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 preaward phase with writing their proposals and in the postaward phase with managing their awarded projects.
Roles: Postdoc
Expertise: Mathematical modelling, parameter estimation, Systems Biology
Tools: Dynamic modelling, parameter estimation, Matlab, ODE
Expertise: Systems Biology, Mathematical modelling, 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 datadriven
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I am had of the Research Group PiDOMICS which aims at the identification of human biomarkers for fungal infection using omicsdata. 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 datawarehouses for visualizing these data.
Projects: Kinetics on the move  Workshop 2016, MultiScale Models for Personalized Liver Function Tests (LiSyMMMPLF), FAIRDOM user meeting, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training
Institutions: Charité University Medicine Berlin, HumboldtUniversität zu Berlin, Humboldt University Berlin
https://orcid.org/000000031725179XRoles: Project Coordinator
Expertise: metabolic networks, Kinetic modelling, Liver, Metabolic Models, Computational modelling, computational biology
Tools: jupyter notebooks, SBML, roadrunner, SEDML, tellurium, ODE, Cytoscape
We are investigating liver metabolism and function with the help of computational models and methods.
Read more about the LiSyM junior group at: www.livermetabolism.com
Junior Group Leader
Dr. Matthias König
Institute for Theoretical Biology
HumboldtUniversity Berlin
Invalidenstraße 43, 10117 Berlin, Germany
phone +49 30 20938450
konigmatt@googlemail.com
The liver is the central metabolic organ of our body playing a crucial role in the clearance of drugs, xenobiotics and numerous metabolites
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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
https://orcid.org/0000000279739902Roles: Postdoc
Expertise: yeast, fungi, Metabolomics, Proteomics, Stoichiometric modelling, carbon metabolism, Systems Biology, dynamics and control of biological networks, coupling metabolome and environome, rapid sampling experiments, Biochemistry
Tools: parameter estimation, ODE, HPLC, GC and LC/MS analysis of metabolites, Mass spectrometry (LCMS/MS), continuous cultivation, Enzyme assay, stimulus response experiments, Material balance based modeling, Chromatography, Fermentation, Matlab, Metabolomics, Biochemistry and protein analysis
I've become a SysMO DB PAL for MOSES project in 2007 being a postdoc 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 “stimulusresponse” methodology for the unraveling the dynamic structure of the network and to
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Projects: ICYSB 2015  International Practical Course in Systems Biology
Institutions: Åbo Akademi University
Projects: SulfoSys  Biotec, ICYSB 2015  International Practical Course in Systems Biology
Institutions: OttovonGuericke University Magdeburg, University of Gothenburg
https://orcid.org/0000000169712530Roles: Project Coordinator
Expertise: Image analysis, Image processing, Dynamic Systems, Signalling networks, Databases, Model selection, Cell Cycle, dynamics of biological networks., Data analysis, Identifiability, parameter estimation, Systems Biology, Cellular Senescence
Tools: Identifiability analysis, Fluorescence and confocal microscopy, parameter estimation, Model selection, ODE, FACS
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: Universität Konstanz
Roles: PhD Student
Expertise: Molecular Biology, Systems Biology, Mathematical modelling
Tools: quantitative western blot analysis, octave, Molecular Biology, R, Java, 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 Bcl2 protein family.
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 decisionmaking processes (differentiation, selfrenewal, 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 celltocellvariability.
Projects: SysMOLAB
Institutions: Wageningen University & Research
Expertise: dynamics of biological networks., Reactor models, Mathematical modelling, Bioinformatics
Tools: Material balance based modeling, SQL, Mathematica, Matlab, Copasi, JWS Online, Linear equations, Algebraic equations, ODE, Partial differential equations, SBML, Metabolomics, Model organisms, Cell biology, Computational and theoretical biology, Molecular Biology
I'm a modeller, specialized in kinetic modeling of biochemical networks. My focus in the SysMOLAB consortium is on creating models of Lactococcus lactis glycolysis and couple this to other related lactic acid bacteria like Streptococcus pyogenes and Enterococcus faecalis. Besides kinetic modeling, I'm also interested in combining various modeling techniques (genomescale modeling, qualitative modeling).
