and Regulation funded by the EU. In addition I am a project manager for the UMCG Research BV where I support scientist in the pre-award phase with writing their proposals and in the post-award phase with managing their awarded projects.
Projects: SulfoSys, SulfoSys - Biotec, HOTSOLUTE, Computational pathway design for biotechnological applications, ScyCode
Institutions: University Duisburg-Essen, Universitity Duisburg-Essen

Roles: Project Coordinator, Vice Coordinator
Expertise: Carbohydrate Metabolism of Archaea, Reconstruction of metabolic pathways, Regulation of carbohydrate metabolism, Archaeal physiology, Hyperthermophiles, Thermoacidohiles, Biotechnology
Tools: Biochemistry, Molecular Biology, Microbiology, Physiology, Systems Biology
Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.
Archaea possess many novel enzymes and pathways and our aim is
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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
Institutions: National Institute of Biology

Roles: PhD Student
Expertise: 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, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
Institutions: Latvia University of Agriculture
Roles: Postdoc
Expertise: Python, Systems Biology, Dynamic modelling, Mathematical modelling
Tools: COBRA toolbox, cobrapy toolbox, Python, SBML, Copasi, Computational Systems Biology
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

Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, FAIRDOM user meeting, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato
Institutions: National Institute of Biology

Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Projects: NTNU Health Druglogics, Colosys
Institutions: Norwegian University of Science and Technology

Roles: PhD Student
Expertise: Systems Biology, Computational Biology
Projects: MESI-STRAT, PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University of Groningen, University of Innsbruck
Prof. Dr. Kathrin Thedieck
MESI-STRAT Coordinator
Leader WP8 – Project Coordination
Projects: INCOME, COVID-19 Disease Map
Institutions: ICB Helmholtz Center Munich, University of Bonn

Expertise: Mathematical modelling, Systems Biology, Parameter estimation
I studied Engineering Cybernetics at the University of Stuttgart and the University of Wisconsin, Madison. After my graduation, I started my PhD studies in systems biology for which I received a Ph.D. degree in 2013. A few months later I became team leader at the Institute of Computational Biology at the Helmholtz Zentrum München. Since August 2015, I lead an independent junior research group at the Helmholtz Zentrum München.
My research focuses on the development of methods for the data-driven
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Projects: Millar group, PlaSMo model repository, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development, Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
Institutions: University of Edinburgh, Heinrich Heine University of Düsseldorf

Roles: Postdoc
Expertise: circadian rhythms, Systems Biology, arabidopsis thaliana, Synthetic Biology, Time Series Analysis, photobiology, NanoLUC, LUC, Automation
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

Roles: Project Coordinator, Vice Coordinator
Expertise: circadian rhythms, arabidopsis thaliana, Mathematical modelling, Data Management, Molecular Biology, Genetics, Deterministic modelling of gene regulation networks, Systems Biology
Tools: Transcriptomics, Proteomics, Deterministic models, Stochastic models, SBML
Projects: WineSys, INBioPharm, BioZEment 2.0, CoolWine, Auromega
Institutions: Norwegian University of Science and Technology

Projects: PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, Light and plant development, Light control of leaf development
Institutions: University of Edinburgh

Roles: Postdoc
Expertise: arabidopsis thaliana, caenorhabditis elegans, circadian rhythms, chronobiology, Transcriptomics, splicing, alternative splicing, R, photobiology, plant architecture, leaf development
Tools: Molecular Biology, Molecular biology techniques (RNA/DNA/Protein), R, Systems Biology, Transcriptomics, Bioinformatics, Databases, Genetics, Plant biology, C. elegans biology
Projects: SAFE-Aqua, Biomics Projects
Institutions: Institut Pasteur

Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, DigiSal, WURSynBio, INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research

Expertise: Metabolic modelling, Systems Biology, Transcriptomics, R, SBML
Associate Professor at Wageningen University & Research
Roles: Postdoc
Expertise: Mathematical modelling, Systems Biology, Parameter estimation
Tools: Dynamic modelling, Matlab, ODE, Parameter estimation
Projects: EmPowerPutida
Institutions: Wageningen University & Research

