refactor: updated documentation links

Author: jonrkarr

Dockerfile

@@ -4,7 +4,7 @@ LABEL \
     org.opencontainers.image.title="BioSimulators Jupyter server" \
     org.opencontainers.image.description="Jupyter server in a Python environment with the validated simulation tools registered with BioSimulators" \
     org.opencontainers.image.url="https://github.com/biosimulators/Biosimulators_tutorials" \
-    org.opencontainers.image.documentation="https://biosimulators.org/help" \
+    org.opencontainers.image.documentation="https://docs.biosimulations.org/" \
     org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_tutorials" \
     org.opencontainers.image.authors="BioSimulators Team <[email protected]>" \
     org.opencontainers.image.vendor="BioSimulators Team"

tutorials/2. Creating simulations/Creating SED-ML and COMBINE archives from model files.ipynb

@@ -48,7 +48,7 @@
    "id": "1574534c-6b52-4148-8896-c7a445d21e07",
    "metadata": {},
    "source": [
-    "[runBioSimuations](https://run.biosimulations.org/create) provides a simple web form for building COMBINE/OMEX archives with SED-ML files from model files (e.g., CellML, SBML). This tool support all of the modeling languages supported by BioSimulators."
+    "[runBioSimuations](https://run.biosimulations.org/utils/create-project) provides a simple web form for building COMBINE/OMEX archives with SED-ML files from model files (e.g., CellML, SBML). This tool support all of the modeling languages supported by BioSimulators."
    ]
   },
   {

tutorials/3. Validating models and simulations/2. Validating simulation experiments (SED-ML files).ipynb

@@ -20,7 +20,7 @@
     "</div>\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
-    "    SED-ML is under active development. The SED-ML community is working toward a single interpretation of SED-ML. BioSimulators supports the interpretation of SED-ML described at <a href=\"https://biosimulators.org/conventions/simulation-experiments\">https://biosimulators.org</a>.\n",
+    "    SED-ML is under active development. The SED-ML community is working toward a single interpretation of SED-ML. BioSimulators supports the interpretation of SED-ML described at <a href=\"https://docs.biosimulations.org/concepts/conventions/simulation-experiments/\">https://docs.biosimulations.org</a>.\n",
     "</div>"
    ]
   },

tutorials/3. Validating models and simulations/3. Validating metadata (OMEX Metadata files).ipynb

@@ -17,7 +17,7 @@
     "\n",
     "BioSimulators supports two minimum information conventions for OMEX Metadata files:\n",
     "* **OMEX Metadata** (`rdf_triples`): No minimum set of information is required. This convention supports anything that can be encoded in RDF. Validation is performed using [libOmexMeta](https://sys-bio.github.io/libOmexMeta/).\n",
-    "* **BioSimulations** (`biosimulations`): We recommend using the BioSimulations minimum information convention. This convention imposes additional requirements beyond the OEMX Metadata convention for minimal metdata about a COMBINE archive, including a title, at least one creator, and a license. More information about this convention is available at [https://biosimulators.org](https://biosimulators.org/conventions/metadata).\n",
+    "* **BioSimulations** (`biosimulations`): We recommend using the BioSimulations minimum information convention. This convention imposes additional requirements beyond the OEMX Metadata convention for minimal metdata about a COMBINE archive, including a title, at least one creator, and a license. More information about this convention is available at [https://docs.biosimulations.org](https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/).\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "    OMEX Metadata files can describe thumbnails for simulation projects. OMEX Metadata files can be validated independently from these thumbnails. However, this will not validate the thumbnails. More comprehensive validation, including related images, is available through the validation of simulation projects (COMBINE/OMEX archives). Please see the <a href=\"4.%20Validating%20simulation%20projects%20(COMBINE-OMEX%20archives).ipynb\">simulation project validation tutorial</a> for more information.\n",

tutorials/3. Validating models and simulations/4. Validating simulation projects (COMBINE-OMEX archives).ipynb

@@ -26,7 +26,7 @@
     "This format uses URIs to describe the format of each file in archives. `biosimulators_utils.combine.data_model.CombineArchiveContentFormat` enumerates many formats commonly used with COMBINE/OMEX archives.\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
-    "    SED-ML is under active development. The SED-ML community is working toward a single interpretation of SED-ML. BioSimulators supports the interpretation of SED-ML described at <a href=\"https://biosimulators.org/conventions/simulation-experiments\">https://biosimulators.org</a>.\n",
+    "    SED-ML is under active development. The SED-ML community is working toward a single interpretation of SED-ML. BioSimulators supports the interpretation of SED-ML described at <a href=\"https://docs.biosimulations.org/concepts/conventions/simulation-experiments/\">https://docs.biosimulations.org</a>.\n",
     "</div>\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
@@ -2387,7 +2387,7 @@
     "\n",
     "Two conventions for minimum metadata are supported:\n",
     "* **OMEX Metadata** (`rdf_triples`): This convention does not require any minimal set of metadata. This convention supports anything that can be encoded in RDF. Validation is performed using [libOmexMeta](https://sys-bio.github.io/libOmexMeta/).\n",
-    "* **BioSimulations** (`BioSimulations`): We recommend using the BioSimulations convention. This convention imposes additional requirements beyond the OMEX Metadata convention for minimal metdata about a simulation project, including a title, at least one creator, and a license. More information about this convention is available at [https://biosimulators.org](https://biosimulators.org/conventions/metadata)."
+    "* **BioSimulations** (`BioSimulations`): We recommend using the BioSimulations convention. This convention imposes additional requirements beyond the OMEX Metadata convention for minimal metdata about a simulation project, including a title, at least one creator, and a license. More information about this convention is available at [https://docs.biosimulations.org](https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/)."
    ]
   },
   {

tutorials/5. Executing simulations/Executing simulation projects.ipynb

@@ -243,7 +243,7 @@
       "  'ALGORITHM_SUBSTITUTION_POLICY': Policy for substituting alternative algorithms.\n",
       "    Options: 'ANY', 'DISTINCT_APPROXIMATIONS', 'DISTINCT_SCALES', 'NONE', 'SAME_FRAMEWORK', 'SAME_MATH', 'SAME_METHOD', 'SAME_VARIABLES', 'SIMILAR_APPROXIMATIONS', 'SIMILAR_VARIABLES'\n",
       "    Default value: 'SIMILAR_VARIABLES'\n",
-      "    More information: https://biosimulators.org/conventions/simulator-interfaces\n",
+      "    More information: https://docs.biosimulations.org/concepts/conventions/simulator-interfaces/\n",
       "\n",
       "  'BUNDLE_OUTPUTS': Whether to bundle all of the exported reports and plots generated by the execution of a COMBINE/OMEX archive into zip files for all reports and all plots.\n",
       "    Options: '0', '1'\n",
@@ -344,7 +344,7 @@
       "  'VERBOSE': Whether to print additional information about simulation runs.\n",
       "    Options: '0', '1'\n",
       "    Default value: '0'\n",
-      "    More information: https://biosimulators.org/conventions/simulator-interfaces\n",
+      "    More information: https://docs.biosimulations.org/concepts/conventions/simulator-interfaces/\n",
       "\n",
       "  'VIZ_FORMATS': Comma-separated list of formats to save each SED-ML plot.\n",
       "    Options: 'jpg', 'pdf', 'png', 'svg'\n",