Expertise: Mathematical and statistical modeling, bioreactor models, dynamics of biological networks, dynamics and control of biological networks, parameter estimation, Reactor models, Mathematical modelling, Bioinformatics, Molecular Biology
Tools: evaluation of process dynamics, continuous cultivation, DIVA, differential algebraic equations, stimulus response experiments, linux, Material balance based modeling, Microarray analysis, Matlab, Linear equations, ODE, Model organisms, Single Cell analysis, SBML, Transcriptomics, Computational and theoretical biology, Bioinformatics
I'm an engineer at the MPI Magdeburg and I'm working in the field of mathematical modeling, model verification, parameter identification, model analysis and experimental design. I'm involved in two projects, KOsmoBac and PSYSMO.
Projects: KOSMOBAC
Institutions: University of Aberdeen
Physicist, working on the modelling side.
Projects: COSMIC, BaCellSysMO, SYSTERACT, HUMET Startup, INCOME, BESTER, iRhythmics
Institutions: University of Rostock
Expertise: Data analysis Mathematical modelling Bioinformatics Systems biology, dynamics of biological networks, dynamics and control of biological networks
Tools: quantitative western blot analysis, Stochastic models, quantitative western blot analyses, differential algebraic equations, stimulus response experiments, Mathematica, Matlab, ODE, Computational and theoretical biology
Projects: COSMIC
Institutions: University of Rostock
biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock
Expertise: Mathematical modelling of biosystems and bioprocesses, Statistically and biologically inspired optimization algorithms, dynamics and control of biological networks, parameter estimation, Mathematical modelling
Tools: including:  Dynamic modelling  Parameter estimation  Optimal experimental design  Dynamic optimization, Computational Systems Biology, Mathematica, Matlab, Partial differential equations, ODE, Computational and theoretical biology
We are very interested in applying a systems approach (i.e. modelbased concepts and related computational tools) to problems from the biological domain. In particular, we are doing research in computational systems biology, targetting the following topics:
 Parameter estimation (inverse problems, model calibration) in biochemical pathways
 Optimal experimental design (optimal dynamic experiments) for Systems Biology
 Dynamic optimization (optimal control) of biosystems and bioprocesses

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Projects: PSYSMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: KOSMOBAC
Institutions: University of Aberdeen
My background is physics engineering & biomedical engineering. I did my PhD in Surrey on the modelling of response of mammalian cells to radiation of different qualities.
I have been working at the University of Aberdeen since November 2007 as a theoreticien research fellow of the KOSMOBAC project. We are investigating the homeostasis of ions in bacteria E. coli. I have been working at a model of the buffering capacity of the cytopplasm, arising from the presence of weak acids and bases. We
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Projects: KOSMOBAC
Institutions: University of Aberdeen
Expertise: Mathematical modelling of biosystems and bioprocesses, Mathematical modelling
Tools: including: Dynamic modelling Parameter estimation Optimal experimental design Dynamic optimization, Deterministic models, Computational Systems Biology, C programming, Stochastic models, enzymatic analyses, data modeling, linux, ODE, Computational and theoretical biology
Projects: KOSMOBAC
Institutions: University of Aberdeen
Expertise: Programming, Physics, Mathematical modelling
Tools: PDE, C programing, Stochastic models, linux, ODE, Computational and theoretical biology
Expertise: Dynamic optimization., Systems Biology, sensitivity analysis, Optimal experimental design, Mathematical modelling of biosystems and bioprocesses, dynamics and control of biological networks, parameter estimation
Tools: Dynamic modelling, Computational Systems Biology, Deterministic models, Stochastic models, parameter estimation, differential algebraic equations, Matlab, Partial differential equations, ODE
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 diffusionreaction systems
Projects: KOSMOBAC
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Projects: BaCellSysMO
Institutions: University of Rostock
Expertise: Systems Biology, sensitivity analysis, stress responses, Deterministic modelling of gene regulation networks, dynamics and control of biological networks, parameter estimation, Bacillus subtilis, Mathematical modelling
Tools: Dynamic modelling, Deterministic models, Stochastic models, linux, Matlab, ODE, Computational and theoretical biology, Biochemistry
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
Projects: TRANSLUCENT
Institutions: University of Applied Sciences Koblenz, Rhein Ahr Campus
Grammar school until 1998
199899 Alternative civilian service
19992002 Professional education as male nurse
20022007 Study of Biomathematics
2007... PhD student in TRANSLUCENT project
Projects: SUMO
Institutions: University of Stuttgart
Expertise: Systems Biology, parameter estimation, Data Management, Mathematical modelling
Tools: Mathematica, Matlab, SBML, ODE
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 SysMODB pals for SUMO.
