Update README

README.md

@@ -1,91 +1,34 @@
 # Angiogenesis
 
-## Project description
+This is the code base for the publication:
+**Bridging scales: A hybrid model to simulate vascular tumor growthand treatment response**
+by Duswald, Lima, Oden, and Wohlmuth (2023) available [here](https://doi.org/10.1016/j.cma.2023.116566).
 
-* Goal: simulate cancer and the related phenomenon angiogenesis with a hybrid
-  (ABM+PDE) model.
-* Stages: 
-  1) Scenario: few hypoxic cancer cells surrounding a vessel. Cells secrete VEGF
-     to trigger sprouting and apical growth. The vessel then grows towards the 
-     cells and if the nutrient concentration at the hypoxic cells is beyond a 
-     threshold (or they are simply close to a vessel), then the cell become 
-     quiescent. Vessels are supposed to follow the gradient.
-  2) Possible extensions:
-     * Include growth of primary tumor
-     * Possibly include complicated initial vessel configurations from image 
-       data
-     * Use more complicated continuum models
-* Data: yet to be defined
-* Metrics: yet to be defined
-
-## Software stack
+## Software Stack and Depndencies
 
 *  BioDynaMo. To install, consult the 
   [BDM dev-guide](https://biodynamo.org/docs/devguide/build/). Install the 
   latest master as described in the link. Following the dev-guide allows us to
   easily upgrade and extend BioDynaMo if necessary.
 
-## Running the simulation
+## Running the simulations
 
-BioDynaMo needs to be installed and sourced, e.g.
-```bash
-source <path_to_biodynamo>/biodynamo/build/bin/thisbdm.sh
-```
-The simulation can then be executed by simply running 
-```bash
-bdm run
+Building on the BioDynaMo platform, the commands to running the simulations
+assume a functional installation of BioDynaMo and are
 ```
-in your project directory. You can verify component of the model by running a 
-very similar command
-```bash
-bdm test
-``` 
-We outsourced all parameters steering the simulation to `src/sim_param.h` and 
-one can modify the parameters in `bdm.json` without the need to recompile the 
-simulation. Further ways to feed parameters to the simulation are the following:
-
-1. ```cpp
-    // Define parameters
-    auto set_param = [&](Param* param) {
-      auto* sparam = param->Get<SimParam>();
-      param->statistics = true;
-      param->calculate_gradients = false;
-      sparam->some_value = some_value
-    };
-
-    // Initialize the simulation
-    Simulation simulation(argc, argv, set_param);
-    ```
-2. We can use BioDynaMo's CLI, e.g. 
-   ```
-   ./build/angiogenesis --inline-config '{ "bdm::SimParam": { "x": 6.28 } }'
-   ```
-
-The output of the simulation is, by default, available in 
-`output/angiogenesis`.
-
-## Visualization
-
-Assuming that one has successfully sourced and executed the simulation, the user
-simply follows up with the paraview command"
-```bash
 source <path>/thisbdm.sh
+bdm build
 bdm run
-paraview
-```
-The place where we call `paraview` is indeed important. This opens a ParaView
-window. Follow with
+bdm view
 ```
-File >> Load State... >> "output/angiogenesis/angiogenesis.pvsm" >> \
-Use File Name from States
-```
-and the simulation output is ready to view. Simply click play.
 
-## Results backup
+## Reproducing the results of the publication
 
-In case we accidentally delete the project, the results are backed up in the 
-Cernbox cloud. The backup is automated, e.g. run
-```
-./backup_results.sh
-```
-to compress the results folder and copy it to the Cernbox.
+Reproducing the results of the different experiments of the publication
+requires setting the correct parameters but also minimal changes to code, i.e.,
+possibly adding a few lines of code to adequately set the initial conditions.
+This process it automated in a second repository that can be found at
+`TobiasDuswald/bdm-angiogenesis-reproducer`. Please consult the
+[README.md](https://github.com/TobiasDuswald/bdm-angiogenesis-reproducer/blob/main/README.md)
+of that [repository](https://github.com/TobiasDuswald/bdm-angiogenesis-reproducer)
+for further instructions.