LN #2
Introduction to the training day
10:00
Antonis KOKOSSIS - NTUA
LN #6
Advanced modeling of bioreactors: An introduction to Siemens gPROMS for bioprocess design and optimization
10:15
LN #1
Sarah FADDA - SIEMENS
Yashita PATEL - SIEMENS
A modular, and scalable compute environment for executing scientific workflows in BIOINDUSTRY4.0. A demo
LN #3
12:10
LN #5
George GEORGAKILAS - ARC
Theodore DALAMAGAS - ARC
Break
12:30
Lunch
LN #4
Metabolomics for efficiency targets & large-scale kinetic models
13:30
Stefanos XENIOS - NTUA
Vitor MARTINS DOS SANTOS - WUR
15:30
Break
LN #3
Twinning technology with Physics Informed Neural Networks (PINNs)
15:45
Antonis KOKOSSIS - NTUA
Konstantinos MEXIS - NTUA
Closure
17:45
Michael O'DONOHUE - INRAE
Dr Georgios Georgakilas is a Scientific Associate at "Athena" Research Center, Information Management Systems Institute. He holds a degree from the Department of Computer Engineering and Informatics at University of Patras in Greece (2009), a MSc in Bioinformatics from University of Athens (2011) and a PhD in Bioinformatics from University of Thessaly (2015). From 2015 to 2023 he has been involved in many research projects related to Epigenomics and RNAi Biology in various institutions such as the University of Pennsylvania in USA, Central European Institute of Technology in Czechia, and the School of Medicine in University of Thessaly in Greece. Since 2003, he works at "Athena" Research Center and is involved in several R&D EU projects related to scientific data infrastructures, e.g. IBISBA-DIALS (HORIZON-CSA) and BIOINDUSTRY4.0 (HORIZON-RIA). His research interests include the ML-based modeling of biological processes, development of explainable ML methods for extracting novel insights from biological data, development of novel approaches for analyzing single-cell RNA-Seq as well as spatial transcriptomics, and scientific data and workflow standardization. He has published more than 25 articles in international scientific journals with more than 7,000 citations (Google Scholar) and 20 h-index.
Yashita Patel is a gPROMS library developer and Solution Consultant at Siemens Industry Software. She graduated from the University of Birmingham (2020) with a Chemical Engineering degree and completed an internship at Roche (Basel) in the MSAT team, where she gained experience in developing data-driven and mechanistic modelling tools to optimise monoclonal antibody manufacturing. In 2020, she joined Siemens, where she had a hand in developing different gPROMS models for pharma applications and worked with clients to deliver consultancy projects and gPROMS trainingYashita Patel is a gPROMS library developer and Solution Consultant at Siemens Industry Software. She graduated from the University of Birmingham (2020) with a Chemical Engineering degree and completed an internship at Roche (Basel) in the MSAT team, where she gained experience in developing data-driven and mechanistic modelling tools to optimise monoclonal antibody manufacturing. In 2020, she joined Siemens, where she had a hand in developing different gPROMS models for pharma applications and worked with clients to deliver consultancy projects and gPROMS training.
Konstantinos Mexis holds a degree in Electrical Engineering and Computer Science from National Technical University of Athens. His expertise centers around Data Science and Machine Learning, particularly in the context of the circular economy. He currently works as a researcher and is pursuing a Ph.D. in the Industrial Process Design & Systems Engineering Unit. Konstantinos is passionate about areas such as machine learning, metabolic engineering, and bioprocesses.
Dr. Kokossis, FIChemE, FIEE, FRSA, and FIET, is Professor of Process Systems Engineering at the National Technical University of Athens. He is a Chartered Engineer with IChemE (UK). He holds a Diploma in Chemical Engineering from NTUA and a PhD from Princeton University. Prior to NTUA, he worked for 17 years in UK. He is now the co-director of the National Technology Platform for Sustainable Chemistry, a National Representative of Directorate I (Climate Change & Environment), Affiliate of IEA Bioenergy and EERA Bioenergy, and the Greek Delegate of the Computer Aided Process Engineering (CAPE) group of EFCE. His expertise includes process systems design, modelling, process integration, and optimization. He has graduated 25 PhD and 46 MSc students. He holds 142 communications in international conferences, 129 publications in peer-reviewed journals and 70 invited lectures in conferences universities, and multinational companies. He serves as the National Representative of the IBISBA EU research infrastructure on Industrial Biotechnology. He is an elected member of the Executive Board of the European Federation of Chemical Engineering (EFCE) and leads the New EFCE Sustanability section.
Michael O’Donohue works for INRAE, France’s National Institute of Research on Agriculture, Food and the Environment.He holds a PhD in protein biochemistry from the University of Portsmouth (UK) and possesses extensive research experience in enzyme engineering and biotechnology.In INRAE, Michael is head of TRANSFORM, a 600-staff research division possessing 29 labs in France.In 2014, Michael launched a European initiative aimed at developing a more systemic approach to research in industrial biotechnology. Since then, this initiative has grown into IBISBA, a distributed European research infrastructure that gained ESFRI recognition in 2018. IBISBA currently mobilizes staff from 21 research institutions located in 10 European countries.
Dr. Kokossis, FIChemE, FIEE, FRSA, and FIET, is Professor of Process Systems Engineering at the National Technical University of Athens. He is a Chartered Engineer with IChemE (UK). He holds a Diploma in Chemical Engineering from NTUA and a PhD from Princeton University. Prior to NTUA, he worked for 17 years in UK. He is now the co-director of the National Technology Platform for Sustainable Chemistry, a National Representative of Directorate I (Climate Change & Environment), Affiliate of IEA Bioenergy and EERA Bioenergy, and the Greek Delegate of the Computer Aided Process Engineering (CAPE) group of EFCE. His expertise includes process systems design, modelling, process integration, and optimization. He has graduated 25 PhD and 46 MSc students. He holds 142 communications in international conferences, 129 publications in peer-reviewed journals and 70 invited lectures in conferences universities, and multinational companies. He serves as the National Representative of the IBISBA EU research infrastructure on Industrial Biotechnology. He is an elected member of the Executive Board of the European Federation of Chemical Engineering (EFCE) and leads the New EFCE Sustanability section.
Vitor Martins Dos Santos has been a professor at Wageningen University & Research since 2010. He is also the CEO and Founder of LifeGlimmer GmbH since 2012. His research activities have focused on using mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. He has a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The goals of his research group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological interactions of microbes, and to translate this knowledge into Synthetic Biology applications of biomedical, biotechnological and environmental interest.
Stefanos Xenios is a passionate chemical engineer with 3 years of experience. Skilled in process design and with a strong background in systems biology and machine learning. Some of his previous works include the design of a curated genome scale model for yeast and the development of large-scale kinetic models muconic acid production. His role in the Industrial Process Design & Systems Engineering Unit (IPSEN) team is to construct detailed metabolic models for bioprocesses of interest and to connect large scale kinetics with bioreactor kinetics.
Dr Sarah Fadda is a Principal Consultant at Siemens Industry Software and the Solution Owner of upstream bioprocessing model libraries. She holds a degree in Chemical Engineering from the University of Cagliari (2005) and a PhD in Industrial Chemistry and Chemical Engineering from the Polytechnic University of Milan (2009). Before joining Siemens in 2017, she worked as an academic research associate, focusing primarily on modelling heterogeneity in biological applications. At Siemens, she leads the development of the gPROMS bioreactor model libraries and works at facilitating the adoption of mechanistic and hybrid modelling solutions for upstream bioprocessing in process industries.
