DateThe program of lectures and other activitiesResponsible Partner institution, Country Downloadable
01.07.2012 Arrival    
02.07.2012

Lectures about differences and common features of biological and technical systems. Communication by means of models.

Practical models: how close do they have to be to the original? Molecular interactions – is it physics, biology or mathematics. Basics of structural biology, tour through the cell.

1. Egils Stalidzans, University of Agriculture, Latvia egils_stalidzans-monday.zip (14MB) test_2012-07-02.docx
03.07.2012

Success stories of modelling of cellular processes.

Building first toy models. Behaviour of models and questions to be asked.

1. David Fell, Oxford Brookes University, UK;

2. Egils Stalidzans, University of Agriculture, Latvia

david_fell.zip (7MB)
egils_stalidzans.zip (25MB)
test_2012-07-03.docx
04.07.2012 Steady states of dynamic processes. Flux balance analysis. Using software COBRA in reconstruction of a biochemical pathway. 1. Maike Aurich and Swagatika Sahoo University of Iceland, Iceland university_of_iceland-wednesday.zip (15MB)
test_2012-07-04.docx
05.07.2012 Applications of flux balance analysis using software COBRA in reconstruction of a biochemical pathway. 1. Maike Aurich and Swagatika Sahoo University of Iceland, Iceland Thursday lectures (7MB)
Tutorials (2MB)
university_of_iceland.zip (15MB)
06.07.2012 Applications of dynamic model development using COPASI software.

1. Pedro Mendes and Juergen Pahle, University of Manchester, UK;

2. Sven Sahle and Katrin Huebner, Ruprecht Karl University of Heidelberg, Germany

Lecture (< 1MB)
Exercise (< 1MB)
Exercise 2 (< 1MB)
07.07.2012 Day off – day for cultural activities. Excursion/trip to Rundale palace, Bauska castle.    
08.07.2012 Day off – day for cultural activities. Jelgava or Riga sightseeing, shopping.    
09.07.2012 Applications of dynamic model optimization using COPASI software.

1. Pedro Mendes and Juergen Pahle, University of Manchester, UK;

2. Sven Sahle and Katrin Huebner, Ruprecht Karl University of Heidelberg, Germany

copasi_monday.zip (2MB)
stochastic_modelling.zip (1.3MB)
10.07.2012 Modelling of biotechnological processes in a bioreactor. Development and tuning of model. Real-time modelling. 1. Vytautas Galvanauskas, Kaunas University of Technology, Lithuania vytautas_galvanauskas-tuesday.zip (9.8MB)
11.07.2012 Synthetic biology and engineering approach in development of new features of a cellular biochemical networks. Building blocks. Modelling tools. 1. David Gilbert Brunel University London, UK readinglist
Workshop
12.07.2012 iGEM competitions. Rules of the competition, brightest ideas. Applications of modelling in iGEM competitions. Synthetic components at Biobrick Registry. Simulations of synthetic systems. 1. Roman Jerala, University of Ljubljana, Slovenia bionanomaterials.pptx (24MB)
overview_igem.pptx (41MB)
tasks.pdf (< 1MB)
13.07.2012 Discussion about future perspectives of biological sciences and biotechnology, educational and training needs. Final test. Closing session of the course. 1. Egils Stalidzans, University of Agriculture, Latvia  
14.07.2012 Departure