= '''S'''olid '''Ea'''rth '''T'''eaching and '''Re'''search '''E'''nvironment = [[PageOutline]] Partial support through NSF-CAREER. SEATREE is a modular and user-friendly software to facilitate using [http://geosys.usc.edu/projects/seatree/wiki/screenshots solid Earth research tools] in the classroom and for interdisciplinary, scientific collaboration. We use python wrappers and make use of modern software design concepts, while remaining compatible with traditional scientific coding. Our goals are to provide a fully contained, yet transparent package that lets users operate in an easy, graphically supported "black box" mode, while also allowing to look under the hood. In the long run, we envision SEATREE to contribute to new ways of sharing scientific research, and making (numerical) experiments truly reproducible again ([http://www-udc.ig.utexas.edu/external/becker/preprints/mbbssw08.pdf Eos Article]). For the current development status, see [http://www-udc.ig.utexas.edu/external/becker/sdata.html the main software download page]. SEATREE is module based, and the [https://github.com/thwbecker/seatree current Github version] includes tools for computing 2-D mantle (thermal) convection, 3-D body wave mantle seismic tomography, 3-D spherical mantle flow, for inverting for Earth structure by means of surface wave, phase velocity tomography, and a two-dimensional synthetic tomography teaching module. A rudimentary module for earthquake location inversions is also available. The main software design consists of transparent python wrappers that drive the modules, including a GMT plotting tool, a VTK/Paraview 3-D visualization interface, and a graphical user interface. SEATREE is freely available under the GNU license; a desktop installation is required to use SEATREE right now but we are planning on a web-based version as well. We encourage you to [wiki:download take the software for a test drive]. If you want to use SEATREE in a classroom setting, we might be able to offer you some installation support and always welcome [wiki:bugs your feedback]. Also, if you like to add your own module to SEATREE, please let us know; we might be able to provide some assistance. [wiki:screenshots Screenshots] Illustrations of software capabilities and design concepts. [wiki:bugs Bug reports, feedback, To-Do list, and version history]. [wiki:UserDocs User Documentation] User-level documentation of SEATREE and the modules. [wiki:DevDocs Developer Documentation] Start here if you want to extend SEATREE and/or add modules. [wiki:PythonSandbox Python Sandbox] Programming tricks (for internal use) == [wiki:download Download] == [wiki:download Download and installation] Instructions on how to obtain and install the whole package, including via a complete VirtualBox install. (Release: version 2.0.2, as of May, 2016). == Modules == The [wiki:UserDocs SEATREE graphical user interface] and our python wrappers provide access to the following computational tools which are provided and shared by different groups of researchers. === Geodynamics === [wiki:hc_docu hc]:: A Hager & O'Connell (1981) mantle flow computation tool for spherical mantle circulation that allow computing flow velocities, tractions, and the geoid given different tomographic models. [wiki:conman conman]:: 2D thermal convection module based on [http://geodynamics.org/cig/software/conman/ ConMan] === Seismology === [wiki:larry3d_docu larry3d]:: a toolkit for performing 3-D, global body wave tomography for the Earth's mantle [wiki:larry_docu larry]:: a toolkit for performing 2-D, global, surface wave phase velocity tomography [wiki:syn2d_docu Syn2D]:: a synthetic 2-D seismic tomography tool Modules under development :: - [wiki:nonlinloc nonlinloc]: non linear earthquake relocations using [http://alomax.free.fr/nlloc/ NonLinLoc] (initial stages) === Visualization === SEATREE provides access to different ways of visualization computational module output, some modules support more than one way of plotting