From 42eebb839e73339b38c4be0500844e387e385271 Mon Sep 17 00:00:00 2001 From: Rui Ribeiro <rui.ribeiro@icloud.com> Date: Thu, 10 Nov 2022 10:42:38 +0100 Subject: [PATCH] release --- README.md | 13 ++++++------ SSBtoolkit-Tutorial1-EBRAINS.ipynb | 13 ++++++------ SSBtoolkit-Tutorial1.ipynb | 22 +++++++-------------- SSBtoolkit-Tutorial2-EBRAINS.ipynb | 14 ++++++------- SSBtoolkit-Tutorial2.ipynb | 13 ++++++------ SSBtoolkit-Tutorial3A-EBRAINS.ipynb | 14 ++++++------- SSBtoolkit-Tutorial3A.ipynb | 15 +++++++------- SSBtoolkit-Tutorial3B-tauRAMD-EBRAINS.ipynb | 14 ++++++------- SSBtoolkit-Tutorial3B-tauRAMD.ipynb | 15 +++++++------- SSBtoolkit-Tutorial4-OXTR-EBRAINS.ipynb | 14 ++++++------- SSBtoolkit-Tutorial4-OXTR.ipynb | 15 +++++++------- docs/index.rst | 16 +++++++-------- 12 files changed, 84 insertions(+), 94 deletions(-) diff --git a/README.md b/README.md index 0738923..85967ef 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 bf243a6..78ee978 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 fb71030..1a80b97 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 b7a2aae..07a4e81 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 476ca87..adb870e 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 656fe15..1d95d69 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 47fecc0..7d097c7 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 9953102..1e42af7 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 cf71cca..b56eab3 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 0ed02cb..ab4b7d5 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 1a92f2f..40b95b6 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 bed7212..e304d48 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} } -- GitLab