I'm currently a PhD student in Laboratory of Systems and Synthetic Biology in Wageningen University & Research. My project involves using genome scale metabolic modelling to understand and improve chemical production capacities of microorganism.
Projects: EmPowerPutida
Institutions: LifeGlimmer GmbH
Expertise: Bioinformatics, Systems Biology, Transcriptomics, R, Genomics, Proteomics, Databases, Data Integration
Tools: Bioinformatics, Molecular Biology, Computational Systems Biology
Computational Biologist and App Designer @LifeGlimmer
Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, WURSynBio
Institutions: Wageningen University & Research

Roles: PhD Student
Expertise: Bioinformatics, Systems Biology, Agent-based modelling, Dynamic modelling, Python, Java, R, pathogen host interaction, Molecular Biology
Tools: Copasi, libRoadrunner, Python, R, semantic web
I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model.
I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation
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Expertise: Transcriptomics, Systems Biology, plant, Data Integration
Projects: SBEpo - Systems Biology of Erythropoietin
Institutions: German Cancer Research Center (DKFZ)

Roles: PhD Student
Expertise: Mathematical modelling, Single Cell analysis, Cell biology, Molecular Biology
Tools: Biochemistry, Systems Biology, Matlab, R
Projects: HUMET Startup, COVID-19 Disease Map
Institutions: Bilkent University

Expertise: Bioinformatics, Systems Biology, SBGN standard, Network Visualization, Graphical Editors
Tools: SBGNViz, cBioPortal, PathwayMapper, ChiBE, Newt Editor
Associate Professor for Systems Biomedicine, Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Projects: Not specified
Institutions: Not specified
Projects: HUMET Startup, EraCoBiotech 2 nd call proposal preparation, COVID-19 Disease Map
Institutions: geneXplain GmbH

Expertise: Systems Biology, promoters and anhancers, gene regulation, signal transduction, drug targets
Tools: geneXplain platform, BioUML, R, c++
Alexander Kel received his Ph.D. in Bioinformatics, Molecular Biology and Genetics in 1990. He studied biology and mathematics at Novosibirsk State University and obtained his M.S. in biology with special focus on mathematical biology in 1985. He worked for 15 years at the Institute of Cytology and Genetics, Russia (ICG) holding positions as a programmer, scientist, senior scientist and Vice-Head of the Laboratory of Theoretical Molecular Genetics. In 1995, he won the Academician Belaev Award.
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Projects: HUMET Startup, COVID-19 Disease Map
Institutions: Centro de Investigación Príncipe Felipe, Fundación Progreso y Salud

Expertise: 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
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Expertise: chromatin, Epigenetics, nuclear organisation, DNA repair
Tools: quantitative microscopy, Biochemistry, Systems Biology, Cell biology
POSITION
I am an emeritus professor in Biochemistry at the University of Amsterdam (retired 2010).
RESEARCH
My research focussed on the human chromatin in its natural environment, i.e. the nucleus of cultured living human cells.
Aspects, such as the dynamic folding of the chromatin fiber inside the nucleus and local chemical modification of histones and DNA at genetic loci, are the physical and chemical basis for epigenetic regulation of gene expression. In my group we worked parallel on human
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I am had of the Research Group PiDOMICS which aims at the identification of human biomarkers for fungal infection using omics-data. Moreover, I am PI Infrastructure project of the Collaborative Research Center / Transregio 124 Pathogenic fungi and their human host: Networks of Interaction - FungiNet. Thereby my expertise is the implementation and usage of pipeline for OMICS (genome, transcriptome, protoem) data analysis, as well as data-warehouses for visualizing these data.
Projects: FAIRDOM user meeting
Institutions: SYSBIO - Centre of Systems Biology

Expertise: Bioinformatics, Data Management, Databases, Microarray analysis, Systems Biology
Projects: FAIRDOM user meeting
Institutions: Peter MacCallum Cancer Centre
Roles: PhD Student
Expertise: Systems Biology, Transcriptomics, Genomics
Tools: Systems Biology, Transcriptomics, Computational Systems Biology, Bioinformatics, R
Projects: FAIRDOM user meeting
Institutions: KAIST
Roles: PhD Student
Expertise: Cell biology, Molecular Biology, Cancer, Stem cell
Tools: Boolean modeling, Systems Biology
Projects: IMOMESIC, FAIRDOM user meeting, Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III)
Institutions: German Cancer Research Center (DKFZ)

