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SyMBioSys SIGNED

Systematic Models for Biological Systems Engineering Training Network

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

SyMBioSys project word cloud

Explore the words cloud of the SyMBioSys project. It provides you a very rough idea of what is the project "SyMBioSys" about.

biotechnological entrepreneurial sciences dynamic models committed behavior predicting academic six edge optimal hypotheses practices bioprocesses usability selecting intervention networks community software experimental innovative biological computational stimulating implementing establishment esrs tools industrial centres treatment principles generation metabolic algorithms engineering justifying universities mathematical generating reverse preceding biosystems integrates joint model biotechnology kinetic pharmaceutical symbiosys cutting biomedical central sectors stage mutual training supporting record beneficiaries convergence mechanistically testable players optimization simulation

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 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.	UK (LONDON)	coordinator	546˙575.00
2	HUMBOLDT-UNIVERSITAET ZU BERLIN HUMBOLDT-UNIVERSITAET ZU BERLIN Organization address address: UNTER DEN LINDEN 6 city: BERLIN postcode: 10117 website: www.hu-berlin.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (BERLIN)	participant	498˙432.00
3	UNIVERSITAETSKLINIKUM AACHEN UNIVERSITAETSKLINIKUM AACHEN Organization address address: Pauwelsstrasse 30 city: AACHEN postcode: 52074 website: www.ukaachen.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (AACHEN)	participant	498˙432.00
4	AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS Organization address address: CALLE SERRANO 117 city: MADRID postcode: 28006 website: http://www.csic.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (MADRID)	participant	495˙745.00
5	PROCESS SYSTEMS ENTERPRISE LIMITED PROCESS SYSTEMS ENTERPRISE LIMITED Organization address address: HAMMERSMITH GROVE 26-28 6TH FLOOR EAST city: LONDON postcode: W6 7HA website: www.psenterprise.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (LONDON)	participant	273˙287.00
6	ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE Organization address address: BATIMENT CE 3316 STATION 1 city: LAUSANNE postcode: 1015 website: www.epfl.ch contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CH (LAUSANNE)	participant	265˙226.00
7	RIJKSUNIVERSITEIT GRONINGEN RIJKSUNIVERSITEIT GRONINGEN Organization address address: Broerstraat 5 city: GRONINGEN postcode: 9712CP website: www.rug.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (GRONINGEN)	participant	255˙374.00
8	INSILICO BIOTECHNOLOGY AG INSILICO BIOTECHNOLOGY AG Organization address address: MEITNERSTRASSE 9 city: STUTTGART postcode: 70563 website: www.insilico-biotechnology.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (STUTTGART)	participant	249˙216.00
9	ARISTOTELIO PANEPISTIMIO THESSALONIKIS ARISTOTELIO PANEPISTIMIO THESSALONIKIS Organization address address: KEDEA BUILDING, TRITIS SEPTEMVRIOU, ARISTOTLE UNIV CAMPUS city: THESSALONIKI postcode: 54636 website: www.auth.gr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	EL (THESSALONIKI)	participant	242˙386.00
10	PROTATOUANS - ETAIREIA EREYNAS VIOTECHNOLOGIAS MONOPROSOPI ETAIREIA PERIORISMENIS EYTHINIS PROTATOUANS - ETAIREIA EREYNAS VIOTECHNOLOGIAS MONOPROSOPI ETAIREIA PERIORISMENIS EYTHINIS Organization address address: ODOS NAVARCHOU VOTSI 3 city: GLYFADA postcode: 16675 website: www.protATonce.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	EL (GLYFADA)	participant	242˙386.00
11	SILICOLIFE LDA SILICOLIFE LDA Organization address address: RUA DO CANASTREIRO 15 city: BRAGA postcode: 4715 387 website: www.silicolife.com contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	PT (BRAGA)	participant	238˙356.00
12	Imperial Innovations Ltd Imperial Innovations Ltd Organization address address: 52 Princes Gate, Exhibition Road city: London postcode: SW7 2PG website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (London)	partner	0.00
13	KAIST KAIST Organization address address: DAEHAK-RO 291 YUSEONG GU city: DAEJEON postcode: 305 701 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	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

List of publications.
year	authors and title	journal	last update
2017	Romuald GyÅ‘rgy, 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 RoÅ¾anc, Theodore Sakellaropoulos, Asier Antoranz, Cristiano GuttÃ , 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, BenoÃ®t 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. Oâ€™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 GyÅ‘rgy, Michail E. Klontzas, Margaritis Kostoglou, Nicki Panoskaltsis, Athanasios Mantalaris, Michael C. Georgiadis Capturing Mesenchymal Stem Cell Heterogeneity during Osteogenic Differentiation: An Experimentalâ€“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 SchÃ¤fer, 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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The information about "SYMBIOSYS" are provided by the European Opendata Portal: CORDIS opendata.