{"id":170002,"date":"2008-11-21T03:48:26","date_gmt":"2008-11-21T03:48:26","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/project\/stochastic-pi-machine\/"},"modified":"2020-03-06T10:54:09","modified_gmt":"2020-03-06T18:54:09","slug":"stochastic-pi-machine","status":"publish","type":"msr-project","link":"https:\/\/www.microsoft.com\/en-us\/research\/project\/stochastic-pi-machine\/","title":{"rendered":"Stochastic Pi Machine"},"content":{"rendered":"<p class=\"asset-content\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-287870 alignleft\" src=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2008\/11\/pi.jpg\" alt=\"pi\" width=\"500\" height=\"371\" srcset=\"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2008\/11\/pi.jpg 967w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2008\/11\/pi-300x223.jpg 300w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2008\/11\/pi-768x570.jpg 768w, https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2008\/11\/pi-80x60.jpg 80w\" sizes=\"(max-width: 500px) 100vw, 500px\" \/><\/p>\n<p class=\"asset-content\">The Stochastic Pi Machine (SPiM) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of biological systems, and can be used to model large systems incrementally, by directly composing simpler models of subsystems<\/p>\n\t\t\t<div class=\"moray-accordion\" data-show=\"false\">\n\t\t\t\t\t\t\t<div class=\"clearfix\">\n\t\t\t\t\t<div\n\t\t\t\t\t\tclass=\"btn-group align-items-center mb-g float-sm-right\"\n\t\t\t\t\t\trole=\"group\"\n\t\t\t\t\t\tdata-mount=\"collapse-controls\"\n\t\t\t\t\t\tdata-bi-aN=\"accordion-collapse-controls\"\n\t\t\t\t\t\tdata-target=\"#accordion-1\">\n\t\t\t\t\t\t<button class=\"btn btn-link m-0\" aria-disabled=\"false\" aria-pressed=\"false\" data-action=\"expand\" type=\"button\" data-bi-cN=\"Expand all\">Expand all<\/button>\n\t\t\t\t\t\t<span aria-hidden=\"true\"> | <\/span>\n\t\t\t\t\t\t<button class=\"btn btn-link m-0\" aria-disabled=\"false\" aria-pressed=\"false\" data-action=\"collapse\" type=\"button\" data-bi-cN=\"Collapse all\">Collapse all<\/button>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t<ul class=\"accordion\" id=\"accordion-1\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<li class=\"m-0\">\n\t\t\t<h4 class=\"accordion-header\">\n\t\t\t\t<button\n\t\t\t\t\tclass=\"btn btn-collapse m-0\"\n\t\t\t\t\ttype=\"button\"\n\t\t\t\t\tdata-mount=\"collapse\"\n\t\t\t\t\tdata-target=\"#collapse-2\"\n\t\t\t\t\taria-expanded=\"false\"\n\t\t\t\t\taria-controls=\"collapse-2\">\n\t\tDocumentation\t\t\t\t<\/button>\n\t\t\t<\/h4>\n\t\t\t<div class=\"collapse\" id=\"collapse-2\">\n\t\t\t\t<div class=\"accordion-body\">\n\t\t\t\t\t\t\t\t\t\t<ul>\n<li>Introductory chapter on SPiM [<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2008\/11\/SSB09-preliminary.pdf\">pdf<\/a>]<\/li>\n<li>Introductory slides on SPiM\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-ssb.ppt\" target=\"_self\" rel=\"noopener noreferrer\">[ppt]<\/a> <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-ssb.pdf\" target=\"_self\" rel=\"noopener noreferrer\">[pdf] <\/a><\/li>\n<li>Basic\u00a0SPiM examples and simulation results\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-examples.pdf\" target=\"_self\" rel=\"noopener noreferrer\">[pdf]<\/a><\/li>\n<li>Coupled chemical reactions in SPiM\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-gillespie.pdf\" target=\"_self\" rel=\"noopener noreferrer\">[pdf]<\/a><\/li>\n<li>The SPiM language definition\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-language.pdf\" target=\"_self\" rel=\"noopener noreferrer\">[pdf]<\/a><\/li>\n<li>Some 3D videos of SPiM simulations: Repressilator\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-repressilator.wmv\" target=\"_new\" rel=\"noopener noreferrer\">[wmv]<\/a> Mapk\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-mapk.wmv\" target=\"_new\" rel=\"noopener noreferrer\">[wmv]<\/a> MHCI\u00a0<a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-mhci.wmv\" target=\"_new\" rel=\"noopener noreferrer\">[wmv]<\/a><\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/li>\n\t\t\t\t\t\t<li class=\"m-0\">\n\t\t\t<h4 class=\"accordion-header\">\n\t\t\t\t<button\n\t\t\t\t\tclass=\"btn btn-collapse m-0\"\n\t\t\t\t\ttype=\"button\"\n\t\t\t\t\tdata-mount=\"collapse\"\n\t\t\t\t\tdata-target=\"#collapse-3\"\n\t\t\t\t\taria-expanded=\"false\"\n\t\t\t\t\taria-controls=\"collapse-3\">\n\t\tOnline Simulator (2011-0506)\t\t\t\t<\/button>\n\t\t\t<\/h4>\n\t\t\t<div class=\"collapse\" id=\"collapse-3\">\n\t\t\t\t<div class=\"accordion-body\">\n\t\t\t\t\t\t\t\t\t\t<ul>\n<li><strong><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/lepton.research.microsoft.com\/VisualSPiM\">Prototype Web Simulator<\/a> <\/strong>(requires <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/www.silverlight.net\/getstarted\/\">Silverlight 4.0<\/a> for Windows or Mac).