results. [wiki:gmt_docu GMT]:: many modules use [http://gmt.soest.hawaii.edu GMT] for plotting geographic data (as for [wiki:hc_docu hc] and [wiki:larry_docu larry]), we wrote a simple python interface. [http://matplotlib.sourceforge.net/ MatplotLib]:: Matlab-like output, used for [wiki:syn2d_docu syn2d] and [wiki:conman ConMan] [http://www.paraview.org/ Paraview]:: Interactive 3-D output via VTK, now available for latest version of the [wiki:hc_docu hc] module, and in the works for larry3d == Contributors == SEATREE has been developed since the Fall of 2007 thanks to [http://www.nsf.gov/ NSF] CAREER funding and the additional support of the Department of Earth Sciences at USC, Los Angeles, and now from UT Austin. === SEATREE design and coding === * Kevin Milner (main Python code design and support) * [http://www-udc.ig.utexas.edu/external/becker/ Thorsten Becker] (project lead, module and some python programming) * Francois Cadieux (larry3d python module and VTK interfacing) * John Yu: Distributed Linux cluster installation, UGESCE implementation, and additional coding * Hannah Waterhouse and Jared Sain (python code contributions) * Danijel Schorlemmer: design advice === Module contributors === The meat of SEATREE lies in the underlying research software. Please see the individual module documentation for full references and copyright notices. In particular, * [wiki:larry_docu Larry], larry3D, and [wiki:syn2d_docu Syn2D] source codes were generously contributed by [http://www.sg.geophys.ethz.ch/geodynamics/lapo/ Lapo Boschi]. * Surface and body wave velocity measurements were generously contributed by [http://www.ldeo.columbia.edu/~ekstrom/ Goran Ekstrom], [http://es.ucsc.edu/~creif/ Christine Houser], Michael Antolik, and [http://www.geo.lsa.umich.edu/~jritsema/ Jeroen Ritsema]. Original references to the data are provided on the module pages. * [wiki:hc_docu hc] is mainly based on ''advect'' by [http://www.geodynamics.no/STEINBERGER/ Bernhard Steinberger], which was rewritten in C by [http://www-udc.ig.utexas.edu/external/becker/ Thorsten Becker] and Craig O'Neill, and the original routines are by Hager & O'Connell (1981). * [wiki:nonlinloc nonlinloc] uses [http://alomax.free.fr/nlloc/ Anthony Lomax's] freely available software packages including !NonLinLoc * [wiki:conman conman] uses Scott King's software !ConMan == Publications and presentations on SEATREE == Please cite * Milner, K., Becker, T. W., Boschi, L., Sain, J., Schorlemmer, D. and H. Waterhouse: The Solid Earth Research and Teaching Environment: a new software framework to share research tools in the classroom and across disciplines. Eos Trans. AGU, 90, 12, 2009. [http://www-udc.ig.utexas.edu/external/becker/preprints/mbbssw08.pdf PDF] if you use SEATREE for your teaching or research efforts, and the appropriate module or data authors as listed on the module pages. Other publications and presentations on SEATREE include * Milner, K; T. W. Becker; L. Boschi; J. Sain; D. Schorlemmer; H. Waterhouse: The Solid Earth Research and Teaching Environment, a new software framework to share research tools inthe classroom and across disciplines. AGU Fall Meeting Abstract ED13D-0620, 2009. * Milner, K., Becker, T. W., Boschi, L., Sain, J., Schorlemmer, D. and H. Waterhouse: The Solid Earth Research and Teaching Environment: a new software framework to share research tools in the classroom and across disciplines. Eos Trans. AGU, 90, 12, 2009. [http://www-udc.ig.utexas.edu/external/becker/preprints/mbbssw08.pdf PDF] * Waterhouse, H. D., K. Milner, T. W. Becker, J. Sain, and D. Schorlemmer: A Solid Earth Research and Teaching Environment, Opportunities and Challenges in Computational Geophysics workshop, Caltech, 2009. [http://www.geodynamics.org/cig/workinggroups/cs/workshops/future-of-cig09/posters/seatree_scec2008.pdf PDF] * Waterhouse, H. D. and K. Milner, and T.W. Becker: SEATREE: An Interactive Visual Environment for Earthquake Science, 2008 SCEC Annual Meeting, 1-007, 2008.