From 626439b9cece6282151cdf44197bc14e7080e87e Mon Sep 17 00:00:00 2001 From: Blair Lyons Date: Thu, 29 Jul 2021 14:24:47 -0700 Subject: [PATCH 1/2] update supported simulators on readme, make docs --- README.md | 14 ++++++++++---- docs/simulariumio.data_objects.rst | 8 ++++++++ docs/simulariumio.filters.rst | 8 -------- 3 files changed, 18 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 59df9508..91101431 100644 --- a/README.md +++ b/README.md @@ -21,9 +21,12 @@ Simulariumio converts simulation outputs to the format consumed by the [Simulari * Converts 3D spatiotemporal trajectories to .simularium JSON format * Accepts spatial trajectories from the following biological simulation engines: * CytoSim (https://gitlab.com/f.nedelec/cytosim) - * ReaDDy (https://readdy.github.io/) - * PhysiCell (http://physicell.org/) + * MCell (https://mcell.org/) * MEDYAN (http://medyan.org/) + * PhysiCell (http://physicell.org/) + * ReaDDy (https://readdy.github.io/) + * Smoldyn (http://www.smoldyn.org/) + * SpringSaLaD (https://vcell.org/ssalad) * Conversions for data from custom engines can be implemented using the TrajectoryConverter class * Also accepts metrics data for plots to display alongside spatial data @@ -36,9 +39,12 @@ ___ ### Convert spatial trajectory from a supported engine See the Tutorial for the simulation engine you're using for details: * [Cytosim Tutorial](examples/Tutorial_cytosim.ipynb) -* [ReaDDy Tutorial](examples/Tutorial_readdy.ipynb) -* [PhysiCell Tutorial](examples/Tutorial_physicell.ipynb) +* [MCell Tutorial](examples/Tutorial_mcell.ipynb) * [MEDYAN Tutorial](examples/Tutorial_medyan.ipynb) +* [PhysiCell Tutorial](examples/Tutorial_physicell.ipynb) +* [ReaDDy Tutorial](examples/Tutorial_readdy.ipynb) +* [Smoldyn Tutorial](examples/Tutorial_smoldyn.ipynb) +* [SpringSaLaD Tutorial](examples/Tutorial_springsalad.ipynb) An overview for data from ReaDDy: ```python diff --git a/docs/simulariumio.data_objects.rst b/docs/simulariumio.data_objects.rst index 36a0827b..60824734 100644 --- a/docs/simulariumio.data_objects.rst +++ b/docs/simulariumio.data_objects.rst @@ -20,6 +20,14 @@ simulariumio.data\_objects.camera\_data module :undoc-members: :show-inheritance: +simulariumio.data\_objects.dimension\_data module +------------------------------------------------- + +.. automodule:: simulariumio.data_objects.dimension_data + :members: + :undoc-members: + :show-inheritance: + simulariumio.data\_objects.histogram\_plot\_data module ------------------------------------------------------- diff --git a/docs/simulariumio.filters.rst b/docs/simulariumio.filters.rst index a5b5cbc8..02a8a7de 100644 --- a/docs/simulariumio.filters.rst +++ b/docs/simulariumio.filters.rst @@ -60,14 +60,6 @@ simulariumio.filters.multiply\_time\_filter module :undoc-members: :show-inheritance: -simulariumio.filters.reorder\_agents\_filter module ---------------------------------------------------- - -.. automodule:: simulariumio.filters.reorder_agents_filter - :members: - :undoc-members: - :show-inheritance: - simulariumio.filters.transform\_spatial\_axes\_filter module ------------------------------------------------------------ From 1f5ec6322c2a491cccbf57582ede7e3a38c43ac0 Mon Sep 17 00:00:00 2001 From: Blair Lyons Date: Thu, 29 Jul 2021 14:30:32 -0700 Subject: [PATCH 2/2] add visualization and sharing instructions to readme --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index 91101431..0460aa47 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,16 @@ We're working to improve performance for converting large trajectories, and also ___ +## Visualize results +1. In a supported browser (Firefox, Chrome, or Edge), navigate to https://simularium.allencell.org/viewer. +2. Drag the file output from SimulariumIO from your file browser onto the window or use the file upload dialogue to choose your file + +## Sharing links to results +1. Upload your Simularium file to one of the supported public cloud providers, currently Dropbox, Google Drive, or Amazon S3, and get a publicly accessible link to the file. +2. In a supported browser, navigate to https://simularium.allencell.org/viewer?trajUrl=[link to your file]. You can share this link with collaborators or post it on your website so that others can interactively view your results. + +___ + ## Quick Start ### Convert spatial trajectory from a supported engine