<\/li>\n<li>Introductory <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-spim_tutorial.pdf\">Tutorial<\/a>.<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/li>\n\t\t\t\t\t\t<li class=\"m-0\">\n\t\t\t<h4 class=\"accordion-header\">\n\t\t\t\t<button\n\t\t\t\t\tclass=\"btn btn-collapse m-0\"\n\t\t\t\t\ttype=\"button\"\n\t\t\t\t\tdata-mount=\"collapse\"\n\t\t\t\t\tdata-target=\"#collapse-4\"\n\t\t\t\t\taria-expanded=\"false\"\n\t\t\t\t\taria-controls=\"collapse-4\">\n\t\tDownload (version 0.05, 2008)\t\t\t\t<\/button>\n\t\t\t<\/h4>\n\t\t\t<div class=\"collapse\" id=\"collapse-4\">\n\t\t\t\t<div class=\"accordion-body\">\n\t\t\t\t\t\t\t\t\t\t<ul>\n<li>The <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/biology.azurewebsites.net\/spim\/setup.msi\">SPiM Player 1.13<\/a> is a graphical interface to SPiM, developed by James Margetson, Luca Cardelli and Andrew Phillips. (Requires the <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/msdn2.microsoft.com\/en-us\/netframework\/aa731542.aspx\">.Net 2.0 Runtime<\/a>)<\/li>\n<li>A command-line version of SPiM is available in three distribution formats, under the <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-license.rtf\" target=\"_self\" rel=\"noopener noreferrer\">SPiM License<\/a>:\n<ul>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-spim.zip\" target=\"_self\" rel=\"noopener noreferrer\">Windows Executable<\/a>.<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-spim.ocaml_.zip\" target=\"_self\" rel=\"noopener noreferrer\">OCaml Bytecode (Linux, MacOS X)<\/a>. (Requires <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/caml.inria.fr\/ocaml\">Objective Caml 3.08<\/a>)<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-spim.source.zip\" target=\"_self\" rel=\"noopener noreferrer\">Source Code<\/a>. (Requires <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/caml.inria.fr\/ocaml\">Objective Caml 3.08<\/a>)<\/li>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-release-notes.txt\" target=\"_self\" rel=\"noopener noreferrer\">Release notes<\/a>\u00a0are also available<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/li>\n\t\t\t\t\t\t<li class=\"m-0\">\n\t\t\t<h4 class=\"accordion-header\">\n\t\t\t\t<button\n\t\t\t\t\tclass=\"btn btn-collapse m-0\"\n\t\t\t\t\ttype=\"button\"\n\t\t\t\t\tdata-mount=\"collapse\"\n\t\t\t\t\tdata-target=\"#collapse-5\"\n\t\t\t\t\taria-expanded=\"false\"\n\t\t\t\t\taria-controls=\"collapse-5\">\n\t\tLinks\t\t\t\t<\/button>\n\t\t\t<\/h4>\n\t\t\t<div class=\"collapse\" id=\"collapse-5\">\n\t\t\t\t<div class=\"accordion-body\">\n\t\t\t\t\t\t\t\t\t\t<ul>\n<li>A tool for translating <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" title=\"\" href=\"https:\/\/sites.google.com\/site\/ozankahramanogullari\/software\/pim\" target=\"_new\" rel=\"noopener noreferrer\">text narrative to SPiM<\/a>, developed by <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" title=\"\" href=\"https:\/\/sites.google.com\/site\/ozankahramanogullari\/\" target=\"_new\" rel=\"noopener noreferrer\">Ozan Kahramanogullari<\/a>.<\/li>\n<li>A tool for translating <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/imt.itc.it\/people\/claudio\/Tesi\/SBML2PI.jar\">SBML to SPiM<\/a>, developed by <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/imt.itc.it\/people\/claudio\/index.html\">Claudio Eccher<\/a>.<\/li>\n<li>Further information on process calculi for biology at <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/lucacardelli.name\/BioComputing.htm\">Luca Cardelli&#8217;s Biocomputing Page<\/a>, including an advanced tutorial.