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Proteomics and SPiM

Nov 3, 2011 at 5:49 PM

Posting Vandana's question and Simon's reply for the community to view.


I would like to know if i could have some proteomics part like calculating the M/Z ratios or charge from MS data by using .net bio or do you have any other tool or project that is available for academic research.? Also i would be glad if you could guide me through the Pi-calculus software spim and how i could model protein network through it.

Looking forward for your reply.




Research assistant

Bioinformatics & Biostatistcs Department

Thrombosis Research Institute



Nov 3, 2011 at 5:50 PM

Thank you for your questions; the .NET Bio project is open source, and the Outercurve Foundation (who own the project) are keen to encourage a community of developers who will extend the basic library of functions to cover areas such as proteomics in the future. While Microsoft continues to extend the functionality of the library, our current focus is genomics, not proteomics – perhaps if you know some programmers interested in the area of proteomics, they could build these functions for you and contribute the code to the project for everyone to use?

With regard to other biology projects – you will find many listed on the CodePlex site, For a list of those started by Microsoft, please visit Please note that these tools are frequently research prototypes and may not have extensive documentation or user support.


Finally regarding your question on SPiM – more details are available at - but this project was not developed in our team and I do not believe there are extensive training materials or user support.


With best wishes,


Simon Mercer