From 0ab204b2ef83d44918608c285c7fbe9466c61f20 Mon Sep 17 00:00:00 2001 From: Eran Date: Mon, 4 Mar 2024 14:02:13 -0500 Subject: [PATCH] v1.0.0 --- README.md | 18 +++++++++++++----- setup.py | 6 +++--- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index ecd3c2e..488375f 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,19 @@ interactions with both membrane bound and soluble factors (e.g., cytokines, cyto environment. Particularly this model is useful for testing variations in T cell immunotherapies and we have integrated with multiplexed imaging datasets for initialization of the model and also verifying expected behavior. +## Citing This Work + +If you use this model in your research, please cite our accompanying paper: + +Hickey, J. W., Agmon, E., Horowitz, N., Lamore, M., Sunwoo, J. B., Covert, M., & Nolan, G. P. (In Press). +Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical +Component of Therapeutic T Cell Efficacy. Cell Systems. + +The figures in the paper were generated using version 1.0.0 of this model, available on PyPI. The notebooks and figures +present in this readme were produced using an earlier version, 0.0.28, which is consistent with the simulations +described in the paper when the lymph node interactions are turned off in version 1.0.0. + + ## Notebook Tutorials ### Static notebooks: @@ -17,11 +30,6 @@ integrated with multiplexed imaging datasets for initialization of the model and Introduces the Vivarium processes, composites, and the full ABM as process bigraph diagrams. * [Killing Experiments](https://nbviewer.org/github/vivarium-collective/tumor-tcell/blob/master/jupyter_notebooks/Killing%20Experiments.ipynb): A notebook for modeling in-vitro killing experiments that can be run from a machine with the repository installed locally. - -### Colab notebooks: -This Model Tutorial can be altered by the user in a online environment and used to run experiments: - * [Model Tutorial](https://colab.research.google.com/github/vivarium-collective/tumor-tcell/blob/master/jupyter_notebooks/tumor_tcell_model.ipynb) - ## Description of models diff --git a/setup.py b/setup.py index 41dc59e..520cede 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ setup( name='tumor-tcell', - version='0.0.47', + version='1.0.0', packages=[ 'tumor_tcell', 'tumor_tcell.composites', @@ -18,7 +18,7 @@ 'tumor_tcell.plots', ], author='John Hickey, Eran Agmon', - author_email='jwhickey@stanford.edu, agmon@uchc.edu', + author_email='john.hickey@duke.edu, agmon@uchc.edu', url='https://github.com/vivarium-collective/tumor-tcell', license='MIT', entry_points={ @@ -28,7 +28,7 @@ package_data={}, include_package_data=True, install_requires=[ - 'vivarium-core>=1.6.0', + 'vivarium-core==1.6.0', 'vivarium-multibody==0.0.12', 'tqdm', 'opencv-python',