Python is a scripting language of the closest to low level programming codes. Intuitive, object oriented, light and versatile, python also counts with numerous extensions, modules and libraries for scientific applications. Once familiar with the main programming components, Python allows to quickly carry out complex scientific tasks with an apparent limitless field of applications. For these reasons, a large number of programs in computational chemistry and molecular modelling have been developed based on a python architecture (i.e. Chimera, Pymol, , Maestro, OpenEye, etc). Moreover, many of which were not built on this particular code have been implemented with a python interface in the recent years.

The aim of our summer school is to introduce the researcher in computational and theoretical chemistry to python programming, focusing on a set of tools nowadays available in this field. The participants will be instructed by several leaders in the development of python codes for scientific analysis, computational chemistry and molecular modelling. The school will be concentrated on 3 days. The first two and half ones will be dedicated to the teaching of fundamental modules like introduction and numerical calculation with python, molecular visualization and modelling, graphical representation (see program for more details) and the remaining half day will be dedicated to the presentation of several challenges. Prizes will be awarded to the winners. Importantly, each teaching module will contain a substantial amount of hands-on where the researcher will be able to experiment by him-/ herself on our computers the interest of coding in python.

Jean-Didier Maréchal i Ramón Crehuet
Universitat Autònoma de Barcelona i IQAC-CSIC
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The coordinators will be helped in his work by a series of people including Enrique Marcos, Victor Muñoz and Elisabeth Ortega.

Speakers

Ramon Crehuet
Institut de Química Avançada de Catalunya (IQAC-CSIC)
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Konrad Hinsen,
Centre de Biophysique Moléculaire, University of Orleans, France
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Conrad Huang
Department of Pharmaceutical Chemistry, University of California at San Francisco (USA)
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John D. Hunter
University of Chicago, USA
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Jean-Didier Maréchal
Departament de Química, Universitat Autònoma de Barcelona
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Fernando Perez
University of Colorado, USA
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Oriol Vendrell-Romagosa
Physikalisch-Chemisches Institut, Universitaet Heidelberg
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Program:

Download slides and exercises (members only)

Wednesday 16th June

9:00-10:00 Registration

10:00-11:00 Introduction to Python, R. Crehuet and J.-D. Maréchal, Universitat and Universitat Autònoma de Barcelona, Spain

11:00-11:30 Coffee break

11:30-13:00 Introduction to Python, R. Crehuet and J.-D. Maréchal, Universitat and Universitat Autònoma de Barcelona, Spain

13:00-14:00 Lunch

14:00-16:00 Introduction to Numerical Python, R. Crehuet, Universitat de Barcelona, Spain

16:00-16:30 Coffee Break

16:30–17:30 A first applicative case, O. Vendrell, University of Heidelberg, Germany

 

Thursday 17th June

9:00 – 11:00 Molecular Manipulation and Visualization, C. Huang, Project leader Chimera, University of California, San Francisco, U.S.A

11:00-11:30 Coffee Break

11:30-13:00 Molecular Manipulation and Visualization, C. Huang, Project leader Chimera, University of California, San Francisco, U.S.A

13:00-14:00 Lunch

14:00-15:30 Molecular Modeling ToolKit, K. Hinsen, Main author of MMTK, University of Orleans, France


15:30-16:00 Coffee Break

16:00-17.30 Molecular Modeling ToolKit, K. Hinsen, Main author of MMTK, University of Orleans, France

Friday 18th June

9:00-11:00 Scientific Analysis and Graphical Representation, J. Hunter and F. Perez, Main authors of Matplotlib and Ipython, University of Chicago and Colorado, U.S.A

11:00-11.30 Coffee break

11:30-13:00 Scientific Analysis and Graphical Representation, J. Hunter and F. Perez, Main authors of Matplotlib and Ipython, University of Chicago and Colorado, U.S.A

13:00-14:00 Lunch

14:00-17:30 Challenge