A worldwide e-Infrastructure for NMR and structural biology

WeNMR workshop: Introduction to python programming

Typetraining
DateSeptember 25, 2012 - September 26, 2012
LocationSpronk NMR Consultancy, Vilnius, Lithuania

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 2-day workshop will get you started with python programming and results in a fully functional script for a real life application in NMR: The conversion from CYANA distance restraints to XPLOR distance restraints (see attached README).
 
It consists of lectures that introduce you to basic python programming concepts, 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 (see attached program).

which are directly applied to build the CYANA to XPLOR conversion script.

Important note: Even though the example is from biological NMR, the concepts taught are suitable for anyone with a structural biology or bioinformatics background!

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