**Mathematical modelling**'.

**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:** 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:** COVID-19 Disease Map

**Institutions:** University of Pittsburgh

**Expertise:** Mathematical modelling, Network Analysis, Dynamics and Control of Biological Networks

**Tools:** R, Matlab, Python, ODE Modelling

**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. ...

**Projects:** COVID-19 Disease Map

**Institutions:** University of Heidelberg

**Projects:** COMBINE Multicellular Modelling

**Institutions:** Indiana University Bloomington

**Expertise:** Mathematical modelling, Multicellular Modelling

Research Scientist, Computer Vision; Intellisense Systems, Inc. Lead Developer for MultiCellDS

Postdoctoral researcher at Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg

**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:** 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:** COMBINE Multicellular Modelling

**Institutions:** Indiana University Bloomington

**Expertise:** 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:** COMBINE Multicellular Modelling

**Institutions:** University College London (UCL)

**Expertise:** Dynamic modelling, Databases, Mathematical modelling, standards, Neuroscience, NeuroML

**Projects:** SAFE-Aqua, Biomics Projects

**Institutions:** Institut Pasteur

**Projects:** INBioPharm

**Institutions:** Norwegian University of Science and Technology

**Roles:** Postdoc

**Expertise:** Mathematical modelling, Systems Biology, Parameter estimation

**Tools:** Dynamic modelling, Matlab, ODE, Parameter estimation

**Projects:** EmPowerPutida, COVID-19 Disease Map

**Institutions:** Wageningen University & Research, University Maastricht

**Roles:** PhD Student, Postdoc

**Expertise:** Systems Biology, Mathematical modelling, Biotechnology, Synthetic Biology, Metabolic Engineering, metabolism, Metabolic Networks, SARS-CoV 2, COVID-19, Pathway Curation, Pathway Analysis, Network Analysis

**Tools:** Matlab, Computational Systems Biology, Flux balance analysis, omics analysis, Python, R, Constraint-based analysis

My research interest is in studying cellular and molecular pathways of COVID-19 disease.

**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 ...

**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

Associate Professor for Systems Biomedicine, Luxembourg Centre for Systems Biomedicine, University of Luxembourg

Lutz Brusch is heading the research group "Spatio-temporal pattern formation in cells and tissues" at the Centre for Information Services and High Performance Computing of TU Dresden, Germany. The group is co-developing the multi-cellular modelling and simulation framework Morpheus (https://morpheus.gitlab.io) and is collaborating with experimental labs on questions of tissue morphogenesis and regeneration.

**Projects:** HUMET Startup, COVID-19 Disease Map

**Institutions:** University of Ulster

POSITION Lecturer/Assistant Prof in Computational Biology at the University of Ulster.

RESEARCH My research focusses principally on cholesterol metabolism and its role in cardiovascular disease and atherosclerosis. I have also studied its role in innate immunity and infection. In addition, I have worked on areas of personalised and stratified medicine for cardiovascular disease and rheumatoid arthritis.

PUBLICATION My publications can be seen at: https://scholar.google.co.uk/citations?user=oMccxPwAAAAJ&hl=en ...

**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 ...

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:** Kinetics on the move - Workshop 2016, de.NBI-SysBio

**Institutions:** University of Heidelberg

**Expertise:** Mathematical modelling, Biofilms, (Bio)Process Design

**Tools:** Numerical modells, Comsol, Matlab

**Projects:** ICYSB 2015 - International Practical Course in Systems Biology

**Institutions:** Åbo Akademi University

**Projects:** ICYSB 2015 - International Practical Course in Systems Biology

**Institutions:** Institute for Experimental Internal Medicine

**Expertise:** Mathematical modelling, Image processing

**Tools:** Matlab, Copasi, c++, Mathematica

I am a PhD student in the field of Systems Biology. In my PhD project I apply mathematical modelling to understand the role of time delay in biological systems containing delayed negative feedbacks.

**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:** 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:** COSMIC

**Institutions:** Beuth University of Applied Sciences Berlin

**Roles:** Project Coordinator

**Expertise:** 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:** 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 ...

**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.

**Institutions:** University of Tuebingen, University of Tübingen

**Projects:** BaCell-SysMO

**Institutions:** University of Goettingen

**Expertise:** Mathematical modelling

**Tools:** Bioinformatics, Computational and theoretical biology, Python, SubtiWiki

I'm a PhD student at the lab of Prof. Dr. Jörg Stülke. My main interest is to analyze the central metabolism of Bacillus subtilis using systems biology software. I have developed an algorithm to find short pathways connecting sets of metabolites and I'm also involved in SubtiWiki, the wiki for all genes of Bacillus subtilis (http://subtiwiki.uni-goettingen.de)

**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:** Noisy-Strep

**Institutions:** University of Cologne

**Expertise:** Mathematical modelling, Statistical Physics

**Tools:** Python, Matlab, Mathematica, Stochastic models, stochastic methods, fortran

I am a phd student working on statistical physics and complex systems and applying concepts from these fields to biology.