Theodore Dalamagas is Research Director and Vice Director of Information Management Systems Institute at ATHENA Research Center, as well as co-founder and Research Director of Symbiolabs (spinoff of ATHENA). He received his Diploma in Electrical Engineering from NTU Athens, Greece (1995), his MSc in Advanced Information Systems from Glasgow University, Scotland (1997), and his PhD from NTUA (2004). He has more than 20 years of R&I experience of running and coordinating EU and national R&I IT projects. His research and technology areas of interest include: scientific databanks and e-research infrastructures, data Web and information retrieval, data interoperability and integration, as well as data services and data science applications for several domains (e.g., health and genomics, industrial biotechnology, manufacturing). He has published more than 100 articles in international journals and conference proceedings.
Dr. Kokossis, FIChemE, FIEE, FRSA, and FIET, is Professor of Process Systems Engineering at the National Technical University of Athens. He is a Chartered Engineer with IChemE (UK). He holds a Diploma in Chemical Engineering from NTUA and a PhD from Princeton University. Prior to NTUA, he worked for 17 years in UK. He is now the co-director of the National Technology Platform for Sustainable Chemistry, a National Representative of Directorate I (Climate Change & Environment), Affiliate of IEA Bioenergy and EERA Bioenergy, and the Greek Delegate of the Computer Aided Process Engineering (CAPE) group of EFCE. His expertise includes process systems design, modelling, process integration, and optimization. He has graduated 25 PhD and 46 MSc students. He holds 142 communications in international conferences, 129 publications in peer-reviewed journals and 70 invited lectures in conferences universities, and multinational companies. He serves as the National Representative of the IBISBA EU research infrastructure on Industrial Biotechnology. He is an elected member of the Executive Board of the European Federation of Chemical Engineering (EFCE) and leads the New EFCE Sustanability section.
Course objectives:
- Showcasing genome scale models and their capability in predicting physiology
- Implementing the large scale kinetic model construction pipeline on an e coli use case
- Showing the predictive capabilities of large scale kinetic models through enzyme perturbation simulations and bioreactor simulations
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Transcript
LN #2
Introduction to the training day
10:00
Antonis KOKOSSIS - NTUA
LN #6
Advanced modeling of bioreactors: An introduction to Siemens gPROMS for bioprocess design and optimization
10:15
LN #1
Sarah FADDA - SIEMENS
Yashita PATEL - SIEMENS
A modular, and scalable compute environment for executing scientific workflows in BIOINDUSTRY4.0. A demo
LN #3
12:10
LN #5
George GEORGAKILAS - ARC
Theodore DALAMAGAS - ARC
Break
12:30
Lunch
LN #4
Metabolomics for efficiency targets & large-scale kinetic models
13:30
Stefanos XENIOS - NTUA
Vitor MARTINS DOS SANTOS - WUR
15:30
Break
LN #3
Twinning technology with Physics Informed Neural Networks (PINNs)
15:45
Antonis KOKOSSIS - NTUA
Konstantinos MEXIS - NTUA
Closure
17:45
Michael O'DONOHUE - INRAE
Dr Georgios Georgakilas is a Scientific Associate at "Athena" Research Center, Information Management Systems Institute. He holds a degree from the Department of Computer Engineering and Informatics at University of Patras in Greece (2009), a MSc in Bioinformatics from University of Athens (2011) and a PhD in Bioinformatics from University of Thessaly (2015). From 2015 to 2023 he has been involved in many research projects related to Epigenomics and RNAi Biology in various institutions such as the University of Pennsylvania in USA, Central European Institute of Technology in Czechia, and the School of Medicine in University of Thessaly in Greece. Since 2003, he works at "Athena" Research Center and is involved in several R&D EU projects related to scientific data infrastructures, e.g. IBISBA-DIALS (HORIZON-CSA) and BIOINDUSTRY4.0 (HORIZON-RIA). His research interests include the ML-based modeling of biological processes, development of explainable ML methods for extracting novel insights from biological data, development of novel approaches for analyzing single-cell RNA-Seq as well as spatial transcriptomics, and scientific data and workflow standardization. He has published more than 25 articles in international scientific journals with more than 7,000 citations (Google Scholar) and 20 h-index.