Now:
Industrial affiliation
Projects: COSMIC, BaCellSysMO
Institutions: University of Rostock
Roles: Postdoc
Expertise: Statistical Physics, Data analysis, Systems Biology, bistability, Physics, dynamics of biological networks, dynamics and control of biological networks, Mathematical modelling
Tools: data modelling, Dynamic modelling, Computational Systems Biology, C programming, Stochastic models, differential algebraic equations, Mathematica, Matlab, ODE, Computational and theoretical biology
Modelling of cellular signalling, Dynamic Motifs and Feedback, Quantitative Measures, Theoretical Aspects of Modelling Biological Systems
Projects: BaCellSysMO
Institutions: University of Stuttgart
Expertise: Signalling networks, metabolic networks, carbon metabolism, Nonlinear Dynamics, Systems Biology, stress responses, Mathematical modelling of biosystems and bioprocesses, Bacillus subtilis, Mathematical modelling, Biochemistry, Microbiology
Tools: fedbatch cultivation, Dynamic modelling, Deterministic models, Computational Systems Biology, continuous cultivation, Enzyme assay, Chromatography, Fermentation, Mathematica, Matlab, ODE, Computational and theoretical biology
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: SysMOLAB
Institutions: University of Heidelberg
I am working on a kinetic model of the central metabolism as well as on a genome wide model of Streptococcus pyogenes.
Projects: COSMIC
Institutions: University of Nottingham
Roles: Postdoc
Expertise: Mathematical modelling
Tools: Partial differential equations, ODE, Computational and theoretical biology
The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6
Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneursrv/biomodelsmain/BIOMD0000000412
Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64
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Contributor: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Snapshots: No snapshots
Investigation: Millar, Andrew (exPlaSMo models)
Study: Arabidopsis clock models P2011.1.2 and P2011.2....
Organisms: Arabidopsis thaliana
Models: Arabidopsis clock model P2011.2.1  PLM_71, ver..., Arabidopsis clock model P2011.2.1  PLM_71, ver...
SOPs: No SOPs
Data files: SBSI output from optimisation 2630 July 2013, ..., Unpacked SBSI optimisation results, PLM_71_ 2
Originally submitted model file for PLaSMo accession ID PLM_71, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Contributor: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (exPlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.1.2  PLM_71, ver...
Originally submitted model file for PLaSMo accession ID PLM_71, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Contributor: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (exPlaSMo models)
Studies: Arabidopsis clock models P2011.1.2 and P2011.2....
Modelling analyses: Arabidopsis clock model P2011.2.1  PLM_71, ver...
Here is a kinetic model (in COPASI format) of L. lactis glycolysis.
Creator: Mark Musters
Contributor: Mark Musters
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Lactococcus lactis
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Abstract (Expand)
Authors: None
Date Published: 11th Nov 2010
Journal: Methods Mol. Biol.
PubMed ID: 21063964
Citation: