volkamerlab · AndreaVolkamer · Jun 29, 2023 · May 24, 2023 · May 24, 2023 · Jun 2, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -9,8 +9,8 @@ on:
       - "master"
       - "dev"
   schedule:
-    # Run a cron job once weekly on Monday
-    - cron: "0 3 * * 1"
+    # every two weeks on Monday at 3 am
+    - cron: "0 3/336 * * 1"
 
 jobs:
   test:

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -11,8 +11,8 @@ on:
       - "dev"
       - "maintenance/.+"
   schedule:
-    # Run a cron job once weekly on Monday
-    - cron: "0 3 * * 1"
+    # every two weeks on Monday at 3 am
+    - cron: "0 3/336 * * 1"
 
 jobs:
   docs:
@@ -58,28 +58,28 @@ jobs:
           sed -i 's|src="images/butina_full.pdf"|src="../_images/butina_full.pdf"|g' \
             _build/html/talktorials/T005_compound_clustering.html
 
-      #- name: Check 404s (Sphinx)
-        #shell: bash -l {0}
-        #run: |
-          #cd docs/_build/html
-          #npx linkinator . --verbosity error --recurse -r --retry-errors-jitter --timeout 10000 \
-            #-s "/*.txt" \
-            #-s "https://onlinelibrary.wiley.com/doi/*" \
-            #-s "https://wires.onlinelibrary.wiley.com/doi/*" \
-            #-s "https://chemistry-europe.onlinelibrary.wiley.com/doi/*" \
-            #-s "https://towardsdatascience.com" \
-            #-s "https://medium.com" \
-            #-s "https://*.medium.com" \
-            #-s "http[s]://quora.com" \
-            #-s "http[s]://doi.org/*" \
-            #-s "http[s]://pubs.acs.org/*" \
-            #-s "ftp://*" \
-            #-s "https://machinelearningmastery.com/*" \
-            #-s "https://www.schrodinger.com/training/videos/*" \
-            #-s "/*.mp4" \
-            #-s "/*.pdf" \
-            #-s "/*.png" \
-            #-s "https://www.icoa.fr/pkidb/index.html" \
+      - name: Check 404s (Sphinx)
+        shell: bash -l {0}
+        run: |
+          cd docs/_build/html
+          npx linkinator . --verbosity error --recurse -r --retry-errors-jitter --timeout 10000 \
+            -s "/*.txt" \
+            -s "https://onlinelibrary.wiley.com/doi/*" \
+            -s "https://wires.onlinelibrary.wiley.com/doi/*" \
+            -s "https://chemistry-europe.onlinelibrary.wiley.com/doi/*" \
+            -s "https://towardsdatascience.com" \
+            -s "https://medium.com" \
+            -s "https://*.medium.com" \
+            -s "http[s]://quora.com" \
+            -s "http[s]://doi.org/*" \
+            -s "http[s]://pubs.acs.org/*" \
+            -s "ftp://*" \
+            -s "https://machinelearningmastery.com/*" \
+            -s "https://www.schrodinger.com/training/videos/*" \
+            -s "/*.mp4" \
+            -s "/*.pdf" \
+            -s "/*.png" \
+            -s "https://www.icoa.fr/pkidb/index.html" \
 
 
       - name: Check 404s (README)

diff --git a/README.md b/README.md
@@ -40,6 +40,9 @@ TeachOpenCADD is a teaching platform developed by students for students, which p
 
 Each topic is covered in an interactive Jupyter Notebook, using open source packages such as the Python packages `rdkit`, `pypdb`, `biopandas`, `nglview`, and `mdanalysis` (find the full list [here](https://projects.volkamerlab.org/teachopencadd/external_dependencies.html)). Topics are continuously expanded and open for contributions from the community. Beyond their teaching purpose, the TeachOpenCADD material can serve as starting point for users’ project-directed modifications and extensions.
 
