{"id":100,"date":"2017-03-24T17:57:28","date_gmt":"2017-03-24T17:57:28","guid":{"rendered":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/?page_id=100"},"modified":"2026-02-20T15:05:12","modified_gmt":"2026-02-20T15:05:12","slug":"software","status":"publish","type":"page","link":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/software\/","title":{"rendered":"Software"},"content":{"rendered":"\n<p>All of the software we develop is open-source and available under Gnu public license.<\/p>\n\n\n\n<p>New <a href=\"https:\/\/github.com\/JohnsonBiophysicsLab\">lab GitHub site<\/a> for shared repos<\/p>\n\n\n\n<p><a href=\"https:\/\/johnsonbiophysicslab.github.io\/NERDSS\/\">ioNERDSS<\/a>: Python package for setting up self-assembly simulations from PDB files (2026)<\/p>\n\n\n\n<p><a href=\"https:\/\/johnsonbiophysicslab.github.io\/NERDSS\/\">NERDSS<\/a><a href=\"https:\/\/github.com\/mjohn218\/NERDSS\">:<\/a> Nonequilibrium Reaction-diffusion self-assembly simulator (2020)<\/p>\n\n\n\n<p><a href=\"https:\/\/github.com\/mjohn218\/KineticAssembly_AD\">Assembly Kinetics<\/a> with Automatic Differentiation (2024)<\/p>\n\n\n\n<p><a href=\"https:\/\/github.com\/mjohn218\/StoichiometricBalance\">SBOPN<\/a>: Stoichiometric Balance Optimized for Protein Networks (2018)<\/p>\n\n\n\n<p><a href=\"https:\/\/github.com\/mjohn218\/FPR_rot\">FPR<\/a> : Structure resolved reaction-diffusion simulator using the Free-propagator Reweighting (FPR) algorithm (2018)<\/p>\n\n\n\n<p><a href=\"https:\/\/github.com\/mjohn218\/network_sampling_MC\">IIN Sampling<\/a>: Monte Carlo sampling of Interface Interaction Networks (IIN) for a defined protein network (2017)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Example networks and Cytoscape files: <a href=\"https:\/\/hollandnetworkmotif.wordpress.com\">David Holland 2017<\/a><\/li>\n<\/ul>\n\n\n\n<p>Check out some movies of biological <a href=\"https:\/\/computersinscience.wordpress.com\/simulations\/\">simulations<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>All of the software we develop is open-source and available under Gnu public license. New lab GitHub site for shared repos ioNERDSS: Python package for setting up self-assembly simulations from PDB files (2026) NERDSS: Nonequilibrium Reaction-diffusion self-assembly simulator (2020) Assembly Kinetics with Automatic Differentiation (2024) SBOPN: Stoichiometric Balance Optimized for Protein Networks (2018) FPR : [&hellip;]<\/p>\n","protected":false},"author":176,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-100","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/pages\/100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/users\/176"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/comments?post=100"}],"version-history":[{"count":5,"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/pages\/100\/revisions"}],"predecessor-version":[{"id":898,"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/pages\/100\/revisions\/898"}],"wp:attachment":[{"href":"https:\/\/sites.krieger.jhu.edu\/johnson-lab\/wp-json\/wp\/v2\/media?parent=100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}