Yashita Patel is a gPROMS library developer and Solution Consultant at Siemens Industry Software. She graduated from the University of Birmingham (2020) with a Chemical Engineering degree and completed an internship at Roche (Basel) in the MSAT team, where she gained experience in developing data-driven and mechanistic modelling tools to optimise monoclonal antibody manufacturing. In 2020, she joined Siemens, where she had a hand in developing different gPROMS models for pharma applications and worked with clients to deliver consultancy projects and gPROMS trainingYashita Patel is a gPROMS library developer and Solution Consultant at Siemens Industry Software. She graduated from the University of Birmingham (2020) with a Chemical Engineering degree and completed an internship at Roche (Basel) in the MSAT team, where she gained experience in developing data-driven and mechanistic modelling tools to optimise monoclonal antibody manufacturing. In 2020, she joined Siemens, where she had a hand in developing different gPROMS models for pharma applications and worked with clients to deliver consultancy projects and gPROMS training.
Konstantinos Mexis holds a degree in Electrical Engineering and Computer Science from National Technical University of Athens. His expertise centers around Data Science and Machine Learning, particularly in the context of the circular economy. He currently works as a researcher and is pursuing a Ph.D. in the Industrial Process Design & Systems Engineering Unit. Konstantinos is passionate about areas such as machine learning, metabolic engineering, and bioprocesses.
Dr. Kokossis, FIChemE, FIEE, FRSA, and FIET, is Professor of Process Systems Engineering at the National Technical University of Athens. He is a Chartered Engineer with IChemE (UK). He holds a Diploma in Chemical Engineering from NTUA and a PhD from Princeton University. Prior to NTUA, he worked for 17 years in UK. He is now the co-director of the National Technology Platform for Sustainable Chemistry, a National Representative of Directorate I (Climate Change & Environment), Affiliate of IEA Bioenergy and EERA Bioenergy, and the Greek Delegate of the Computer Aided Process Engineering (CAPE) group of EFCE. His expertise includes process systems design, modelling, process integration, and optimization. He has graduated 25 PhD and 46 MSc students. He holds 142 communications in international conferences, 129 publications in peer-reviewed journals and 70 invited lectures in conferences universities, and multinational companies. He serves as the National Representative of the IBISBA EU research infrastructure on Industrial Biotechnology. He is an elected member of the Executive Board of the European Federation of Chemical Engineering (EFCE) and leads the New EFCE Sustanability section.
Michael O’Donohue works for INRAE, France’s National Institute of Research on Agriculture, Food and the Environment.He holds a PhD in protein biochemistry from the University of Portsmouth (UK) and possesses extensive research experience in enzyme engineering and biotechnology.In INRAE, Michael is head of TRANSFORM, a 600-staff research division possessing 29 labs in France.In 2014, Michael launched a European initiative aimed at developing a more systemic approach to research in industrial biotechnology. Since then, this initiative has grown into IBISBA, a distributed European research infrastructure that gained ESFRI recognition in 2018. IBISBA currently mobilizes staff from 21 research institutions located in 10 European countries.
Dr. Kokossis, FIChemE, FIEE, FRSA, and FIET, is Professor of Process Systems Engineering at the National Technical University of Athens. He is a Chartered Engineer with IChemE (UK). He holds a Diploma in Chemical Engineering from NTUA and a PhD from Princeton University. Prior to NTUA, he worked for 17 years in UK. He is now the co-director of the National Technology Platform for Sustainable Chemistry, a National Representative of Directorate I (Climate Change & Environment), Affiliate of IEA Bioenergy and EERA Bioenergy, and the Greek Delegate of the Computer Aided Process Engineering (CAPE) group of EFCE. His expertise includes process systems design, modelling, process integration, and optimization. He has graduated 25 PhD and 46 MSc students. He holds 142 communications in international conferences, 129 publications in peer-reviewed journals and 70 invited lectures in conferences universities, and multinational companies. He serves as the National Representative of the IBISBA EU research infrastructure on Industrial Biotechnology. He is an elected member of the Executive Board of the European Federation of Chemical Engineering (EFCE) and leads the New EFCE Sustanability section.
