diff --git a/jupyter-prometheus/combined_demos/TCIA_notebook.ipynb b/jupyter-prometheus/combined_demos/TCIA_notebook.ipynb index 36b4ef1c..7ecf9c2c 100644 --- a/jupyter-prometheus/combined_demos/TCIA_notebook.ipynb +++ b/jupyter-prometheus/combined_demos/TCIA_notebook.ipynb @@ -927,11 +927,39 @@ "With these extensions the notebook evolves from a showcase into a\n", "production-ready radiogenomic analysis scaffold.\n" ] + }, + { + "cell_type": "markdown", + "id": "c8ae151d", + "metadata": {}, + "source": [ + "## 📚 References & Recommended Resources\n", + "\n", + "1. **Do, N., Grossman, R. L., Feldman, T., _et al._ (2019).** “The Veterans Precision Oncology Data Commons: Transforming VA data into a national resource for research in precision oncology.” *Seminars in Oncology* **46**(4-5), 314–320. \n", + "\n", + "2. **Clark, K., Vendt, B., Smith, K., _et al._ (2013).** “The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository.” *Journal of Digital Imaging* **26**, 1045–1057. \n", + "\n", + "3. **VA Precision Oncology Data Commons Portal.** Accessed July 2025. \n", + "\n", + "4. **The Cancer Imaging Archive (TCIA) Portal.** Accessed July 2025. \n", + "\n", + "---\n", + "\n", + "### 🔗 Helpful How‑Tos & Client Tools\n", + "\n", + "* **Gen3 Client Documentation:** \n", + "* **Gen3 Commons Portal:** \n", + "* **VPODC Project Overview:** \n", + "\n", + "> **Tip:** If you encounter HTTP 403 errors when downloading data, verify that your Gen3 credentials JSON is present in `~/.gen3/credentials.json` and that your account has the proper access policies.\n", + "\n", + "For additional assistance, contact your program’s system administrator or open a ticket with Gen3 Support." + ] } ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3", "language": "python", "name": "python3" }, @@ -945,7 +973,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.6.10" } }, "nbformat": 4, diff --git a/jupyter-prometheus/combined_demos/VPODC_data_download_guide.ipynb b/jupyter-prometheus/combined_demos/VPODC_data_download_guide.ipynb index 6d8fe1f9..fd3dc58b 100644 --- a/jupyter-prometheus/combined_demos/VPODC_data_download_guide.ipynb +++ b/jupyter-prometheus/combined_demos/VPODC_data_download_guide.ipynb @@ -2111,20 +2111,36 @@ "metadata": {}, "source": [ "---\n", - "## 📚 References and Next Steps\n", - "- [Gen3 Client Documentation](https://gen3.org/resources/user/gen3-client/)\n", - "- [Gen3 Commons Portal](https://gen3.datacommons.io/)\n", + "## 📚 References\n", + "\n", + "\n", + "\n", + "1. **Do N, Grossman RL, Feldman T, et al. (2019)**. “The Veterans Precision Oncology Data Commons: Transforming VA data into a national resource for research in precision oncology.” *Seminars in Oncology* **46**(4–5):314–320. DOI: [10.1053/j.seminoncol.2019.09.002](https://doi.org/10.1053/j.seminoncol.2019.09.002) \n", + "\n", + "2. **Elbers DC, Fillmore NR, Sung F‑C, et al. (2020)**. “The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database.” *Patterns* **1**:100083. DOI: [10.1016/j.patter.2020.100083](https://doi.org/10.1016/j.patter.2020.100083) \n", + "\n", + "3. **Cheng D, Ramos‑Cejudo J, Tuck D, et al. (2019)**. “External validation of a prognostic model for mortality among patients with non‑small‑cell lung cancer using the Veterans Precision Oncology Data Commons.” *Seminars in Oncology* **46**(4–5):327–333. DOI: [10.1053/j.seminoncol.2019.09.006](https://doi.org/10.1053/j.seminoncol.2019.09.006) \n", + "\n", + "\n", + "\n", + "---\n", + "\n", + "### 🔗 Useful Resources\n", + "\n", + "- [Gen3 Client Documentation](https://gen3.org/resources/user/gen3-client/) \n", + "- [Gen3 Commons Portal](https://gen3.datacommons.io/) \n", "- [VPODC Project Overview](https://vpodc.data-commons.org/)\n", "\n", - "If you encounter download errors (e.g., HTTP 403), ensure your Gen3 credentials are correctly configured and your profile has access permissions.\n", + "---\n", "\n", - "For additional help, contact your system administrator or Gen3 support." + "> ⚠️ If you encounter download errors (e.g., HTTP 403), ensure your Gen3 credentials are correctly configured and your profile has appropriate access. \n", + "> For additional support, contact your system administrator or the Gen3 support team.\n" ] } ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3", "language": "python", "name": "python3" }, @@ -2138,7 +2154,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.6.10" } }, "nbformat": 4,