Roles: Postdoc
Expertise: Mass spectrometry (LC-MS/MS), Proteomics, Systems Biology
Roles: PhD Student
Expertise: Corynebacterium glutamicum, Systems Biology, Stoichiometric modelling, Automation, Bioreactor cultivation
Tools: Matlab, COBRA toolbox, Liquid handling systems, Automation
PhD student @ "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany
Team leader "Quantitative Microbial Phenotyping"
Institute of Bio- and Geosciences, IBG-1: Biotechnology
Forschungszentrum Jülich GmbH
52425 Jülich, Germany
POSITION
Prof. Dr. Natal van Riel is Professor in Computational Modelling at the Academic Medical Center - University of Amsterdam (AMC - UvA) and Associate Professor in Systems Biology and Metabolic Diseases at the Department of Biomedical Engineering of the Eindhoven University of Technology (TU/e).
RESEARCH
My research applies mathematical modelling and computation to study metabolic diseases, in particular Metabolic Syndrome and co-morbidities. Systems biology approaches are developed for
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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)

Expertise: 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, CausalDB, COMBINE Multicellular Modelling, Colosys, NTNU Health Druglogics
Institutions: Kinetics on the move Workshop at HITS, Norwegian University of Science and Technology

Expertise: Bioinformatics, Systems Biology, SBGN standard
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
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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
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Data 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
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Roles: Postdoc
Expertise: Systems Biology, Dynamic optimization., Metabolic Networks
Projects: ZucAt, Modelling COVID-19 epidemics
Institutions: Institute of Cytology and Genetics, Novosibirsk State University
Expertise: Systems Biology, molecular genetic systems, gene networks, gene expression, Modeling
Tools: Java, Vaadin, Kinetic Modeling
I am staff scientist in the lab of molecular-genetic systems at the Department of Systems Biology, Institute of Cytology and Genetics SB RAS and Postdoc Research Fellow at San Diego State University.
My research focus is dynamical modeling of gene network functioining.
Projects: Not specified
Institutions: Not specified
Expertise: Systems Biology, marine, microbiomics
Tools: Pathway Tools
Projects: SysMetEx
Institutions: Universitity Duisburg-Essen
My research is intended to contribute to the elucidation of the physiological and molecular processes involved in the biofilm formation of acidophilic leaching bacteria with emphasis in their cell-cell communication mechanisms.
In SysMetEx, our role is to understand biofilm formation at a microscopical and OMICS levels, in order to optimize it.
Projects: MetApp, INBioPharm, SYSTERACT, Auromega
Institutions: SINTEF

Research scientist
Projects: SulfoSys - Biotec, ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Otto-von-Guericke University Magdeburg, University of Gothenburg

Roles: Project Coordinator
Expertise: Signalling networks, dynamics of biological networks., Databases, Data analysis, Systems Biology, Model selection, Identifiability, Cellular Senescence, Cell Cycle, Dynamic Systems, Image processing, Image analysis, Parameter estimation
Tools: ODE, FACS, Model selection, Fluorescence and confocal microscopy, Identifiability analysis, Parameter estimation
My group investigates dynamic regulation and control mechanisms of cellular signal transduction networks by a combination of theoretical, experimental and computational methods. We seek to make sense of our biological data with the help of mathematical models, which ideally enable us to make valid predictions for new experiments, thereby generating novel biological insights.
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
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Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: University of Goettingen
Roles: PhD Student
Expertise: Systems Biology, High-throughput data analysis, Data Integration
Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Universität Konstanz
Roles: PhD Student
Expertise: Molecular Biology, Systems Biology, Mathematical modelling
Tools: quantitative western blot analysis, Molecular Biology, Java, octave, R, ODE
I studied Life Science (which is similar to chemical biology) at the University of Konstanz and became interested in Bioinformatics, Systems Biology and quantitative analyses during my Master's. In my PhD project I combine experimental analyses with modeling and parameter estimation approaches to quantitatively analyse regulation of apoptosis at the level of the Bcl-2 protein family.
Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Radboud University Nijmegen
Expertise: Molecular Biology, Microbiology, Escherichia coli, Systems Biology
I am a first year graduate student in the lab of Prof. Wilhelm Huck at the Radboud University Nijmegen. I am working on a project to create an artificial cell. This involves implementing complex genetic networks in cell-free systems which are far from equilibrium. My project involves designing, quantifying, modeling such networks. I am a molecular biologist by training and have basic modeling skills. I am looking to expand my skill-set to include microscopy, microfluidics and a little bit of
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Projects: ICYSB 2015 - International Practical Course in Systems Biology
Institutions: Imperial College London
I am a PhD student in the Theoretical Systems Biology group, based at Imperial College London.
The aim of my PhD is to understand how noise can be the driving force of decision-making processes (differentiation, self-renewal, apoptosis or tumorgenesis), and what are our chances to control them. So far I have been working on method development for stochastic models, a moment closure framework and a stochastic reachability method, to look into cell-to-cell-variability.
Projects: SulfoSys, SulfoSys - Biotec
Institutions: University Duisburg-Essen
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, FAIRDOM Templates
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

