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International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies 


June 29 - July 5, 2008 - Bucharest, Romania


T1. WiMAX Technologies: Architectures, Protocols, Resource Management and Applications
by Prof. Dr. Eugen Borcoci

T2. Computational Models in Systems Biology
by Prof. Dr. Ion Petre


T1. WiMAX Technologies: Architectures, Protocols, Resource Management and Applications
by Prof. Dr. Eugen Borcoci

The IEEE/802.16/WiMAX emerging technology provides attractive metropolitan area broadband wireless access (BWA), highly efficient and suitable to support a large range of applications for residential and enterprise environments. This tutorial discusses the key aspects, emphasizing both the current state of the art and future trends. Basic architectures IEEE 802.16/WiMAX Forum are presented, for point to multipoint and mesh topologies with focus on layer two and above, related protocols, resource management and mobility.

The following specific topics will be discussed:

  • Main standards in BWA
  • Applications
  • IEEE 802.16 and WiMAX Forum Architectures
  • Basic PHY,  MAC and Convergence layer aspects
  • QoS and WiMAX Resource Management and Control
  • IEEE 802.16/WiMAX Integration in End to END Architectures
  • Micro and Macromobility
  • Media Independent Handover Approach
  • WiMAX versus other Broadband Technologies
  • Relevant Actors on WiMAX Market
  • Future Trends: WiMAX and  4G networks

T2. Computational Models in Systems Biology
by Prof. Dr. Ion Petre


Biology is witnessing nowadays a transformation towards a more quantitative science, based on major technological breakthroughs in the past decade. In this transformation, biology is incorporating mathematical modeling techniques and computational approaches towards numerical simulations, model analysis, and predictions. Systems biology is perhaps the best example in this respect. A major effort here goes into understanding the biological functioning of the whole based on the well-understood function of its parts. The aim is to formalize and analyze the ever-changing interconnections between components (often on different time and space scales), their influence on one another, regulatory patterns, alternative pathways, etc. This is a typical example of a branch of biology where formal reasoning rather than empirical observations is the main driving force.

The importance of biology as a new application area for applied mathematics and computer science has been recognized in our community. There are already significant contributions in this field from well-established computer science research groups (from the formal methods community see D.Harel, L.Cardelli, G.Plotkin, and others), as well as a number of international conferences and journals dedicated to the topic, having computer science as the main target community.

The main difficulties for a computer scientist entering this field are on one hand, the lack of a proper (if minimal) biological background and on the other hand, the lack of training in the mathematical and computational techniques most often used in this field. Through this one-day (6 hours) tutorial, we aim to give an introduction to computational systems biology, starting with a crash course on molecular biology for computer scientist, continuing with continuous and discrete modeling techniques, as well as formal methodsbased modeling approaches. We also plan to give a computer tutorial on Copasi (Complex Pathway Simulator), a useful tool for modeling and simulating sysbio projects.

Finally, we plan to give an overview of a well-rounded off sysbio project (on the heat shock response) that we have been working on in our groups for a couple of years now. We believe that this combination of basic notions and techniques, computer tutorial, and a well-defined complex research project should give our audience a valuable insight into the beauty and the challenges of systems biology. We also hope to give them an insight into the potential of their already existing computer science tools and techniques in this new application area.


  • Molecular biology for computer scientists - a crash course
  • Mathematical modeling techniques in biology: differential equations and stochastic processes
  • Computer science modeling techniques in biology: Petri nets, temporal logic, process algebra, membrane systems
  • Copasi tutorial: model implementation and simulation, parameter estimation, sensitivity analysis, steady state analysis
  • A sysbio project: the heat shock response


It is the aim of the course to give the audience a minimum background on molecular biology and so, no prerequisites are required in this respect. With respect to the mathematical and computational techniques we plan to discuss, we will only consider them with respect to their applications to systems biology. As such, an elementary background on the notions of differentials, probabilities, Petri nets, temporal logic, process algebra, etc would be welcome. We expect this should be no problem for our target audience of graduate students and senior researchers in formal methods.

Past experience of instructors:

Ion Petre is leading a research group in systems biology and has given a number of graduate courses on the topic. He has given several tutorials on mathematical modeling techniques in biology in international conferences and workshops. He has been involved himself in organizing several such events. The second lecturer is Andrzej Mizera, a PhD student in the Petre lab. He has a very strong background in mathematics, with applications to systems biology.


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