A worldwide e-Infrastructure for NMR and structural biology

Bio-NMR workshop "Automating NMR workflows: Introduction to python programming"

DateAugust 27, 2012 - August 30, 2012
LocationSpronk NMR Consultancy, Vilnius



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 4-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.

Learning to program requires a lot of practice, and there is no better way to learn it than using building your application of choice. During day 3 and 4 you will practice your knowledge on an application of your own choice, guided by us so you will go home with an application that is going to speed up your daily work.



Chris Spronk

Cite WeNMR

Usage of the WeNMR portals should be acknowledged in any publication:
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
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.


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