Roles: Postdoc
Expertise: Systems Biology, Metabolic Engineering, Stoichiometric modelling, Kinetic modelling, Data Management, Metabolic Networks
Tools: Python, Copasi, Matlab, COBRA toolbox
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects: COSMIC
Institutions: Wageningen University & Research
Expertise: Microbiology, Genetics, Molecular Biology, Systems Biology, Anaerobic Microbiology, Clostridial Genetics, Metabolic Engineering, Synthetic Biology, bacterial metabolism, carbon metabolism, Clostridium
Tools: Microbiology, Molecular Biology, Chromatography, Molecular biology techniques (RNA/DNA/Protein)
I'm an experimentalist 'Pre-doc' (I still have to finish my PhD thesis) and my work on the COSMIC project will focus on setting up a metabolomic analysis method for Clostridium acetobutylicum.
In the past I have worked on metabolic engineering of the same organism by disrupting genes to asses their impact on acid and solvent formation.
I'm looking forward to joining the COSMIC web-community. It hopefully will all us to stay in touch and update each other on advances in the (computer)lab.
Projects: STREAM, SilicoTryp
Institutions: University of Groningen
Roles: Project Coordinator
Expertise: Transcriptomics, Metabolomics, Systems Biology
I am currently Professor of Systems Biology at the University of Manchester. My research interests focus on the development of innovative computational approaches for post-genomic systems biology, statistical methods for high-throughput biological experimentation and the dynamic modelling of cellular systems. This work is highly interdisciplinary and usually involves close collaboration with experimental biologists and clinicians. A recurrently theme is the study of complex cellular networks at
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Expertise: Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, sensitivity analysis, Dynamic optimization., Dynamics and Control of Biological Networks, Parameter estimation
Tools: ODE, Partial differential equations, Matlab, differential algebraic equations, Stochastic models, Computational Systems Biology, Deterministic models, Dynamic modelling, Parameter estimation
I am a postdoctoral researcher in the group of Julio Banga. My research is focused on computational systems biology with particular attention to the mathematical modelling of biosystems and bioprocesses. Some of the topics we address are:
- Parameter estimation
- Model identifiability
- Global sensitivity analysis
- Optimal experimental design
- Dynamic optimization
- Robust control of diffusion-reaction systems
Institutions: University of Tuebingen, University of Tübingen
Projects: BaCell-SysMO
Institutions: University of Rostock
Expertise: Mathematical modelling, Bacillus subtilis, Deterministic modelling of gene regulation networks, stress responses, Systems Biology, sensitivity analysis, Dynamics and Control of Biological Networks, Parameter estimation
Tools: Biochemistry, Computational and theoretical biology, ODE, Matlab, linux, Stochastic models, Deterministic models, Dynamic modelling
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
Projects: BaCell-SysMO
Institutions: University of Groningen
Expertise: Microbiology, Genetics, Molecular Biology, Bacillus subtilis, translational control of gene expression, sporulation, phenotypic heterogeneity, bistability, gene regulation, stress responses, Signal transduction in Gram-negative bacteria; Synthetic Microbiology; Single cell gene expression; Regulatory networks; biochemistry; histidine ki..., regulation of gene expression, Systems Biology
Tools: Microbiology, Genetics, Molecular Biology, Genetic analysis, Genetic modification, Model organisms, Single Cell analysis, PCR, Fluorecence based reporter gene analyses/single cell analyses, Molecular biology techniques (RNA/DNA), time lapse microscopy, Time-lapse fluorescence microscopy Flow cytometry
Projects: STREAM
Institutions: University of Warwick
Systems Biologist specialising in data integration, high-throughput sequence analysis, and evolutionary and comparative analyses.
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: SUMO
Institutions: University of Stuttgart
From 2005 to 2008 I was group leader at the Institute for System Dynamics at the University of Stuttgart. Since 2008 I am now Professor of Systems Biology at the University of Luxembourg.
The research of the Systems Biology Group at the University of Luxembourg is focussed in the area of experimental and theoretical systems biology. We are applying different modelling techniques (mainly ODE and logical) to biological systems to develop suitable computational models. The analysis of these models
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Projects: BaCell-SysMO
