Add JOSS citation (#208)

* add joss citation

* fix broken link

* Revert "Mention MOD and morph files in LICENSE (#33)"

This reverts commit baebfcb.

* keep main license intact

Author: ilkilic

LICENSE

@@ -1,10 +1,3 @@
-BlueCellulab is licensed under the Apache License, unless noted otherwise, 
-e.g., for external dependencies such as MOD or morphology files.
-For MOD files for which the original source is available on ModelDB, 
-any specific licenses on mentioned on ModelDB, or the generic License of ModelDB apply.
-The licenses of the morphology files used in this repository are available on: https://zenodo.org/record/5909613
-
-
                                  Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/

README.rst

@@ -16,9 +16,10 @@ BlueCelluLab
 +----------------+------------+
 | Gitter         | |gitter|   |
 +----------------+------------+
-| Citation       | |zenodo|   |
+| Paper          | |joss|     |
++----------------+------------+
+| Zenodo         | |zenodo|   |
 +----------------+------------+
-
 
 The Blue Brain Cellular Laboratory is designed for simulations and experiments on individual cells or groups of cells.
 Suitable use cases for BlueCelluLab include:
@@ -38,20 +39,25 @@ Suitable use cases for BlueCelluLab include:
 Citation
 ========
 
-When you use this BlueCelluLab software for your research, we ask you to cite the following reference(this includes poster presentations):
+When using the BlueCelluLab software for your research, please cite the following paper (including for poster presentations): `BlueCelluLab: Biologically Detailed Neural Network Experimentation API <https://doi.org/10.21105/joss.07026>`_
 
 .. code-block::
 
-    @software{bluecellulab_zenodo,
-      author       = {Tuncel, Anil and Van Geit, Werner and Gevaert, Mike and Torben-Nielsen, Benjamin and Mandge, Darshan and Kilic, Ilkan and Jaquier, Aurélien and Muller, Eilif and Kanari, Lida and Markram, Henry},
-      title        = {BlueCelluLab},
-      month        = jul,
-      year         = 2023,
-      publisher    = {Zenodo},
-      doi          = {10.5281/zenodo.8113483},
-      url          = {https://doi.org/10.5281/zenodo.8113483}
+    @article{Tuncel2024,
+        doi = {10.21105/joss.07026},
+        url = {https://doi.org/10.21105/joss.07026},
+        year = {2024},
+        publisher = {The Open Journal},
+        volume = {9},
+        number = {100},
+        pages = {7026},
+        author = {Anıl Tuncel and Werner Van Geit and Mike Gevaert and Benjamin Torben-Nielsen and Darshan Mandge and İlkan Kılıç and Aurélien Jaquier and Eilif Muller and Lida Kanari and Henry Markram},
+        title = {BlueCelluLab: Biologically Detailed Neural Network Experimentation API},
+        journal = {Journal of Open Source Software}
     }
 
+If you need to cite a specific version, please use the DOI provided by `Zenodo <https://zenodo.org/records/8113483>`_, which you can access via the "Cite this repository" button at the top of the repository page.
+
 Support
 =======
 
@@ -161,6 +167,10 @@ The licenses of the morphology files used in this repository are available on: h
                  :target: https://gitter.im/BlueBrain/BlueCelluLab
                  :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab
 
+.. |joss| image:: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg
+                :target: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff
+                :alt: JOSS
+
 .. |zenodo| image:: https://zenodo.org/badge/640805129.svg
                  :target: https://zenodo.org/badge/latestdoi/640805129
 

examples/2-sonata-network/sonata-network.ipynb

@@ -42,16 +42,6 @@
     "**Note**: The compiled mechanisms need to be provided before importing bluecellulab."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# hack that imports libsonata before NEURON to avoid libc conflict\n",
-    "import libsonata  # https://github.com/BlueBrain/libsonata/issues/273"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

examples/6-stimuli-sequence/stimuli-sequence.ipynb

@@ -231,14 +231,14 @@
     "        ax[1].plot(recording.time, recording.voltage, label=label_txt, alpha=0.8)\n",
     "\n",
     "    ax[0].legend(fontsize=legend_fontsize)\n",
-    "    ax[0].set_title(f'Injected Current', fontsize=title_fontsize)\n",
+    "    ax[0].set_title('Injected Current', fontsize=title_fontsize)\n",
     "    ax[0].set_xlabel('Time (ms)', fontsize=label_fontsize)\n",
     "    ax[0].set_ylabel('Injected Current (nA)', fontsize=label_fontsize)\n",
     "    ax[0].tick_params(axis='both', which='major', labelsize=tick_fontsize)\n",
     "    ax[0].tick_params(axis='both', which='minor', labelsize=tick_fontsize)\n",
     "\n",
     "    ax[1].legend(fontsize=legend_fontsize, loc='upper right')\n",
-    "    ax[1].set_title(f'Cell Response', fontsize=title_fontsize)\n",
+    "    ax[1].set_title('Cell Response', fontsize=title_fontsize)\n",
     "    ax[1].set_xlabel('Time (ms)', fontsize=label_fontsize)\n",
     "    ax[1].set_ylabel('Membrane Potential (mV)', fontsize=label_fontsize)\n",
     "    ax[1].tick_params(axis='both', which='major', labelsize=tick_fontsize)\n",
@@ -250,11 +250,11 @@
     "\n",
     "    title = ''\n",
     "    if \"FIRE_PATTERN\" in stimulus:\n",
-    "        title = f'FirePattern Stimulus Cell Response'\n",
+    "        title = 'FirePattern Stimulus Cell Response'\n",
     "    elif \"IV\" in stimulus:\n",
-    "        title = f'IV Stimulus Cell Response'\n",
+    "        title = 'IV Stimulus Cell Response'\n",
     "    elif \"POS_CHEOPS\" in stimulus:\n",
-    "        title = f'POSCHEOPS Stimulus Cell Response'\n",
+    "        title = 'POSCHEOPS Stimulus Cell Response'\n",
     "\n",
     "    fig.suptitle(title ,fontsize=20)\n",
     "\n",
@@ -535,7 +535,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -549,7 +549,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.7.4"
   }
  },
  "nbformat": 4,