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SyMBioSys SIGNED

Systematic Models for Biological Systems Engineering Training Network

Total Cost €

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EC-Contrib. €

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Partnership

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Project "SyMBioSys" data sheet

The following table provides information about the project.

Coordinator
IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE 

Organization address
address: SOUTH KENSINGTON CAMPUS EXHIBITION ROAD
city: LONDON
postcode: SW7 2AZ
website: http://www.imperial.ac.uk/

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Project website http://www.h2020symbiosys.eu/
 Total cost 3˙805˙423 €
 EC max contribution 3˙805˙423 € (100%)
 Programme 1. H2020-EU.1.3.1. (Fostering new skills by means of excellent initial training of researchers)
 Code Call H2020-MSCA-ITN-2015
 Funding Scheme MSCA-ITN-ETN
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2019-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE UK (LONDON) coordinator 546˙575.00
2    HUMBOLDT-UNIVERSITAET ZU BERLIN DE (BERLIN) participant 498˙432.00
3    UNIVERSITAETSKLINIKUM AACHEN DE (AACHEN) participant 498˙432.00
4    AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS ES (MADRID) participant 495˙745.00
5    PROCESS SYSTEMS ENTERPRISE LIMITED UK (LONDON) participant 273˙287.00
6    ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE CH (LAUSANNE) participant 265˙226.00
7    RIJKSUNIVERSITEIT GRONINGEN NL (GRONINGEN) participant 255˙374.00
8    INSILICO BIOTECHNOLOGY AG DE (STUTTGART) participant 249˙216.00
9    ARISTOTELIO PANEPISTIMIO THESSALONIKIS EL (THESSALONIKI) participant 242˙386.00
10    PROTATOUANS - ETAIREIA EREYNAS VIOTECHNOLOGIAS MONOPROSOPI ETAIREIA PERIORISMENIS EYTHINIS EL (GLYFADA) participant 242˙386.00
11    SILICOLIFE LDA PT (BRAGA) participant 238˙356.00
12    Imperial Innovations Ltd UK (London) partner 0.00
13    KAIST KR (DAEJEON) partner 0.00

Map

 Project objective

Mathematical, computational models are central in biomedical and biological systems engineering; models enable (i) mechanistically justifying experimental results via current knowledge and (ii) generating new testable hypotheses or novel intervention methods.

SyMBioSys is a joint academic/industrial training initiative supporting the convergence of engineering, biological and computational sciences. The consortium's mutual goal is developing a new generation of innovative and entrepreneurial early-stage researchers (ESRs) to develop and exploit cutting-edge dynamic (kinetic) mathematical models for biomedical and biotechnological applications. SyMBioSys integrates: (i) six academic beneficiaries with a strong record in biomedical and biological systems engineering research, these include four universities and two research centres; (ii) four industrial beneficiaries including key players in developing simulation software for process systems engineering, metabolic engineering and industrial biotechnology; (iii) three partner organisations from pharmaceutical, biotechnological and entrepreneurial sectors. SyMBioSys is committed to supporting the establishment of a Biological Systems Engineering research community by stimulating programme coordination via joint activities.

The main objectives of this initiative are:

* Developing new algorithms and methods for reverse engineering and identifying dynamic models of biosystems and bioprocesses

* Developing new model-based optimization algorithms for exploiting dynamic models of biological systems (e.g. predicting behavior in biological networks, identifying design principles and selecting optimal treatment intervention) * Developing software tools, implementing the preceding novel algorithms, using state-of-the-art software engineering practices to ensure usability in biological systems engineering research and practice

* Applying the new algorithms and software tools to biomedical and biological test cases.

