Sunday 09.06.2013

Arrival of participants. Accommodation at hostel.

Day1 - Monday 10.06.2013

1-st lecture

Introduction to the course.

Interplay of scientific branches of bioinformatics, systems biology and synthetic biology. Different types of models and their application in systems biology and synthetic biology. (E. Stalidzans, LUA, Latvia)

2-nd lecture Types of metabolic models. Structural modelling of metabolism. Elementary modes analysis Success stories. (D. Fell, Oxford-Brookes, UK)
3-rd lecture Practical 1: Familiarisation with sequence and enzyme databases. (D. Fell, M. Poolman, H. Hartman, Oxford-Brookes, UK)
4th lecture Intro to kinetic modelling of biological systems. (D. Fell, Oxford-Brookes, UK)
5-th lecture Computer practical 2: Introduction to Python and ScrumPy; examining the stoichiometry matrix of a simple metabolic model. (D. Fell, M. Poolman, H. Hartman, Oxford-Brookes, UK)

Supplementary materials

Day2 - Tuesday 11.06.2013

1-st lecture Genome-scale metabolic modelling – building and analysing models. (D. Fell & M. Poolman, Oxford-Brookes UK)
2-nd lecture Kinetic modelling. Sensitivity analysis / metabolic control analysis. (D.Fell, Oxford-Brookes, UK)
3-rd lecture ScrumPy practical. Elementary modes analysis of metabolism. (D. Fell & M. Poolman, Oxford-Brookes UK)
4-th lecture ScrumPy practical. Flux balance analysis of a medium scale metabolic model / Demonstration of genome-scale analysis. (D. Fell & M. Poolman, Oxford-Brookes UK)

Day3 - Wednesday 12.06.2013

1-st lecture Web modelling tool FAME (Flux Analysis and Modeling Environment). (J. Boele, UA, The Netherlands)
2-nd lecture Creating, analyzing, visualizing of stoichiometric models using FAME. Part 1. (J. Boele, UA, The Netherlands)
3-rd lecture Creating, analyzing, visualizing of stoichiometric models using FAME. Part 2. (J. Boele, UA, The Netherlands)
4-th lecture Comparison of models with software tool ModeRator (Model Comparator) (M. Mednis, LUA, Latvia)

Supplementary materials

Day4 - Thursday 13.06.2013

1-st lecture Applications of dynamic model development using COPASI software. (S. Sahle, Heidelberg, Germany)
2-nd lecture Creation of dynamic models with COPASI. (S. Sahle, Heidelberg, Germany)
3-rd lecture Deterministic modelling of dynamic processes with COPASI. (S. Sahle, Heidelberg, Germany)
4-th lecture Stochastic modeling of dynamic processes with COPASI. (S. Sahle, Heidelberg, Germany)

Supplementary materials

Day5 - Friday 14.06.2013

1-st lecture Applications of dynamic model optimization in parameter estimation and design tasks using COPASI software. Part 1 (P. Mendes and J. Pahle, Manchester, UK)
2-nd lecture Applications of dynamic model optimization in parameter estimation and design tasks using COPASI software. Part 2. (P. Mendes and J. Pahle, Manchester, UK)
3-rd lecture Convergence properties of optimization methods. Part1. (P. Mendes and J. Pahle, Manchester, UK)
4-th lecture Convergence properties of optimization methods. Part2. (P. Mendes and J. Pahle, Manchester, UK), 60 min. Applications or parallel optimization runs of global stochastic optimization methods (E. Stalidzans, LUA, Latvia), 30 min.

Supplementary materials

Saturday 15.06.2013

Free time or social activities.

Sunday 16.06.2013

Free time or social activities.

Day6 - Monday 17.06.2013

1-st lecture Scope of synthetic biology from the perspective of ERASynBio project (E.Stalidzans, LUA, Latvia)
2-nd lecture Synthetic biology and engineering approach in development of new features of cellular biochemical networks. (D. Gilbert, Brunel, UK)
3-rd lecture Building blocks. Modelling tools. (D. Gilbert, Brunel, UK)
4-th lecture Practical success of implementation of synthetic networks. (A. Wipat, Newcastle, UK)

Day7 - Tuesday 18.06.2013

1-st lecture Standardisation of virtual biological parts. SBOL standard. (M. Pocock, Newcastle, UK)
2-nd lecture Design and reality in development of synthetic circuits (J. Hallinan, Newcastle, UK).
3-rd lecture Modelling practical in synthetic biology (A. Wipat, M. Pocock & J. Hallinan, Newcastle, UK).
4-th lecture Modelling practical in synthetic biology (A. Wipat, M. Pocock & J. Hallinan, Newcastle, UK).

Supplementary materials

Day8 - Wednesday 19.06.2013

1-st lecture Modelling of biotechnological processes in a bioreactor scale. (V. Galvanauskas, KTU, Lithuania)
2-nd lecture Development and tuning of model. Real-time modelling. (V. Galvanauskas, KTU, Lithuania)
3-rd lecture Matlab practical in modeling of bioreactor scale processes. Part 1 (V. Galvanauskas, KTU, Lithuania)
4-th lecture Matlab practical in modeling of bioreactor scale processes. Part 2 (V. Galvanauskas, KTU, Lithuania)

Supplementary materials

Day9 - Thursday 20.06.2013

1-st lecture Synthetic gene Switches and networks. Installing synthetic networks in cells. (M. Benčina, Ljubljana, Slovenia)
2-nd lecture iGEM competitions. Rules of the competition, brightest ideas. (M. Benčina, Ljubljana, Slovenia)
3-rd lecture Work in groups: micro iGEM competition. (M. Benčina, Ljubljana, Slovenia)
4-th lecture Work in groups: micro iGEM competition. (M. Benčina, Ljubljana, Slovenia)

Day10 - Friday 21.06.2013

1-st lecture “Tick box” test for students.
2-nd lecture Ethical aspects of synthetic biology. Discussion. (E. Stalidzans, LUA, Latvia)
3-rd lecture Project evaluation discussions. Teamwork. (E. Stalidzans, LUA, Latvia)
4-th lecture Closing session with discussions about the future of systems biology and synthetic biology. Educational and training needs. (moderated by E. Stalidzans, LUA, Latvia)

Saturday 22.06.2013

Departure

Contact information

Coordinators: Agris Dobrovolskis, This email address is being protected from spambots. You need JavaScript enabled to view it. , Tel.0037163005698, Fax.0037163027238
and Natalja Bulipopa, This email address is being protected from spambots. You need JavaScript enabled to view it.