Institutions: University of Newcastle
Expertise: Microbiology, Molecular Biology, Gram positive bacteria (Bacillus, Systems Biology, Genetics)
Tools: Microbiology, Molecular Biology, Biochemistry and protein analysis, Cell biology, Genetic analysis, Genomics, Transcriptomics, Proteomics, Model organisms, Proteomics (2D-PAGE), gene regulation, DNA technology RNA technology Protein analysis Fermentation Mutagenesis, molecular biological techniques (RNA/DNA techniques), protein interaction studies
Optimisation of Bacillus subtilis for the secretion of heterologous proteins Therapeutic proteins (including those required for experimental purposes and clinical trials) are major products of biomanufacturing processes and considerable time and expense are expended to maximise the yield and quality of proteins produced in heterologous hosts. The production host of choice is the Gram-negative bacterium Escherichia coli for which many strains and expression systems have been developed. However,
...
Projects: COSMIC, BaCell-SysMO
Institutions: University of Rostock
Roles: Postdoc
Expertise: Mathematical modelling, dynamics of biological networks, Physics, bistability, Systems Biology, Data analysis, Statistical Physics, Dynamics and Control of Biological Networks
Tools: Computational and theoretical biology, ODE, Matlab, Mathematica, differential algebraic equations, Stochastic models, C programming, Computational Systems Biology, Dynamic modelling, Data Modelling
Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems
Projects: BaCell-SysMO
Institutions: University of Stuttgart
Expertise: Microbiology, Biochemistry, Mathematical modelling, Bacillus subtilis, Mathematical modelling of biosystems and bioprocesses, stress responses, Systems Biology, Nonlinear Dynamics, carbon metabolism, Signalling networks, Metabolic Networks
Tools: Computational and theoretical biology, ODE, Matlab, Mathematica, Fermentation, Chromatography, continuous cultivation, Enzyme assay, Computational Systems Biology, Deterministic models, Dynamic modelling, fed-batch cultivation
I am a biologist in the lab of Prof. Reuss at the University of Stuttgart and I am working in the field of biotechnology and mathematical modelling.
Projects: SUMO
Institutions: University of Sheffield
I am a first year PhD student, working with Professor Robert Poole (University of Sheffield), Professor Jeff Green (University of Sheffield) and Dr Jamie Wood (University of York) using a systems biology approach to study respiration in Escherichia coli.
Projects: PSYSMO, MOSES, COSMIC, BaCell-SysMO
Institutions: University of Stuttgart
Expertise: Reactor models, rapid sampling experiments, Systems Biology, Mathematical modeling, Regulatory Networks, Dynamics and Control of Biological Networks
Tools: Fermentation, stimulus response experiments, evaluation of process dynamics, continuous cultivation, Computational Systems Biology, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization, Dynamic modelling, In silico Metabolic Network Analysis, fed-batch cultivation
Professor for Biochemcial Engineering, University Stuttgart
Projects: COSMIC
Institutions: University of Nottingham
Expertise: Microbiology, Genetics, Molecular Biology, Systems Biology, Synthetic Biology
Tools: Genetic analysis, Genetic modification
I'm an 'experimentalist' (molecular microbiologist) Postdoc working on regulation and peptide signaling in Clostridium acetobutylicum.
I'm also a SysMO-DB PAL (Product Application Liason) for COSMIC, working on data management including standards and integration with SysMO SEEK.
Projects: SulfoSys, PSYSMO, SulfoSys - Biotec
Institutions: University of Braunschweig
Projects: COSMIC
Institutions: University of Rostock
biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock
Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua, INDIE - Biotechnological production of sustainable indole
Institutions: Helmholtz Centre for Infection Research Braunschweig, Wageningen University & Research
Roles: Project Coordinator
Expertise: Microbiology, Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, Biotechnology
Tools: Bioinformatics, Genetic modification, Proteomics, Fermentation, Microarray analysis, Computational Systems Biology, Metabolic Engineering, microbiology techniques, reverse engineering, computational platform development, metabolic netwlrk visualization
My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological
...
Projects: MOSES, ExtremoPharm, ZucAt, GenoSysFat, DigiSal, EraCoBiotech 2 nd call proposal preparation, FAIRDOM & LiSyM & de.NBI Data Structuring Training
Institutions: University of Stuttgart, University of Hohenheim, Norwegian University of Life Sciences, Norwegian University of Science and Technology