+
+**New edition**: we have extended the TeachOpenCADD platform with 6 notebooks introducing deep learning and its application to CADD related topics. 
+
 ## Get started
 
 <!-- markdown-link-check-disable -->
@@ -77,4 +80,4 @@ If you prefer to work in the context of a graphical interface, talktorials T001-
 
 Please refer to our TeachOpenCADD website to find a list of external resources:
 - [External packages and webservices](https://projects.volkamerlab.org/teachopencadd/external_dependencies.html) that are used in the TeachOpenCADD material
-- [Further reading material](https://projects.volkamerlab.org/teachopencadd/external_tutorials_collections.html) on Python programming, cheminformatics, structural bioinformatics, and more.
+- [Further reading material](https://projects.volkamerlab.org/teachopencadd/external_tutorials_collections.html) on Python programming, cheminformatics, structural bioinformatics, and more.
diff --git a/devtools/test_env.yml b/devtools/test_env.yml
@@ -3,9 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - mkl < 2022
-  - pytorch::pytorch==1.13.0
-  #- pyg::pyg==2.2.0
   - python>=3.8
   - pip
   - jupyterlab>=3
@@ -42,6 +39,9 @@ dependencies:
   - mdtraj
   - plip
   - openmm
+  - mkl < 2022
+  - pytorch::pytorch==1.13.0
+  #- pyg::pyg==2.2.0  # installed manually for now
   # Dependency not included, see https://github.com/volkamerlab/teachopencadd/issues/313
   # - openmmforcefields
   - pdbfixer

diff --git a/docs/_static/images/thumbnails/T011.svg b/docs/_static/images/thumbnails/T011.svg
diff --git a/docs/_static/images/thumbnails/T033.png b/docs/_static/images/thumbnails/T033.png
diff --git a/docs/_static/images/thumbnails/T034.png b/docs/_static/images/thumbnails/T034.png
diff --git a/docs/_static/images/thumbnails/T035.png b/docs/_static/images/thumbnails/T035.png
diff --git a/docs/_static/images/thumbnails/T036.png b/docs/_static/images/thumbnails/T036.png
diff --git a/docs/_static/images/thumbnails/T037.png b/docs/_static/images/thumbnails/T037.png
diff --git a/...ion_prediction/images/basic_structure.png → docs/_static/images/thumbnails/T038.png b/...ion_prediction/images/basic_structure.png → docs/_static/images/thumbnails/T038.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -62,6 +62,7 @@
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinx_copybutton",
     "sphinxext.opengraph",
+    "sphinx_gallery.load_style",
 ]
 
 autosummary_generate = True
@@ -231,3 +232,16 @@
 ogp_image = "https://raw.githubusercontent.com/volkamerlab/teachopencadd/master/docs/_static/images/TeachOpenCADD_topics.png"
 ogp_description_length = 300
 ogp_type = "website"
+
+
+# -- Thumbnails --
+
+nbsphinx_thumbnails = {
+    'talktorials/T011_query_online_api_webservices': '_static/images/thumbnails/T011.svg',
+    'talktorials/T033_molecular_representations': '_static/images/thumbnails/T033.png',
+    'talktorials/T034_recurrent_neural_networks': '_static/images/thumbnails/T034.png',
+    'talktorials/T035_graph_neural_networks': '_static/images/thumbnails/T035.png',
+    'talktorials/T036_e3_equivariant_gnn': '_static/images/thumbnails/T036.png',
+    'talktorials/T037_uncertainty_estimation': '_static/images/thumbnails/T037.png',
+    'talktorials/T038_protein_ligand_interaction_prediction': '_static/images/thumbnails/T038.png',
+}
diff --git a/docs/index.rst b/docs/index.rst
@@ -14,6 +14,8 @@ TeachOpenCADD is a teaching platform developed by students for students, which p
 
 For each topic, an interactive Jupyter Notebook is offered, using open source packages such as the Python packages ``rdkit``, ``pypdb``, ``biopandas``, ``nglview``, and ``mdanalysis``. Topics are continuously expanded and open for contributions from the community. Beyond their teaching purpose, the TeachOpenCADD material can serve as starting point for users’ project-directed modifications and extensions.
 
+*New edition*: we have extended the TeachOpenCADD platform with 6 notebooks introducing deep learning and its application to CADD related topics. 
+
 .. raw:: html
 
    <p align="center">

diff --git a/docs/installing.rst b/docs/installing.rst
@@ -14,6 +14,11 @@ Installing
 
 Install from the conda package
 ------------------------------
+.. note::
+
+    The conda package does not yet include all packages necessary to run the deep learning edition talktorials (T033-T038).
+
+    We are working on it and will post an update as soon as the new package is available.
 
