A Programming Interface for Modelling with SPiM

- ozank at doc dot ic dot ac dot uk -

Last updated on 14.12.2008

PIM - SPiM

A Programming Interface for Modelling with SPiM

PIM - SPiM is a tool which aims at making life easy while building models of biological systems.

If you are interested in building a stochastic model of a (considerably large) biological system, you might like to
describe the interactions of the species of the considered system as a model by writing down English sentences.
Then you can use this tool to translate these sentences into a SPiM program to run simulations on the model.

See the talk slides (PPS), given at the Noise in Life 2009 and BioSysBio 2009.

The windows binary of the latest version (28.1.09) of PIM are available for download.

Here are some example files for getting started. Check the quick-start-instructions here as well.

Here is a short abstract (BioSysBio'09), and an extended abstract (submitted).

You can download the SPiM stochastic simulation tool from Andrew Phillips' web-site.

An Intuitive Automated Modelling Interface for Systems Biology,
with Luca Cardelli and Emmanuelle Caron
Poster presentation at the Imperial College, Institute of Systems and Synthetic Biology - Autumn Symposium, 13/14 November 2008
Oral presentation at the BioSysBio'09, 23-25 March 2009
Oral presentation at the Noise in Life'09, 30 March - 1 April 2009
Download: Short Abstract:PDF

Extended Abstract: PDF

The K-calculus and the work by Guerriero et al. on Beta-binders have been source of inspiration for PIM-SPiM.

EE Vincent Danos, Jerome Feret, Walter Fontana, Russell Harmer, Jean Krivine: Rule-Based Modelling of Cellular Signalling. CONCUR 2007: 17-41

EE Maria Luisa Guerriero, John K. Heath, Corrado Priami: An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra. CMSB 2007: 136-151