 Deliverables

List of deliverables.
Methodology for reverse engineering: model selection and parameter identification Documents, reports 2020-03-20 15:39:22
Public dissemination of project results Documents, reports 2020-03-20 15:39:22
Kinetic model describing E.coli central metabolism Documents, reports 2020-03-20 15:39:21
Transferable skills courses Other 2020-03-20 15:39:21
Final report Documents, reports 2020-03-20 15:39:22
Multi-scale models to capture heterogeneity in biological systems Documents, reports 2020-03-20 15:39:21
Conference organization Other 2020-03-20 15:39:21
Science-based courses Other 2020-03-20 15:39:21
Methodology to identify both structure and parameters of large signalling models Documents, reports 2020-03-20 15:39:20
Methodology for global dynamic optimization of cellular processes Documents, reports 2020-03-20 15:39:20
Methodology to model jointly signaling, regulatory and metabolic networks Documents, reports 2020-03-20 15:39:20
Doctoral degrees Other 2020-03-20 15:39:22
\"Optimal operation profile capturing heterogeneity of \"\"high-fidelity\"\" bioprocess\" Documents, reports 2020-03-20 15:39:19
Mathematical model-based strategy for the detection of drug targets Documents, reports 2020-03-20 15:39:22
Mathematical model to describe regulation of metabolism by dynamic cell Documents, reports 2020-03-20 15:39:22
SyMBioSys Website Other 2020-03-20 15:39:19
SyMBioSys vacancies published Other 2020-03-20 15:39:19
Researchers declaration of conformity Documents, reports 2020-03-20 15:39:19
Methodology for a more systematic model building, and subsequent model Documents, reports 2020-03-20 15:39:22
Integrated experimental-modeling platform to tailor treatments in a patient-specific Documents, reports 2020-03-20 15:39:21
Model-based dynamic optimization methods to explain (a posteriori use) or predict Documents, reports 2020-03-20 15:39:22
Kinetic model of human metabolism derived Documents, reports 2020-03-20 15:39:19
Development of an in silico leukemia model Documents, reports 2020-03-20 15:39:19

Take a look to the deliverables list in detail:  detailed list of SyMBioSys deliverables.

