{"id":139,"date":"2019-03-15T13:47:17","date_gmt":"2019-03-15T18:47:17","guid":{"rendered":"http:\/\/my.dev.vanderbilt.edu\/lopezlab\/?page_id=139"},"modified":"2021-08-12T07:35:37","modified_gmt":"2021-08-12T12:35:37","slug":"tools","status":"publish","type":"page","link":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/tools\/","title":{"rendered":"Tools"},"content":{"rendered":"

Tools from the Lopez Lab<\/h1>\n

\"pysb-swirl\"<\/a>PySB – A Python framework for\u00a0systems biology modeling.<\/h2>\n

Publication: Programming biological models in Python using PySB<\/a> (Molecular Systems Biology, 2013)<\/p>\n

GitHub repository<\/a><\/p>\n

Documentation and Tutorials<\/a><\/p>\n

For examples of models built with PySB, see the Models page.<\/p>\n

Contact: Lolab<\/a><\/p>\n

\"thunor\"<\/a>\u00a0Thunor – Manage, visualize, and analyze high throughput cell proliferation data.<\/h2>\n

Web interface<\/h3>\n

Demo<\/a><\/p>\n

Introduction Video<\/a><\/p>\n

GitHub repository<\/a><\/p>\n

Documentation<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

Core\u00a0package (for standalone analysis or integration into a pipeline)<\/h3>\n

GitHub repository<\/a><\/p>\n

Documentation<\/p>\n

Contact: Lolab<\/a><\/p>\n

PyDREAM – Bayesian model calibration with Python.<\/h2>\n

Publication: PyDREAM: high-dimensional parameter inference for biological models in Python<\/a> (Bioinformatics, 2017)<\/p>\n

Github repository<\/a><\/p>\n

Documentation<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

cupSODA – Parallel biological simulations with GPUs and PySB.<\/h2>\n

Publication:\u00a0GPU-powered model analysis with PySB\/cupSODA.<\/a> (Bioinformatics, 2017)<\/p>\n

Included in PySB Github repository<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

MAGINE – Network enrichment and analysis for -omics data.<\/h2>\n

Github repository<\/a><\/p>\n

Documentation<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

\"pybilt\"<\/a>PyBILT – Python toolkit for analysis of lipid bilayer molecular simulation trajectories.<\/h2>\n

Github repository<\/a><\/p>\n

Documentation<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

ParticleSwarmOptimization – PSO based PySB model calibration.<\/h2>\n

Github repository<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

\u00a0\"pyvipr_logo\"<\/a>PyViPR – Dynamic and static visualizations of PySB models.<\/h2>\n

Github repository<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

TroPy – Identify signal drivers within a dynamic PySB network.<\/h2>\n

Github repository<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

HypBuilder –\u00a0Automatically construct multiple large physiochemical PySB models.<\/h2>\n

Github repository<\/a><\/p>\n

Contact: Lolab<\/a><\/p>\n

QQSB\u00a0– Incorporate qualitative and quantitative experimental data in model calibration.<\/h2>\n

Contact: Lolab<\/a><\/p>\n

 <\/p>\n

\n","protected":false},"excerpt":{"rendered":"

Tools from the Lopez Lab PySB – A Python framework for\u00a0systems biology modeling. Publication: Programming biological models in Python using PySB (Molecular Systems Biology, 2013) GitHub repository Documentation and Tutorials For examples of models built with PySB, see the Models page. Contact: Lolab \u00a0Thunor – Manage, visualize, and analyze high throughput cell proliferation data. Web…<\/p>\n","protected":false},"author":8228,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"tags":[],"class_list":["post-139","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/pages\/139","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/users\/8228"}],"replies":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/comments?post=139"}],"version-history":[{"count":11,"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/pages\/139\/revisions"}],"predecessor-version":[{"id":181,"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/pages\/139\/revisions\/181"}],"wp:attachment":[{"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/media?parent=139"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/lopezlab\/wp-json\/wp\/v2\/tags?post=139"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}