diff --git a/README.md b/README.md
index 073892372e881e551ee3bff25d796b77b80f9dbb..85967ef28580ec3ce06e677ae4a781f535d86275 100644
--- a/README.md
+++ b/README.md
@@ -38,12 +38,13 @@ How to do:
If you use or adapt the SSBtoolkit for your own research projects please cite us.
```
-@article{XXX,
- title={XXX},
- author={XXX},
- publisher={XXX},
- note={\url{XXX}},
- year={XXX}
+@article{ribeiro_ssb_2022,
+ title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},
+ author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},
+ publisher={bioRxiv},
+ url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},
+ doi={10.1101/2022.11.08.515595},
+ year={2022}
}
```
diff --git a/SSBtoolkit-Tutorial1-EBRAINS.ipynb b/SSBtoolkit-Tutorial1-EBRAINS.ipynb
index bf243a6160351fd2e68fcc78a5c3cf61326aaec4..78ee9789da3d2331d227298e406becb79ce58a75 100644
--- a/SSBtoolkit-Tutorial1-EBRAINS.ipynb
+++ b/SSBtoolkit-Tutorial1-EBRAINS.ipynb
@@ -429,12 +429,13 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
diff --git a/SSBtoolkit-Tutorial1.ipynb b/SSBtoolkit-Tutorial1.ipynb
index fb71030d7632b1b8f23e08525946fbd05cb7e982..1a80b971fda1a9d09cb12aeb703d5119d546eafa 100644
--- a/SSBtoolkit-Tutorial1.ipynb
+++ b/SSBtoolkit-Tutorial1.ipynb
@@ -466,17 +466,17 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
"\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
@@ -486,14 +486,6 @@
" <img src=\"https://res.cloudinary.com/djz27k5hg/image/upload/v1642677502/logos/COFUNDED_EU_j2ktlp.jpg\" width=\"300\" align='left' style=\"margin-left:50px\">\n",
"</div> "
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "690b7ff2",
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
diff --git a/SSBtoolkit-Tutorial2-EBRAINS.ipynb b/SSBtoolkit-Tutorial2-EBRAINS.ipynb
index b7a2aae4983bedac3732c2fcc032378ccca2ada8..07a4e81548048dd4111bd179c19005c062e32a5f 100644
--- a/SSBtoolkit-Tutorial2-EBRAINS.ipynb
+++ b/SSBtoolkit-Tutorial2-EBRAINS.ipynb
@@ -455,17 +455,17 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
"\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/SSBtoolkit-Tutorial2.ipynb b/SSBtoolkit-Tutorial2.ipynb
index 476ca872c35e5178dd1e9fbc27ca1ce47abbd200..adb870e1c4727883f88c512d5b53005810998c54 100644
--- a/SSBtoolkit-Tutorial2.ipynb
+++ b/SSBtoolkit-Tutorial2.ipynb
@@ -489,12 +489,13 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
diff --git a/SSBtoolkit-Tutorial3A-EBRAINS.ipynb b/SSBtoolkit-Tutorial3A-EBRAINS.ipynb
index 656fe1569f65c2540cb2a22f11bf123214b28a11..1d95d69430476367203e7c0c3c2027f75cbf80c8 100644
--- a/SSBtoolkit-Tutorial3A-EBRAINS.ipynb
+++ b/SSBtoolkit-Tutorial3A-EBRAINS.ipynb
@@ -398,17 +398,17 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
"\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/SSBtoolkit-Tutorial3A.ipynb b/SSBtoolkit-Tutorial3A.ipynb
index 47fecc0d5c87adce65363d8730f9ffdda0adc900..7d097c7203796bd7872c5c1ec10eea14ca7b5369 100644
--- a/SSBtoolkit-Tutorial3A.ipynb
+++ b/SSBtoolkit-Tutorial3A.ipynb
@@ -434,17 +434,16 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
- "\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb b/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb
index 9953102d96ae95f328d113b639ee3f811eebba34..1e42af74e339cd3e186b4809cab2f04bbc197138 100644
--- a/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb
+++ b/SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb
@@ -472,17 +472,17 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
"\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/SSBtoolkit-Tutorial3B-tauRAMD.ipynb b/SSBtoolkit-Tutorial3B-tauRAMD.ipynb
index cf71cca84cd5ba99e5b27936f76dfc84565c4ecf..b56eab307c4be11ea9f8b9d3045b2f4f711a0ba4 100644
--- a/SSBtoolkit-Tutorial3B-tauRAMD.ipynb
+++ b/SSBtoolkit-Tutorial3B-tauRAMD.ipynb
@@ -201836,17 +201836,16 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
- "\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb b/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb
index 0ed02cb64d492dc626399a52b10661456fccd0b0..ab4b7d5edf4de2e12e6552d8c417466f3a4641a7 100644
--- a/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb
+++ b/SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb
@@ -299,17 +299,17 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
"\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/SSBtoolkit-Tutorial4-OXTR.ipynb b/SSBtoolkit-Tutorial4-OXTR.ipynb
index 1a92f2fc5161d890ca8289720b1bfdd8b4ddbab0..40b95b6dbd060bbd7c512bb49406655dba08d6b2 100644
--- a/SSBtoolkit-Tutorial4-OXTR.ipynb
+++ b/SSBtoolkit-Tutorial4-OXTR.ipynb
@@ -335,17 +335,16 @@
"If you use or adapt this tutorial for your own research projects please cite us.\n",
"\n",
"```\n",
- "@article{XXX,\n",
- " title={XXX},\n",
- " author={XXX},\n",
- " publisher={XXX},\n",
- " note={\\url{XXX}},\n",
- " year={XXX}\n",
+ "@article{ribeiro_ssb_2022,\n",
+ " title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},\n",
+ " author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},\n",
+ " publisher={bioRxiv},\n",
+ " url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},\n",
+ " doi={10.1101/2022.11.08.515595},\n",
+ " year={2022}\n",
"}\n",
"```\n",
"\n",
- "\n",
- "\n",
"## Acknowledgments\n",
"\n",
"EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).\n",
diff --git a/docs/index.rst b/docs/index.rst
index bed72126fdb0bf0710fbe945d210a121f0b736ed..e304d48faaa089e104fb7ef79fab308cbcfe5c23 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -82,15 +82,13 @@ publications, please cite it. The BibTeX reference is
::
- @article{,
- title = {},
- author = {},
- journal = {},
- volume = {},
- number = {},
- pages = {},
- year = {},
- doi = {}
+ @article{ribeiro_ssb_2022,
+ title={{SSB} toolkit: from molecular structure to subcellular signaling pathways.},
+ author={Ribeiro, Rui Pedro and Gossen, Jonas and Rossetti, Giulia and Giorgetti, Alejandro},
+ publisher={bioRxiv},
+ url={https://www.biorxiv.org/content/10.1101/2022.11.08.515595v1},
+ doi={10.1101/2022.11.08.515595},
+ year={2022}
}