**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:** 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

**Expertise:** Mathematical modelling, Nonlinear Dynamics, Parameter estimation

PI of the SUMO work package "Detailed kinetic modelling, identification and analysis of the citric acid cycle and respiratory chains of E. coli". Director of the Institute for System Dynamics, Universität Stuttgart, Germany.

**Projects:** COSMIC

**Institutions:** University of Nottingham

**Roles:** Postdoc

**Expertise:** Mathematical modelling

**Tools:** Computational and theoretical biology, ODE, Partial differential equations

**Projects:** MOSES

**Institutions:** VU University Amsterdam

**Projects:** COSMIC

**Institutions:** University of Nottingham

I am a Birmingham and MRC Fellow in mathematical biology. Specialising in the modelling of gene regulation networks using both numerical and analytical approaches, my work spans a range of biological applications, from drug development to bioenergy to understanding bacterial behaviour. My MRC fellowship gave me the opportunity to gain experimental training in order to generate the complementary data required to adopt a truly interdisciplinary approach to mathematical modelling in biology.

I worked ...

**Projects:** PSYSMO

**Institutions:** Max Planck Institute for Dynamics of Complex Technical Systems

**Projects:** KOSMOBAC

**Institutions:** University of Aberdeen

**Expertise:** Mathematical modelling, Mathematical modelling of biosystems and bioprocesses

**Tools:** Computational and theoretical biology, ODE, linux, data modeling, enzymatic analyses, Stochastic models, C programming, Computational Systems Biology, Deterministic models, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization

**Projects:** SysMO-LAB

**Institutions:** Wageningen University & Research

**Expertise:** Bioinformatics, Mathematical modelling, Reactor models, dynamics of biological networks.

**Tools:** Molecular Biology, Cell biology, Computational and theoretical biology, Metabolomics, Model organisms, SBML, ODE, Partial differential equations, Algebraic equations, Linear equations, Copasi, JWS Online, Matlab, Mathematica, SQL, Material balance based modeling

I'm a modeller, specialized in kinetic modeling of biochemical networks. My focus in the SysMO-LAB 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 (genome-scale modeling, qualitative modeling).

**Expertise:** Molecular Biology, Bioinformatics, Mathematical modelling, Reactor models, dynamics of biological networks, Mathematical and statistical modeling, bioreactor models, Dynamics and Control of Biological Networks, Parameter estimation

**Tools:** Bioinformatics, Computational and theoretical biology, Transcriptomics, Model organisms, Single Cell analysis, SBML, ODE, Linear equations, Matlab, Microarray analysis, linux, Material balance based modeling, stimulus response experiments, DIVA, differential algebraic equations, evaluation of process dynamics, continuous cultivation

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:** 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

**Expertise:** Mathematical modelling, Statistically and biologically inspired optimization algorithms, Mathematical modelling of biosystems and bioprocesses, Dynamics and Control of Biological Networks, Parameter estimation

**Tools:** Computational and theoretical biology, ODE, Partial differential equations, Matlab, Mathematica, Computational Systems Biology, including:
- Dynamic modelling
- Parameter estimation
- Optimal experimental design
- Dynamic optimization

We are very interested in applying a systems approach (i.e. model-based 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

...

**Projects:** KOSMOBAC

**Institutions:** Max-Planck-Institute of Biochemistry Martinsried

**Expertise:** Microbiology, Biochemistry, Molecular Biology, Bioinformatics, Mathematical modelling, sequencing

**Tools:** Microbiology, Molecular Biology, Bioinformatics, Biochemistry and protein analysis, Matlab, Fermentation, rtPCR, molecular biological techniques (RNA/DNA techniques, qPCR, Transcriptomics

Professor in Jinan University, Guangzhou, China. My research interest is in the modeling of translation. Connecting various processes in translation, we can investigate the impact of different factors on protein biosynthesis and biogenesis in genome-wide scale. This may reveal various general mechanisms on control level of gene expression and folding efficiency regulation in different growth conditions.

**Projects:** KOSMOBAC

**Institutions:** Max Planck Institute for Dynamics of Complex Technical Systems

**Projects:** KOSMOBAC

**Institutions:** University of Aberdeen

Physicist, working on the modelling side.

**Projects:** COSMIC

**Institutions:** University of Rostock

biomathematician, PhD student at the University of Rostock, Systems Biology Group Rostock

**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 ...

**Projects:** KOSMOBAC

**Institutions:** University of Aberdeen

**Expertise:** Mathematical modelling, Physics, Programming

**Tools:** Computational and theoretical biology, ODE, linux, Stochastic models, PDE, C programing