Roles: Postdoc
Expertise: Biochemistry, coupling metabolome and environome, rapid sampling experiments, Systems Biology, carbon metabolism, Stoichiometric modelling, Proteomics, Metabolomics, yeast, fungi, Dynamics and Control of Biological Networks
Tools: Biochemistry and protein analysis, Metabolomics, Matlab, Fermentation, Chromatography, Material balance based modeling, stimulus response experiments, continuous cultivation, Enzyme assay, Mass spectrometry (LC-MS/MS), HPLC, GC and LC/MS analysis of metabolites, ODE, Parameter estimation
I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to
...
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.
Assay: _A_05_BUSCO
Short Name: 05_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO post filtering and reassignment
Description: BUSCO post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar, /transfer/transfer.zip
Assay: _A_04_TransRate
Short Name: 04_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate post filtering and reassignment
Description: TransRate post filtering and reassignment
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output.tar, /scripts/run_TransRate_commands.sh
Assay: _A_03.2_components
Short Name: 03.2_components
Assay Class: DRY
Assay Type: components
Title: Components: tr2aacds headers, cdhit-2d
Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters
pISA Assay creation date: 2019-10-22
pISA Assay creator: Ziva Ramsak
Phenodata: None
Featuredata:
Data:
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar
Assay: _A_03.1_filtering
Short Name: 03.1_filtering
Assay Class: DRY
Assay Type: filtering
Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /intermediate/intermediate.tar, /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /output/other/output_full.tar.gz, /output/other/output_summary.tar.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /scripts/scripts.tar
Assay: _A_02.8_DIAMOND
Short Name: 02.8_DIAMOND
Assay Class: DRY
Assay Type: DIAMOND
Title: DIAMOND on raw tr2aacds output
Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Assay: _A_02.7_VecScreen
Short Name: 02.7_VecScreen
Assay Class: DRY
Assay Type: VecScreen
Title: VecScreen on raw tr2aacds output
Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum, Potato virus Y
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl
Assay: _A_02.6_TransRate
Short Name: 02.6_TransRate
Assay Class: DRY
Assay Type: TransRate
Title: TransRate stat on raw tr2aacds transcriptomes
Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: Nonde
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Assay: _A_02.5_STARlong_matchAnnot
Short Name: 02.5_STARlong_matchAnnot
Assay Class: DRY
Assay Type: matchAnnot
Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
...
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...
Assay: _A_02.4_STAR
Short Name: 02.4_STAR
Assay Class: DRY
Assay Type: STAR
Title: mapping reads back to evigene .tr output
Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt
Assay: _A_02.3_InterProScan
Short Name: 02.3_InterProScan
Assay Class: DRY
Assay Type: InterProScan
Title: InterProScan on tr2aacds output
Description: InterProScan on tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd
Assay: _A_02.2_assembly-contribution-count
Short Name: 02.2_assembly-contribution-count
Assay Class: DRY
Assay Type: count
Title: assembly contribution count
Description: assembly contribution count, input/output tr2aacds
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar
Assay: _A_02.1_BUSCO
Short Name: 02.1_BUSCO
Assay Class: DRY
Assay Type: BUSCO
Title: BUSCO on assemblies and tr2aacds output
Description: BUSCO on assemblies and tr2aacds output
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar
Assay: _A_01_evigene
Short Name: 01_evigene
Assay Class: DRY
Assay Type: evigene
Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11
Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum, Potato virus Y
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh
First draft of Genome-scale metabolic model (GEM) for reconstraction of flavonoids biosynthetic pathways. This model includes as a chassis , the Pseudomonas Putida GEM (iJN1411) .
Creators: David San León Granado, Juan Nogales, Álvaro Gargantilla Becerra
Submitter: David San León Granado
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Organism: Pseudomonas putida
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Model that can be used to obtain the figures of Abudulikemu et al 2018:
Abudukelimu, A., Barberis, M., Redegeld, F.A., Sahin, N., and Westerhoff, H.V. (2018). Predictable Irreversible Switching Between Acute and Chronic Inflammation. Front Immunol 9, 1596.
Creators: Hans Westerhoff, Ablikim Abudukelimu
Submitter: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that
...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl... and 1 hidden item
Studies: Analysis of central carbon and energy metabolis... and 1 hidden item
Modelling analyses: Flux Balance Analysis of multi-compartment meta... and 1 hidden item
Abstract (Expand)
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
Citation: 2017 Winter Simulation Conference (WSC),pp.884-895,IEEE
Abstract (Expand)
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
DOI: 10.1093/bib/bby087
Citation: Briefings in Bioinformatics 20(2):540-550
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: 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
Citation: Journal of Integrative Bioinformatics 16(2)
Abstract (Expand)
Authors: Alexey Kolodkin, Raju Prasad Sharma, Anna Maria Colangelo, Andrew Ignatenko, Francesca Martorana, Danyel Jennen, Jacco J. Briede, Nathan Brady, Matteo Barberis, Thierry D.G.A. Mondeel, Michele Papa, Vikas Kumar, Bernhard Peters, Alexander Skupin, Lilia Alberghina, Rudi Balling, Hans V. Westerhoff
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/647776
Citation: Design principles of ROS dynamic networks relevant to precision therapies for age-related diseases 74 : 324
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 (Expand)
Authors: K. van Eunen, C. M. Volker-Touw, A. Gerding, A. Bleeker, J. C. Wolters, W. J. van Rijt, A. M. Martines, K. E. Niezen-Koning, R. M. Heiner, H. Permentier, A. K. Groen, D. J. Reijngoud, T. G. Derks, B. M. Bakker
Date Published: 7th Dec 2016
Publication Type: Journal
PubMed ID: 27927213
Citation: BMC Biol. 2016 Dec 7;14(1):107. doi: 10.1186/s12915-016-0327-5.
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 (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Alison M. Smith, Mark Stitt, Andrew J Millar
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/105437
Citation: Linking circadian time to growth rate quantitatively via carbon metabolism
Abstract (Expand)
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
PubMed ID: 28187405
Citation: J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.
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
Written and presented by Mihai Glont (EMBL-EBI, UK), at the Reproducible and Citable Data and Model Workshop, September 14th -16th 2015.
Creators: Natalie Stanford, Mihai Glont (EMBL-EBI, UK)
Submitter: Natalie Stanford
The Minimum Information about a Molecular Interaction Causal Statement to guide the curation of causal statements.
Creator: Vasundra Toure
Submitter: Vasundra Toure
Investigations: WP1: Creation of an integrated and curated canc...
Studies: Deliverable 1.1: Draft curation guidelines for ...
Assays: MI2CAST curation guidelines
Creators: Lutz Brusch, Jörn Starruß
Submitter: Lutz Brusch
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Lutz Brusch, Jochen Kursawe, Jörn Starruß
Submitter: Lutz Brusch
Investigations: No Investigations
Studies: No Studies
Assays: No Assays