{"id":277,"date":"2011-08-16T03:38:10","date_gmt":"2011-08-16T03:38:10","guid":{"rendered":"http:\/\/mseas.net16.net\/?page_id=277"},"modified":"2011-10-11T22:05:12","modified_gmt":"2011-10-12T02:05:12","slug":"software","status":"publish","type":"page","link":"https:\/\/mseas.mit.edu\/?page_id=277","title":{"rendered":"Software"},"content":{"rendered":"The MIT Multidisciplinary Simulation, Estimation, and Assimilation Systems (MSEAS) group creates, develops and utilizes new mathematical models and computational methods for ocean predictions and dynamical diagnostics, for optimization and control of autonomous ocean observation systems, and for data assimilation and data-model comparisons. Our systems are used for basic and fundamental research and for realistic simulations and predictions in varied regions of the world&#8217;s ocean, recently including monitoring (Lermusiaux, Physica-2007<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/lermusiaux_physd2007.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>), naval exercises including real-time acoustic-ocean predictions (Xu et al., POMA-2008<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/xu_etal_poma_2008.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>) and environmental management (Cossarini et al., JGR-2009<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/cossarini_etal_jgr_2009.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>).\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Dynamical Models<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<\/ul><ul class=\"big-space\">\r\n<li>New free-surface 2-way nested primitive-equation ocean model (Haley and Lermusiaux, 2010<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/haley_lermusiaux_od_2010.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>). New open boundary conditions and tidal parameterizations. Vertical coordinate options include sigma, hybrid and multiple sigma coordinate transformations<\/li>\r\n<li>Stochastic modeling component to represent sub-grid-scales (Lermusiaux, 2006<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/lermusiaux_jcp_2006.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Uncertainty Prediction and Data Assimilation Schemes<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Three-dimensional Kalman update with specified error covariances (Optimal Interpolation, Lozano et al, 1996; Lermusiaux, MWR-1999<a href=\"http:\/\/web.mit.edu\/pierrel\/www\/Papers\/mwr2_99.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>Non-linear Bayesian-based scheme that predicts field error covariances, Error Subspace Statistical Estimation (ESSE, Lermusiaux, JAOT-2002<a href=\"http:\/\/web.mit.edu\/pierrel\/www\/Papers\/pfjl_jaot02.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>, JCP-2006<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/lermusiaux_jcp_2006.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>). ESSE includes: error subspace initialization, state and uncertainty prediction, minimum error variance data assimilation, adaptive error correction, smoothing, adaptive sampling, path planning and adaptive modeling using varied optimization tools (Lermusiaux, Physica-2007<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/lermusiaux_physd2007.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>New Dynamically-Orthogonal decomposition for uncertainty predictions using prognostic equations (Sapsis and Lermusiaux, 2009<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/sapsis_lermusiaux_DO_SDE_PhysD2009.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>Objective analysis schemes to map gappy ocean data in complex geometries based on the fast-marching method, numerical diffusion and scale estimation (Agarwal and Lermusiaux, 2011<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/agarwal_lermusiaux_FMM_OA_OM2011.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Tidal Model<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Barotropic tides from an inverse tidal model (Logutov, Oc. Dyn.-2008<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/logutov_oc_dyn_2008.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>Nested data-assimilative barotropic tidal prediction system (Logutov and Lermusiaux, Oc. Model.-2008<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/logutov_lermusiaux_inv_baro_tides_OM2008.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Biological Models<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Adaptable biogeochemical models (Besiktepe et al., JMS-2003<a href=\"http:\/\/web.mit.edu\/pierrel\/www\/Papers\/besiktepe_pfjl_arr_jms03.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>; Tian, Eco. Model.-2006)<\/li>\r\n<li>Unstructured-grid biogeochemical ocean modeling based on high-order discontinuous Galerkin finite elements (Ueckermann and Lermusiaux, 2010<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/ueckermann_lermusiaux_od_2010.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Multi-model Fusion and Model Training<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Model training via the two-fold problem of error estimation and subsequent model correction based on observational data (Logutov and Robinson, QJRMS-2005<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/logutov_robinson_qjrms_2005.