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QuantRef Quantitative model refinement

  • Computational Biomodelling Laboratory
  • Projects
  • QuantRef
Academy of Finland, 2013 — 2017

We focus in this project on computational techniques allowing mathematical models in biology to be presented and used at different levels of detail. We aim to construct and investigate a computational framework for quantitative model refinement where details may be added to (or removed from) a model in a systematic, semi-automatic way, while preserving its numerical behavior.

Our methodology addresses a major current challenge in computational systems biology, that of specifying a model at various levels of resolution while formally ensuring that once the model is quantitatively fit and validated at some level, it remains so at any other level. In this way, a model can be specified first at a lower level of detail, so that its numerical fit is computationally efficient. Once the model is fit and validated it can then be formally refined to higher levels of detail based on our framework. This approach provides the basis for creating and handling flexible hierarchical models, able to integrate data and processes across scales. The project is of a methodological nature, focusing on the development of a sound computational framework for quantitative model refinement. Its tools and methods belong mainly to theoretical computer science. The main contribution of the project will be to computer science by establishing a framework for the quantitative refinement of computational models, a topic not yet investigated much in computer science. This framework is a quantitative development of work done in connection to program specification and (qualitative) refinement, at the borderline between computer science and software engineering. The project will also contribute to computational systems biology as an application area of our methodology, by creating a sound basis for multi-resolution modeling of biochemical systems. We test the applicability of our methodology on several biomodeling case studies.

Throughout our project we focus on the following three objectives:

  1. Construct algorithmic foundations for quantitative model refinement;
  2. Construct a framework for quantitative model comparison;
  3. Demonstrate the applicability of quantitative model refinement in systems biology.

People

Sepinoud Azimi Postdoctoral Researcher
Sepinoud Azimi
sepinoud.azimi@abo.fi
+358 (0)2 215 3315
Room: 340B

Alumni

Vladimir Rogojin Diana-Elena Gratie, M.Sc.
Bogdan Iancu Charmi Panchal
Cristian Gratie

Location of room

Current projects

  • EDGE (EDGE)
    2018 – 2020
  • Allied ICT Finland (AIF)
    2018 – 2020
  • Evolvable platform for designing cancer treatment strategies using nanoparticles (EVO-NANO)
    H2020 - FET OPEN, 2018 – 2021
  • Reboot IoT Factory (Reboot)
    2018 – 2019
  • Integrated Energy Solutions to Smart and Green Shipping (INTENS)
    2018 – 2021
  • Finnish Grid and Cloud Infrastructure, stage 2: enabling datascience (FGCI)
    Academy of Finland , 2018 – 2019
  • Learning and Assessing Risks for Enhancing Dependability of Autonomous Socio- Technical Systems (LARA)
    2018 – 2019
  • AlgoNano (AlgoNano)
    Academy of Finland, 2017 – 2021
  • Efficient Stream Computing by Fitting Computations to Cores (ESC)
    Academy of Finland, 2017 – 2021
  • Development of High-Assured Autonomous Systems (AutoSys)
    Nordplus, 2017 – 2019
  • MegaModelling at Runtime - scalable model-based framework for continuous development and runtime validation of complex systems (MegaM@Rt2)
    ECSEL JU, Tekes, 2017 – 2020
  • Towards a More Advanced Loaning and Reading Culture. A Study, Based on Digital Material, of Contemporary Finnish Loaning and Reading Habits (LibDat)
    Academy of Finland, 2017 – 2021
  • Novel Predictive Analytics Technologies for Future Maintenance Business (OPENS)
    Tekes, 2016 – 2019
  • Continuous Resilience Assurance of Complex Software-Intensive Systems (CoRA)
    2016 – 2020
  • High-performance geoscientific computing in multi-scale mineral potential studies (Gecco)
    Academy of Finland, 2015 – 2019

