A worldwide e-Infrastructure for NMR and structural biology

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

Event Date: 
Tue, 2012-08-28 (All day) - Fri, 2012-08-31 (All day)


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.

Costs and reimbursements

Bio-NMR offers the workshop for free for 6 selected participants from non-profit institutes and provides a reimbursement of up to €475 to cover their travel and accommodation costs. Value Added Tax is excluded from reimbursement. To be eligible for free participation and reimbursement, applicants must send a Curriculum Vitae, with research interests and a short letter of motivation. Details on the selection procedure are available under "Other downloads".

Applicants that have not been selected for the free participation, and applicants from for-profit institutes, may take part at a special reduced workshop fee of €200 (non-profit) and €400 (for-profit).


Workshop requirements

The workshop is open to applicants working in EU-member states or in EU associated countries. From all applications, a total of 6 will be selected for free participation and these will be eligible for reimbursements of expenses (see above). To be selected, applicants must send a Curriculum Vitae, with research interests and a short letter of motivation. Details on the selection procedure are attached.


More information and sign up

For more information and sign up for the workshop, please go to the workshop website


Bio-NMR workshop Automating NMR workflows - Introduction to python programming.pdf141.93 KB
README.pdf152.12 KB
Bio-NMR Workshop application and selection.pdf31.38 KB

Cite WeNMR/WestLife

Usage of the WeNMR/WestLife 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

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858