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>Schemes that estimate the spatial distribution of errors in the individual modeling systems and fuse multi-model estimates based on Bayesian principles (Logutov, Oc. Dyn.-2008<a href=\"hhttp:\/\/mseas.mit.edu\/publications\/PDF\/logutov_oc_dyn_2008.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>Empirical neural-network calibration based on prior model misfits (Leslie et al., JMS-2008<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/leslie_etal_jmarsys_2008.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Adaptive Sampling and Path Planning Schemes<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Mixed Integer Linear Programming (MILP; Yilmaz et al, 2006<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/yilmaz_et_al_path_planning_oceans06.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>, et al, 2008<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/yilmaz_etal_path_plan_MILP_IEEE-OE2008.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>; Yilmaz and Lermusiaux, 2009)<\/li>\r\n<li>Genetic algorithms (Heaney et al, 2007<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/heaney_etal_final_jfr2007.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>) to solve the optimization problem.<\/li>\r\n<li>Combined predictive adaptive sampling and onboard adaptive routing for thermocline tracking and adaptive sampling for acoustic fields with AUVs (Wang, 2007<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/wang_thesis_2007.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>; Wang et al., JMS-2009<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/Wang-etal-2009_ac-adapt-sampling-MSEAS.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Data Analysis and Management<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Software for processing, analysis and management of data (Leslie, et al., 2009)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Computer Science<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>Automated relocatable configuration and control of MSEAS codes: web-based software to configure and control multiple ocean modeling codes (Evangelinos et al., Oc. Model.-2006<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/evangelinos_et_al_oc_modelling_2006.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>Many-Task Computing for distributed ocean uncertainty predictions using Error Subspace Statistical Estimation (Evangelinos et al, 2009<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/evangelinos_etal_mtags09_final2.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<\/ul>\r\n\r\n<p>&nbsp;<\/p>\r\n<b><u>Software to Couple MSEAS to Acoustic Models<\/u><\/b><br \/>\r\n<ul class=\"big-space\">\r\n<li>NPS two-way coupled normal mode model (COUPLE, Chiu et al., JASA-1996<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/chiu_etal_jasa_1996.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>) for 2D acoustic sections<\/li>\r\n<li>Range-dependent Parabolic Equation Acoustic Model (RAM, Collins, JASA-1989a<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/collins_jasa_1989a.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>,JASA-1989b<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/collins_jasa_1989b.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>)<\/li>\r\n<li>C-Snap, the one-way Coupled SACLANTCEN normal mode acoustic propagation loss model<\/li>\r\n<li>3d Parabolic Equation method (FOR3D, Lee, et al., JASA-1992<a href=\"http:\/\/mseas.mit.edu\/publications\/PDF\/lee_etal_jasa_1992.pdf\"><img decoding=\"async\" class=\"pdficon\" src=\"http:\/\/mseas.mit.edu\/wp-content\/themes\/mseas-2\/img\/pdficon.gif\" alt=\"\" \/><\/a>))<\/li>\r\n<li>High-resolution embedded 2-D and 3-D non-hydrostatic models developed for internal waves studies (refraction, radial spreading, scattering, dispersion)<\/li>\r\n<\/ul>","protected":false},"excerpt":{"rendered":"<p>The MIT Multidisciplinary Simulation, Estimation, and Assimilation Systems (MSEAS) group creates, develops and utilizes new mathematical models and computational methods for ocean predictions and dynamical diagnostics, for optimization and control of autonomous ocean observation systems, and for data assimilation and data-model comparisons. Our systems are used for basic and fundamental research and for realistic simulations [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"subpage.php","meta":{"footnotes":""},"class_list":["post-277","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=\/wp\/v2\/pages\/277","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=277"}],"version-history":[{"count":52,"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=\/wp\/v2\/pages\/277\/revisions"}],"predecessor-version":[{"id":279,"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=\/wp\/v2\/pages\/277\/revisions\/279"}],"wp:attachment":[{"href":"https:\/\/mseas.mit.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=277"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}