update README

Author: jcschaff

README.md

@@ -7,45 +7,59 @@
 [![License](https://img.shields.io/github/license/virtualcell/pyvcell)](https://img.shields.io/github/license/virtualcell/pyvcell)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/101BPDYqu4_PupqmunT6Qhextks_VT-8X?usp=sharing)
 
-This is the python wrapper for vcell modeling and simulation
+This is the python wrapper for vcell modeling and simulation for
 
-- **Github repository**: <https://github.com/virtualcell/pyvcell/>
-- **Documentation** <https://virtualcell.github.io/pyvcell/>
+1. local scripting of spatial modeling, simulation, data analysis and visualization workflows using Virtual Cell technology
+2. access to Virtual Cell remote APIs - with public access or as an authenticated Virtual Cell user.
 
-## Getting started with your project
+## Local simulation, analysis and visualization with pyvcell
 
-First, create a repository on GitHub with the same name as this project, and then run the following commands:
+### download or create new spatial models
 
-```bash
-git init -b main
-git add .
-git commit -m "init commit"
-git remote add origin git@github.com:virtualcell/pyvcell.git
-git push -u origin main
-```
+- load/save VCML (Virtual Cell’s native format - import/export to VCell UI)
+- load/save SBML (Systems Biology Markup Language)
+- load from Antimony (friendly textual language for SBML)
+- create/edit any VCML object (e.g. species, model, geometry) programmatically
 
-Finally, install the environment and the pre-commit hooks with
+### local editing with Python objects
 
-```bash
-make install
-```
+- edit parameters. add/remove/edit species, compartments, reactions, initial conditions, diffusion coefficients
+- create/edit geometry objects, create/edit vcell applications and simulations
+
+### run local simulations
+
+- run local spatial simulations (for reactions, diffusion, and advection) stored in local workspace.
+
+### analyze local simulation result:
 
-You are now ready to start development on your project!
-The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
+- Time-series summary statistics available as NumPy arrays.
+- spatiotemporal arrays stored as Zarr datastores and available as NumPy arrays.
+- 3D mesh data using VTK unstructured grids, analyzed with VTK
 
-To finalize the set-up for publishing to PyPi or Artifactory, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/publishing/#set-up-for-pypi).
-For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/mkdocs/#enabling-the-documentation-on-github).
-To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/codecov/).
+### local visualization
 
-## Releasing a new version
+- built-in plotting and 3D visualization via Matplotlib and VTK/PyVista
+- make your own plots or 3D renderings.
 
-- Create an API Token on [Pypi](https://pypi.org/).
-- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/virtualcell/pyvcell/settings/secrets/actions/new).
-- Create a [new release](https://github.com/virtualcell/pyvcell/releases/new) on Github.
-- Create a new tag in the form `*.*.*`.
+# installation
 
-For more details, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/cicd/#how-to-trigger-a-release).
+The easiest way to install pyvcell is by using the Python Package Index and pip.
+We highly recommend setting up a virtual environment for dependency management.
+Run the following command to install pyvcell from PyPI
+
+```shell
+pip install pyvcell
+```
+
+# Usage
+
+```python
+import pyvcell.vcml as vc
+biomodel = vc.load_vcml_file('path/to/your/model.vcml')
+results = vc.simulate(biomodel, "sim1")
+results.plotter.plot_concentrations()
+```
 
----
+# Documentation
 
-Repository initiated with [fpgmaas/cookiecutter-poetry](https://github.com/fpgmaas/cookiecutter-poetry).
+coming soon.