A worldwide e-Infrastructure for NMR and structural biology

5 day WeNMR workshop: Python programming for structural bioinformatics

Typetraining
DateOctober 21, 2012 - October 25, 2012
LocationCampusX Roma Tor Vergata, Rome, Italy

Introduction

To work efficiently and reliably with the large amount and complexity of data that typically need to be analyzed in (structural) bioinformatics, automation of workflows is a must. In some cases it is possible to find existing software packages to achieve your goal. However, often no suitable package is available for your specific tasks and development of your own piece of software is needed.

Fortunately these days you can find programming platforms with a simple syntax and which require minimal knowledge about computer technology. Python is a programming language that is perfectly suitable for scientific programming: It is simple to learn, but powerful enough even for complicated tasks.

Workshop outline

The 5-day workshop will not only get you started with python programming, but will let you go up to a level of programming that will allow you to build your own graphical user interfaces (GUI) and plotting scripts. The workshop will start assuming that you have no knowledge in python programming, but is perfectly suitable for participants with some experience in (python) programming that want to refresh their knowledge before touching on the more advanced techniques such as object oriented programming (OO) and GUI development.

The workshop consists of lectures that introduce you to all the necessary concepts for effective python programming, such as

  • preparation of the programming environment
  • where to search for information
  • an introduction to Python basics, with topics like text manipulation, file handling etcetera.
  • object oriented programming (classes, objects and methods)
  • plotting
  • GUI programming - PySide

From the lectures, live demonstrations and many exercises the participants will learn how to apply the knowledge in practice on realistic examples from structural biology.

 

Contacts

Chris Spronk
chris@spronknmr.eu

Cite WeNMR

 
Usage of the WeNMR portals should be acknowledged in any publication:
 
"The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project, the International Desktop Grid Federation (IDGF) with its volunteers and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities. "
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572