Vitor Martins Dos Santos has been a professor at Wageningen University & Research since 2010. He is also the CEO and Founder of LifeGlimmer GmbH since 2012. His research activities have focused on using mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. He has a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The goals of his research group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological interactions of microbes, and to translate this knowledge into Synthetic Biology applications of biomedical, biotechnological and environmental interest.
Stefanos Xenios is a passionate chemical engineer with 3 years of experience. Skilled in process design and with a strong background in systems biology and machine learning. Some of his previous works include the design of a curated genome scale model for yeast and the development of large-scale kinetic models muconic acid production. His role in the Industrial Process Design & Systems Engineering Unit (IPSEN) team is to construct detailed metabolic models for bioprocesses of interest and to connect large scale kinetics with bioreactor kinetics.
Dr Sarah Fadda is a Principal Consultant at Siemens Industry Software and the Solution Owner of upstream bioprocessing model libraries. She holds a degree in Chemical Engineering from the University of Cagliari (2005) and a PhD in Industrial Chemistry and Chemical Engineering from the Polytechnic University of Milan (2009). Before joining Siemens in 2017, she worked as an academic research associate, focusing primarily on modelling heterogeneity in biological applications. At Siemens, she leads the development of the gPROMS bioreactor model libraries and works at facilitating the adoption of mechanistic and hybrid modelling solutions for upstream bioprocessing in process industries.
Theodore Dalamagas is Research Director and Vice Director of Information Management Systems Institute at ATHENA Research Center, as well as co-founder and Research Director of Symbiolabs (spinoff of ATHENA). He received his Diploma in Electrical Engineering from NTU Athens, Greece (1995), his MSc in Advanced Information Systems from Glasgow University, Scotland (1997), and his PhD from NTUA (2004). He has more than 20 years of R&I experience of running and coordinating EU and national R&I IT projects. His research and technology areas of interest include: scientific databanks and e-research infrastructures, data Web and information retrieval, data interoperability and integration, as well as data services and data science applications for several domains (e.g., health and genomics, industrial biotechnology, manufacturing). He has published more than 100 articles in international journals and conference proceedings.
Dr. Kokossis, FIChemE, FIEE, FRSA, and FIET, is Professor of Process Systems Engineering at the National Technical University of Athens. He is a Chartered Engineer with IChemE (UK). He holds a Diploma in Chemical Engineering from NTUA and a PhD from Princeton University. Prior to NTUA, he worked for 17 years in UK. He is now the co-director of the National Technology Platform for Sustainable Chemistry, a National Representative of Directorate I (Climate Change & Environment), Affiliate of IEA Bioenergy and EERA Bioenergy, and the Greek Delegate of the Computer Aided Process Engineering (CAPE) group of EFCE. His expertise includes process systems design, modelling, process integration, and optimization. He has graduated 25 PhD and 46 MSc students. He holds 142 communications in international conferences, 129 publications in peer-reviewed journals and 70 invited lectures in conferences universities, and multinational companies. He serves as the National Representative of the IBISBA EU research infrastructure on Industrial Biotechnology. He is an elected member of the Executive Board of the European Federation of Chemical Engineering (EFCE) and leads the New EFCE Sustanability section.
Course objectives:- Showcasing genome scale models and their capability in predicting physiology
- Implementing the large scale kinetic model construction pipeline on an e coli use case
- Showing the predictive capabilities of large scale kinetic models through enzyme perturbation simulations and bioreactor simulations