Savas Konur

Projects

Current Projects:

Towards Programmable Defensive Bacterial Coatings & Skins (ROADBLOCK): This application-driven research project, within the EPSRC’s Synthetic Biology signpost, seeks to integrate the creation of new computational algorithms, tools and theories for synthetic biology (SB) with well-established wet lab techniques to develop an integrated and validated software suite (i.e. an in silico workbench) for SB. This project focuses on synthetic biology (SB) routes for creating engineered coatings, based on modified bacteria, which will act as bio-programmable shields against colonisation. The target application is healthcare, using SB to develop biological based tools to tackle infection, however it is envisaged that ROADBLOCK constructs could be applicable in other medical, environmental or industrial applications in which bacterial colonisation or biofilm formation should be avoided. The new computational tools permit rapid bio-model prototyping and specification, simulation, verification, analysis and optimisation. Moreover, the project considers creating ROADBLOCK biological parts, devices and systems. In this project, computer science takes centre stage as we look to push its boundaries in the context of ROADBLOCK bio-devices. The project directly drives the development of cutting-edge computer science activities. The research programme necessitates close interdisciplinary collaboration spanning computer sciences, biochemical engineering, microbiology and social sciences. The research groups involved in the project stem from the schools of Computer Science (Newcastle, Sheffield, Warwick), Chemical and Biological Engineering (Sheffield), and Molecular Medicine (Nottingham).

Multi-scale Modeling, Verification and Testing (MuVet): This project aims to develop a modelling approach, focused on multi-scale systems, based on a combination of membrane systems and X-machines. This will strengthen both these formalisms, by using their existing capabilities and their existing tools, and also by addressing (some of) their limitations with regard to modelling complex multi-scale systems and phenomena. By considering several case studies from different areas (biology, economics, engineering), the project develops domain-specific high-level specification languages, based on membrane systems and X-machines, enabling complex systems and multi-scale phenomena to be expressed in a natural manner. These languages are also accompanied by domain-specific logics and test generation techniques for such systems and phenomena, providing the necessary means for formally verifying and validating the obtained models. Furthermore, all modelling, verification and testing methods emerging from the project are accompanied by powerful simulators and a toolkit integrating all these techniques. The project is led by Universities of Bucharest (Romania) and Sheffield in a close collaboration with Universities of Seville (Spain) and Newcastle.

Previous Projects:

Verifying Interoperability Requirements in Pervasive Systems (VPS): The VPS project project is an EPSRC-funded collaboration between the Liverpool, Birmingham and Glasgow universities. The project brings together qualitative techniques, including deductive methods, model checking, and abstraction methods, with quantitative techniques, including probabilistic and performance analysis, in order to tackle the problem of verifying pervasive systems. In order to tackle the challenge of pervasive system verification, the project aims to leverage the power of established techniques, notably model checking, deduction and abstraction and process calculi. Within the overall aim of developing viable and appropriate techniques for verifying interoperability requirements in pervasive systems, the project will address the following research objectives: develop frameworks for modelling interoperability requirements in pervasive systems (specifically, interaction requirements, performance and security); develop verification techniques that are tailored to analysing the requirements in models of pervasive systems; and evaluate the techniques on significant case studies in a realistic application domain of distributed systems.

Temporal Logics for Real-time and Safety-critical System Specification: The main objective of this research, carried out at the School of Computer Science, the University of Manchester, is to develop a formal language which can be used to specify properties of real-time systems and natural language semantics. In particular, the aim of the research is to establish a decidable interval temporal logic which is computationally manageable, and which has the ability to model real-time system requirements and express assertions concerning temporal propositions of a natural language. The computational complexity analysis of the logic is also part of the work. Generally speaking, this thesis comprises theoretical and practical aspects of artificial intelligence.

Cybernetic Incident Management (CIM): The CIM project is a consortium comprising of both industrial and academic partners. Almende B.V., Group 4 Falck, and CMotions B.V. constitute the industrial partners in CIM. The Dutch National Research Institute for Mathematics and Computer Science (CWI), Vrije Universiteit Amsterdam, and Technical University Delft constitute the academic partners in CIM. This project addresses the problem of automated support for incident management. The aim of the project is to gather knowledge in order to create a constantly adapting system that encompasses both people and supporting software and that has the ability to process and assess information in an adaptive, interactive and intelligent fashion to support human decisions. One specific part of the project deals with the development of methods to provide automated support for the analysis of what may have gone wrong in specific (simulated or empirical) traces of incident management.

Distributed Engine for Advanced Logistics (DEAL): DEAL is a research project, a collaboration between VU Amsterdam, Erasmus Universiteit Rotterdam, Almende, Groeneveld IT and Vos Logistics. Current ICT-systems for planning and execution of transportation are centralized and usually ignore the high dynamics and low predictability of external factors. They often lack intelligence, usually automate only part of the market transaction, or feature an inappropriate incentive scheme for the potential participants. This project aims at designing, implementing and evaluating a distributed, agent-based intelligent logictic planner for executing, planning, and automated trading of capacity within transportation networks.

RoboCup: RoboCup is an international research and education initiative. Its goal is to foster artificial intelligence and robotics research by providing a standard problem where a wide range of technologies can be examined and integrated. In order for a robot team to actually perform a soccer game, various technologies must be incorporated including: design principles of autonomous agents, multi-agent collaboration, real-time reasoning, robotics, planning and sensor-fusion. The RoboCup computations are held annually with the participation of many researchers from all over the world. Aachen University of Technology (RWTH Aachen) participates in the computations with a team called AllemaniACs.

Web-based Service for Automated Tracking of Digital Assets: In this project, carried out at the Department of Computer Science, RWTH Aachen, a Media Digital Asset Management solution was provided. This was a web-based software suite for organising, distributing and approving documents, images, logos, photos, graphics and branding elements. Some of the languages and tools that were used during the project development are Java, PHP, Tomcat Server, MySQL, XML.

Brokering and Negotiation in Electronic Commerce: In this project, carried out at the Department of Computer Science, RWTH Aachen, a component-based generic agent architecture for multi-attribute (integrative) negotiation was designed and applied in a prototype system for negotiation about cars. This approach can be characterised as co-operative one-to-one multi-criteria negotiation in which the privacy of both parties is protected as much as possible. A prototype has been implemented in which also brokering based on multi-attribute buyer and seller profiles is covered.