 1. Create a new conda environment for TeachOpenCADD::
 

diff --git a/docs/talktorials.rst b/docs/talktorials.rst
@@ -25,7 +25,7 @@ Talktorials as presented in the original `JCIM 2019 article <https://jcheminf.bi
 Edition 2021
 ------------
 
-Talktorials of the second major release as presented in the `ChemRxiv preprint <https://doi.org/10.26434/chemrxiv-2021-8x13n>`_:
+Talktorials of the second major release as presented in the `Nucleic Acids Research 2022 article <https://academic.oup.com/nar/article/50/W1/W753/6582172>`_:
 
 .. nbgallery::
    :name: edition2021
@@ -103,7 +103,7 @@ Online API/servers for structural bioinformatics and cheminformatics
 Kinase similarity
 -------------------
 
-Kinase similarity comparison using various methods
+Kinase similarity comparison using various methods as presented in the `LiveCoMS 2021 article <https://doi.org/10.33011/livecoms.3.1.1599>`_:
 
 .. nbgallery::
    :name: kinasesimilarity
@@ -119,7 +119,7 @@ Kinase similarity comparison using various methods
 Deep learning 
 -------------------
 
-Various deep learning architectures for drug discovery tasks
+Various deep learning architectures for drug discovery tasks as presented in the `ChemRxiv preprint 2023 <https://doi.org/10.26434/chemrxiv-2023-kz1pb>`_:
 
 .. nbgallery::
    :name: deeplearning

diff --git a/teachopencadd/talktorials/T033_molecular_representations/README.md b/teachopencadd/talktorials/T033_molecular_representations/README.md
@@ -4,7 +4,7 @@
 
 Authors:
 
-- Gerrit Großmann, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/people/gerrit/), Saarland University
+- Gerrit Großmann, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/people/gerrit/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University
 
 
 __Talktorial T033__: This talktorial is part of the TeachOpenCADD pipeline described in the TeachOpenCADD publication, consisting of Talktorials T033 to T038.

diff --git a/teachopencadd/talktorials/T033_molecular_representations/talktorial.ipynb b/teachopencadd/talktorials/T033_molecular_representations/talktorial.ipynb
@@ -13,7 +13,7 @@
     "\n",
     "Authors:\n",
     "\n",
-    "- Gerrit Großmann, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/people/gerrit/), Saarland University"
+    "- Gerrit Großmann, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/people/gerrit/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University"
    ]
   },
   {

diff --git a/teachopencadd/talktorials/T034_recurrent_neural_networks/README.md b/teachopencadd/talktorials/T034_recurrent_neural_networks/README.md
@@ -4,7 +4,7 @@
 
 Authors:
 
-- Azat Tagirdzhanov, 2022, [Chair for Clinical Bioinformatics](https://www.ccb.uni-saarland.de/), Saarland University
+- Azat Tagirdzhanov, 2022, [Chair for Clinical Bioinformatics](https://www.ccb.uni-saarland.de/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University
 
 
 ## Aim of this talktorial

diff --git a/teachopencadd/talktorials/T034_recurrent_neural_networks/talktorial.ipynb b/teachopencadd/talktorials/T034_recurrent_neural_networks/talktorial.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "Authors:\n",
     "\n",
-    "- Azat Tagirdzhanov, 2022, [Chair for Clinical Bioinformatics](https://www.ccb.uni-saarland.de/), Saarland University"
+    "- Azat Tagirdzhanov, 2022, [Chair for Clinical Bioinformatics](https://www.ccb.uni-saarland.de/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University"
    ]
   },
   {

diff --git a/teachopencadd/talktorials/T035_graph_neural_networks/README.md b/teachopencadd/talktorials/T035_graph_neural_networks/README.md
@@ -5,7 +5,7 @@
 
 Authors:
 
-* Paula Linh Kramer, 2022, [Volkamer Lab](https://volkamerlab.org/), Saarland University
+* Paula Linh Kramer, 2022, [Volkamer Lab](https://volkamerlab.org/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University
 
 
 ## Aim of this talktorial

diff --git a/teachopencadd/talktorials/T035_graph_neural_networks/talktorial.ipynb b/teachopencadd/talktorials/T035_graph_neural_networks/talktorial.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "Authors:\n",
     "\n",
-    "* Paula Linh Kramer, 2022, [Volkamer Lab](https://volkamerlab.org/), Saarland University"
+    "* Paula Linh Kramer, 2022, [Volkamer Lab](https://volkamerlab.org/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University"
    ]
   },
   {

diff --git a/teachopencadd/talktorials/T036_e3_equivariant_gnn/README.md b/teachopencadd/talktorials/T036_e3_equivariant_gnn/README.md
@@ -4,7 +4,7 @@
 