<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/li>\n\t\t\t\t\t\t<li class=\"m-0\">\n\t\t\t<h4 class=\"accordion-header\">\n\t\t\t\t<button\n\t\t\t\t\tclass=\"btn btn-collapse m-0\"\n\t\t\t\t\ttype=\"button\"\n\t\t\t\t\tdata-mount=\"collapse\"\n\t\t\t\t\tdata-target=\"#collapse-6\"\n\t\t\t\t\taria-expanded=\"false\"\n\t\t\t\t\taria-controls=\"collapse-6\">\n\t\tAcknowledgements\t\t\t\t<\/button>\n\t\t\t<\/h4>\n\t\t\t<div class=\"collapse\" id=\"collapse-6\">\n\t\t\t\t<div class=\"accordion-body\">\n\t\t\t\t\t\t\t\t\t\t<ul>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/lucacardelli.name\/\">Luca Cardelli<\/a>\u00a0worked on\u00a0the formal specification of SPiM, the design of the SPiM language, and\u00a0on extensive testing and debugging.<\/li>\n<li>Rich Williams developed the Network 3D software for visualising simulations in 3D.<\/li>\n<li>Stefan Leye assisted with debugging the SPiM scheduling algorithm.<\/li>\n<li>James Margetson and Luca Cardelli developed the SPiM GUI.<\/li>\n<li><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/www-sop.inria.fr\/mimosa\/Pascal.Zimmer\/\">Pascal Zimmer<\/a> assisted with debugging the OCaml bytecode distribution.<\/li>\n<li>The <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/www.wisdom.weizmann.ac.il\/~biospi\/\">BioSpi<\/a> project was the main inspiration for SPiM, and many of the SPiM chemical examples are adaptations of earlier BioSpi models.<\/li>\n<li>The core\u00a0SPiM language was developed in <a href=\"https:\/\/www.microsoft.com\/en-us\/research\/project\/f\/\">F#<\/a>.<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/li>\n\t\t\t\t\t\t<li class=\"m-0\">\n\t\t\t<h4 class=\"accordion-header\">\n\t\t\t\t<button\n\t\t\t\t\tclass=\"btn btn-collapse m-0\"\n\t\t\t\t\ttype=\"button\"\n\t\t\t\t\tdata-mount=\"collapse\"\n\t\t\t\t\tdata-target=\"#collapse-7\"\n\t\t\t\t\taria-expanded=\"false\"\n\t\t\t\t\taria-controls=\"collapse-7\">\n\t\tArchive\t\t\t\t<\/button>\n\t\t\t<\/h4>\n\t\t\t<div class=\"collapse\" id=\"collapse-7\">\n\t\t\t\t<div class=\"accordion-body\">\n\t\t\t\t\t\t\t\t\t\t<ul>\n<li><a href=\"https:\/\/www.microsoft.com\/en-us\/research\/uploads\/prod\/2016\/02\/spim-cmsb2010.zip\" target=\"_self\" rel=\"noopener noreferrer\">CMSB 2010<\/a> (Updated 2010-05-17)<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/li>\n\t\t\t\t\t\t\t\t\t<\/ul>\n\t\t<\/div>\n\t\t\n","protected":false},"excerpt":{"rendered":"<p>The Stochastic Pi Machine (SPiM) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of [&hellip;]<\/p>\n","protected":false},"featured_media":287876,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"footnotes":""},"research-area":[13546,13553],"msr-locale":[268875],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-170002","msr-project","type-msr-project","status-publish","has-post-thumbnail","hentry","msr-research-area-computational-sciences-mathematics","msr-research-area-medical-health-genomics","msr-locale-en_us","msr-archive-status-active"],"msr_project_start":"2008-11-21","related-publications":[158490,148014,160258,148015,161363,148018,161467,148019,162142,148020,148021,148022,148025,157040,157181],"related-downloads":[],"related-videos":[],"related-groups":[],"related-events":[],"related-opportunities":[],"related-posts":[],"related-articles":[],"tab-content":[],"slides":[],"related-researchers":[{"type":"guest","display_name":"Luca Cardelli","user_id":640428,"people_section":"Group 1","alias":""}],"msr_research_lab":[199561],"msr_impact_theme":[],"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/170002"}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-project"}],"version-history":[{"count":4,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/170002\/revisions"}],"predecessor-version":[{"id":641496,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/170002\/revisions\/641496"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media\/287876"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=170002"}],"wp:term":[{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=170002"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=170002"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=170002"},{"taxonomy":"msr-pillar","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-pillar?post=170002"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}