Completed projects

  • Network Pharmacology: drug re-purposing and discovery of multi-drug therapies by analytical approaches (NetPharma)
    TEKES, 2016 – 2018
  • Modular Interoperability for Healthcare Cyber-Physical Systems (INTERSYS)
    Academy of Finland, 2016 – 2017
  • Efficient Distributed Media Transcoding Platforms (EASYTRANS)
    Tekes - New knowledge and business from research ideas, 2015 – 2016
  • N4S (N4S)
    Tekes, DIGILE, 2014 – 2016
  • Adaptive Integrated Formal Design of Safety-Critical Systems (ADVICeS)
    Academy of Finland, 2013 – 2017
  • Synthetic controllability of biological networks through understanding and engineering their control elements (NetControl)
    Academy of Finland / Synthetic Biology Programme (FinSynBio), 2013 – 2017
  • Quantitative model refinement (QuantRef)
    Academy of Finland, 2013 – 2017
  • Parallel Acceleration (ParallaX)
    2013 – 2016
  • High-quality Measurement Infrastructure for Future Resilient Control Systems (FResCo)
    Academy of Finland, 2013 – 2015
  • Joint curriculum development for doctoral studies in eBusiness (KURRI)
    CIMO, 2012 – 2014
  • Practical Applications of Model-based technologies to continuous integration & testing methodologies (PAM)
    TEKES, 2012 – 2015
  • Agent Based Management of Embedded Data Reserve (AMEBA)
    2012 – 2014
  • DIGILE Digital Services - SME Services (Digital Services )
    Tekes, 2012 – 2014
  • Collaborative Research into Exascale Systemware, Tools and Applications (CRESTA)
    European Community, 2011 – 2014
  • Dataflow ORiented Automated Design tOolchain (DORADO)
    2011 – 2015
  • E-Math (E-Math)
    2011 – 2013
  • Energy Efficient Digital Hydraulic Hybrid Machines (eDiHy)
    Academy of Finland, 2011 – 2014
  • Regenerative hydraulic hybrid with digi-valve and multi chamber cylinder technology (EFFIMA-Digihybrid)
    2011 – 2014
  • IMPEd (IMPEd)
    2011 – 2014
  • Autonomic software-intensive systems: foundations of safety and resilience (ASSURE)
    Academy of Finland, 2010 – 2013
  • FCEP (CLEEN)
    2010 – 2014
  • Cloud Software Program (Cloud)
    2010 – 2013
  • DISCO (DISCO)
    2010 – 2013
  • Enabling Next GeneratIon NEtworks for broadcast Services (ENGINES)
    TEKES, 2010 – 2012
  • Work and Leadership in a Liminal Space: Projects and Innovations (LIMINARI)
    TEKES, 2010 – 2013
  • Reduced Certification Costs Using Trusted Multi-core Platforms (Recomp)
    Tekes and ARTEMIS-JU, 2010 – 2013
  • SimlTER (SimlTER)
    Academy of Finland, 2010 – 2013
  • TeachEd (TeachEd)
    Finnish National Board of Education, 2010 – 2014
  • Digital Microhydraulics (EFFIMA-DiHy)
    2009 – 2014
  • Validation of Many Models in Many Languages (VAMOLA)
    2009 – 2011
  • Industrial deployment of system engineering methods providing high dependability and productivity (DEPLOY)
    2008 – 2012
  • Device and Interoperability and Ecosystems (DIEM)
    2008 – 2013
  • Distributed Jointly Operating Networks (DIJON)
    Academy of Finland, 2008 – 2011
  • EU Fusion fOR Iter Applications (EUFORIA)
    European Union (FP7), 2008 – 2009
  • Computational modeling of the eukaryotic heat shock response (HeatShock)
    Academy of Finland, 2008 – 2010
  • Titan (Titan)
    2008 – 2011
  • LightweIght formal Methods for distributed component-based Embedded systems (LIME)
    Tekes, 2007 – 2009
  • Deployment of Model-Based Technologies to Industrial Testing (D-Mint)
    ITEA2, Tekes, 2007 – 2010
  • Broadcasting for the 21st Century (B21C)
    2007 – 2009
  • VIBRA (VIBRA)
    2007 – 2009
  • Power and Energy Consumption Testing for NoTA Devices (PECOS)
    Subcontracted from Nokia Research Center, 2006 – 2008
  • Efficient Feature Combination (EFCO)
    2006 – 2008
  • Computational processes in living cells (COMPROC)
    Academy of Finland, 2005 – 2010
  • Improving Transient Control and Energy Efficiency by digital hydraulics (ITCEE)
    TEKES, KITARA-programme, 2005 – 2008
  • Louhi (Louhi)
    Tekes, 2005 – 2008
  • MDA In Co-design ArchitectureS (MICAS)
    Subcontracted by Nokia Research Center, Helsinki, 2004 – 2005
  • Rigorous Open Development Environment for Complex Systems (RODIN)
    EC IST FP6 framework, 2004 – 2007
  • Architecture-driven software engineering for embedded systems (ADSEES)
    TEKES (The National Technology Agency), 2001 – 2003
  • Asynchronous Circuit Design Working Group (ACID-WG)
    EU, 2000 – 2004
  • Asynchronous design of DSP architectures (Asynkron)
    The Academy of Finland, 2000 – 2002
  • Methodologies and Technologies for Industrial Strength Systems Engineering (MATISSE)
    EU FP5-project, 2000 – 2003

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Contact

Phone: +358 (0)2 215 4475
Fax: +358 (0)2 251 5557

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Åbo Akademi, Agora
Informationsteknologi
Vattenborgsvägen 3
20500 Åbo

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Åbo Akademi
Informationsteknologi
Agora
Domkyrkotorget 3
20500 Åbo

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