 Authors:
 
-- Joschka Groß, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/), Saarland University
+- Joschka Groß, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University
 
 
 ## Aim of this talktorial

diff --git a/teachopencadd/talktorials/T036_e3_equivariant_gnn/talktorial.ipynb b/teachopencadd/talktorials/T036_e3_equivariant_gnn/talktorial.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "Authors:\n",
     "\n",
-    "- Joschka Groß, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/), Saarland University"
+    "- Joschka Groß, 2022, [Chair for Modelling and Simulation](https://mosi.uni-saarland.de/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University"
    ]
   },
   {

diff --git a/teachopencadd/talktorials/T037_uncertainty_estimation/README.md b/teachopencadd/talktorials/T037_uncertainty_estimation/README.md
@@ -4,7 +4,7 @@
 
 Authors:
 
-- Michael Backenköhler, 2022, [Volkamer lab](https://volkamerlab.org), Saarland University
+- Michael Backenköhler, 2022, [Volkamer lab](https://volkamerlab.org), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University
 
 
 *The predictive setting (and the model class) used in this talktorial is adapted from __Talktorial T022__.*

diff --git a/teachopencadd/talktorials/T037_uncertainty_estimation/talktorial.ipynb b/teachopencadd/talktorials/T037_uncertainty_estimation/talktorial.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "Authors:\n",
     "\n",
-    "- Michael Backenköhler, 2022, [Volkamer lab](https://volkamerlab.org), Saarland University"
+    "- Michael Backenköhler, 2022, [Volkamer lab](https://volkamerlab.org), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University"
    ]
   },
   {

diff --git a/teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/README.md b/teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/README.md
@@ -4,7 +4,7 @@
 
 Authors:
 
-- Roman Joeres, 2022, [Chair for Drug Bioinformatics, UdS and HIPS](https://www.helmholtz-hips.de/de/forschung/teams/team/wirkstoffbioinformatik/)
+- Roman Joeres, 2022, [Chair for Drug Bioinformatics, UdS and HIPS](https://www.helmholtz-hips.de/de/forschung/teams/team/wirkstoffbioinformatik/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University
 
 
 ## Aim of this talktorial

diff --git a/...orials/T038_protein_ligand_interaction_prediction/images/basic_structure_nn.png b/...orials/T038_protein_ligand_interaction_prediction/images/basic_structure_nn.png
diff --git a/teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/talktorial.ipynb b/teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/talktorial.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "Authors:\n",
     "\n",
-    "- Roman Joeres, 2022, [Chair for Drug Bioinformatics, UdS and HIPS](https://www.helmholtz-hips.de/de/forschung/teams/team/wirkstoffbioinformatik/)"
+    "- Roman Joeres, 2022, [Chair for Drug Bioinformatics, UdS and HIPS](https://www.helmholtz-hips.de/de/forschung/teams/team/wirkstoffbioinformatik/), [NextAID](https://nextaid.cs.uni-saarland.de/) project, Saarland University"
    ]
   },
   {
@@ -114,7 +114,7 @@
     "\n",
     "The last component of our network architecture is a simple multilayer perceptron (MLP) as presented in __Talktorial T022__. The other two components are graph neural networks (GNNs) to extract features from the proteins and ligands in each pair of the dataset. As discussed in __Talktorial T035__ GNNs are used to compute a representation of graph-structured data that holds information about the structure. These representations are concatenated into one vector which serves as input for the final MLP.\n",
     "\n",
-    "![Basic structure](./images/basic_structure.png)\n",
+    "![Basic structure](./images/basic_structure_nn.png)\n",
     "\n",
     "*Figure 1:*\n",
     "Visualization of the model in this notebook. The shown exemplary structures are taken from the PDB entry with ID [4O75](https://www.rcsb.org/structure/4O75) (see __Talktorial T008__ for an introduction to PDB)."
@@ -996,7 +996,9 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "source": [
     "![TrainGraph](./images/train_perf.png)\n",
     "\n",