 Publications

year authors and title journal last update
List of publications.
2017 Romuald Győrgy, Michail E. Klontzas, Margaritis Kostoglou, Nicki Panoskaltsis, Michael C. Georgiadis, Athanasios Mantalaris
An Integrated Experimental-Modelling Approach of Mesenchymal Stem Cell Bioprocess towards Osteogenic Differentiation
published pages: 9877-9882, ISSN: 2405-8963, DOI: 10.1016/j.ifacol.2017.08.1603
IFAC-PapersOnLine 50/1 2020-03-20
2019 Anika Liu, Panuwat Trairatphisan, Enio Gjerga, Athanasios Didangelos, Jonathan Barrat, Julio-Saez Rodriguez
From expression footprints to causal pathways: Contextualizing large signalling networks with CARNIVAL
published pages: , ISSN: , DOI: 10.1101/541888
biorxiv 2020-03-20
2019 Tajti, F., Antoranz, A., Ibrahim, M.M., Kim, H., Ceccarelli, F., Kuppe, C., Alexopoulos, L.G., Kramann, R. and Saez-Rodriguez, J
A functional landscape of chronic kidney disease entities from public transcriptomic data
published pages: , ISSN: , DOI:
bioRxiv 2020-03-20
2019 Jan Rožanc, Theodore Sakellaropoulos, Asier Antoranz, Cristiano Guttà, Biswajit Podder, Vesna Vetma, Nicole Rufo, Patrizia Agostinis, Vaia Pliaka, Thomas Sauter, Dagmar Kulms, Markus Rehm, Leonidas G. Alexopoulos
Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma
published pages: 1365-1378, ISSN: 1350-9047, DOI: 10.1038/s41418-018-0210-8
Cell Death & Differentiation 26/8 2020-03-20
2019 Alejandro F. Villaverde, Nikolaos Tsiantis, Julio R. Banga
Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models
published pages: 20190043, ISSN: 1742-5689, DOI: 10.1098/rsif.2019.0043
Journal of The Royal Society Interface 16/156 2020-03-20
2019 Michail E. Klontzas, Supachai Reakasame, Raquel Silva, Jose C.F. Morais, Spyros Vernardis, Robert J. MacFarlane, Manolis Heliotis, Eleftherios Tsiridis, Nicki Panoskaltsis, Aldo R. Boccaccini, Athanasios Mantalaris
Oxidized alginate hydrogels with the GHK peptide enhance cord blood mesenchymal stem cell osteogenesis: A paradigm for metabolomics-based evaluation of biomaterial design
published pages: 224-240, ISSN: 1742-7061, DOI: 10.1016/j.actbio.2019.02.017
Acta Biomaterialia 88 2020-03-20
2018 Nikolaos Tsiantis, Eva Balsa-Canto, Julio R Banga
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework
published pages: 2433-2440, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty139
Bioinformatics 34/14 2020-03-20
2018 Jake Alan Pitt, Lucian Gomoescu, Constantinos C. Pantelides, Benoît Chachuat, Julio R. Banga
Critical Assessment of Parameter Estimation Methods in Models of Biological Oscillators
published pages: 72-75, ISSN: 2405-8963, DOI: 10.1016/j.ifacol.2018.09.040
IFAC-PapersOnLine 51/19 2020-03-20
2018 Osvaldo D. Kim, Miguel Rocha, Paulo Maia
A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2018.01690
Frontiers in Microbiology 9 2020-03-20
2018 Chris Fotis, Asier Antoranz, Dimitris Hatziavramidis, Theodore Sakellaropoulos, Leonidas G. Alexopoulos
Network-based technologies for early drug discovery
published pages: 626-635, ISSN: 1359-6446, DOI: 10.1016/j.drudis.2017.12.001
Drug Discovery Today 23/3 2020-03-20
2019 Jake Alan Pitt, Julio R. Banga
Parameter estimation in models of biological oscillators: an automated regularised estimation approach
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-019-2630-y
BMC Bioinformatics 20/1 2020-03-20
2018 Sara Barbosa, Bastian Niebel, Sebastian Wolf, Klaus Mauch, Ralf Takors
A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints
published pages: 37-48, ISSN: 0303-2647, DOI: 10.1016/j.biosystems.2018.10.008
Biosystems 174 2020-03-20
2018 Edoardo Gaude, Christina Schmidt, Payam A. Gammage, Aurelien Dugourd, Thomas Blacker, Sew Peak Chew, Julio Saez-Rodriguez, John S. O’Neill, Gyorgy Szabadkai, Michal Minczuk, Christian Frezza
NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction
published pages: 581-593.e7, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2018.01.034
Molecular Cell 69/4 2020-03-20
2019 Romuald Győrgy, Michail E. Klontzas, Margaritis Kostoglou, Nicki Panoskaltsis, Athanasios Mantalaris, Michael C. Georgiadis
Capturing Mesenchymal Stem Cell Heterogeneity during Osteogenic Differentiation: An Experimental–Modeling Approach
published pages: 13900-13909, ISSN: 0888-5885, DOI: 10.1021/acs.iecr.9b01988
Industrial & Engineering Chemistry Research 58/31 2020-03-20
2018 Bosisio, F.M., Antoranz, A., Bolognesi, M.M., Chinello, C., Wouters, J., Magni, F., Alexopoulos, L., Cattoretti, G. and van den Oord, J.
High-dimensional single cell-analysis of lymphocytic activation in melanoma
published pages: , ISSN: , DOI:
bioRxiv 2020-03-20
2019 Alexander Schäfer, Enio Gjerga, Richard WD Welford, Imke Renz, Francois Lehembre, Peter MA Groenen, Julio Saez-Rodriguez, Ruedi Aebersold, Matthias Gstaiger
Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data
published pages: e8828, ISSN: 1744-4292, DOI: 10.15252/msb.20198828
Molecular Systems Biology 15/8 2020-03-20

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