From 89ee3e58a3589fce2b2666d571b5f6ddc524e581 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 27 Dec 2023 18:18:29 +0000 Subject: [PATCH 01/11] adding contents and acknowledment --- new-website/utils/tutorials/acknowledgement.md | 0 new-website/utils/tutorials/build_pdf_book.py | 3 +-- new-website/utils/tutorials/contents.md | 0 3 files changed, 1 insertion(+), 2 deletions(-) create mode 100644 new-website/utils/tutorials/acknowledgement.md create mode 100644 new-website/utils/tutorials/contents.md diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md new file mode 100644 index 00000000..e69de29b diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index b3319186..0556bcff 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -72,8 +72,7 @@ def merge_pdf_pages(a: List[str]): command = "pdfunite " for i in a: command = command + i + ' ' - return command - #os.system(command, "merged.pdf") + os.system(command, "merged.pdf") if __name__ == "__main__": os.system("mkdir " + PDF_PATH) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md new file mode 100644 index 00000000..e69de29b From f2dbfc8126fbf59c3cef8c437a23ce59f6cfad90 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 9 Jan 2024 14:27:57 +0000 Subject: [PATCH 02/11] acknowledgement --- new-website/utils/tutorials/acknowledgement.md | 1 + new-website/utils/tutorials/build_pdf_book.py | 11 +++++++++++ new-website/utils/tutorials/contents.md | 1 + 3 files changed, 13 insertions(+) diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md index e69de29b..a3b81c1f 100644 --- a/new-website/utils/tutorials/acknowledgement.md +++ b/new-website/utils/tutorials/acknowledgement.md @@ -0,0 +1 @@ +# Acknowledgement \ No newline at end of file diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index 0556bcff..376d6e2e 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -4,6 +4,7 @@ Requirements: - pdfunite - pdfkit + - mdpdf Example Usage: - Run the script "fetch_tutorials.py" // It will fetch all the tutorials. @@ -74,7 +75,17 @@ def merge_pdf_pages(a: List[str]): command = command + i + ' ' os.system(command, "merged.pdf") +def compile_information_pages(): + """Converts the Acknowledgent page and content page from + Markdowns to pdf, then they can be merged with the content + pdf using `merge_pdf_pages` function. + + """ + os.system('mdpdf -o storage/acknowledgement.pdf acknowledgement.md') + os.system('mdpdf -o storage/contents.pdf contents.md') + if __name__ == "__main__": os.system("mkdir " + PDF_PATH) html_to_pdf() merge_pdf() + compile_information_pages() diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index e69de29b..31a9fe20 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -0,0 +1 @@ +# Contents \ No newline at end of file From 4857afd3ff6b3f08a3e558940ec8452dd8b20e6b Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 9 Jan 2024 14:30:47 +0000 Subject: [PATCH 03/11] mdpdf --- new-website/utils/requirements.txt | Bin 770 -> 784 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/new-website/utils/requirements.txt b/new-website/utils/requirements.txt index 0fed149c707087d4271f1fc90ee3b5bb5e468536..299b57f76877c1886ea1290da16e3a87a7cf253c 100644 GIT binary patch delta 22 ccmZo-o4~e#iFtAWBMVn9LkdFy5T`K!06r=N(EtDd delta 7 OcmbQh*2K1fi5UP0)B)50 From 1fc19e5373c2a8f953db28b3515d4efaa3a5b8f6 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Fri, 12 Jan 2024 14:47:51 +0000 Subject: [PATCH 04/11] updated info --- .../utils/tutorials/acknowledgement.md | 3 +- new-website/utils/tutorials/contents.md | 46 ++++++++++++++++++- 2 files changed, 47 insertions(+), 2 deletions(-) diff --git a/new-website/utils/tutorials/acknowledgement.md b/new-website/utils/tutorials/acknowledgement.md index a3b81c1f..448e8843 100644 --- a/new-website/utils/tutorials/acknowledgement.md +++ b/new-website/utils/tutorials/acknowledgement.md @@ -1 +1,2 @@ -# Acknowledgement \ No newline at end of file +# Acknowledgement +We acknowledge the DeepChem community for their contributions and support. \ No newline at end of file diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index 31a9fe20..89c2bed2 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1 +1,45 @@ -# Contents \ No newline at end of file +# Con +About_nODE_Using_Torchdiffeq_in_Deepchem +Advanced_Model_Training +Advanced_model_training_using_hyperopt +An_Introduction_To_MoleculeNet +Atomic_Contributions_for_Molecules +Conditional_Generative_Adversarial_Networks +Creating_Models_with_TensorFlow_and_PyTorch +Creating_a_high_fidelity_model_from_experimental_data +DeepQMC_tutorial +Deep_probabilistic_analysis_of_single-cell_omics_data +Exploring_Quantum_Chemistry_with_GDB1k +Generating_molecules_with_MolGAN +Going_Deeper_on_Molecular_Featurizations +Hierarchial_Moelcular_Generation_with_HierVAE +Interactive_Model_Evaluation_with_Trident_Chemwidgets +Introducing_JaxModel_and_PINNModel +Introduction_To_Material_Science +Introduction_to_Bioinformatics +Introduction_to_Equivariance +Introduction_to_GROVER +Introduction_to_Gaussian_Processes +Introduction_to_Graph_Convolutions +Introduction_to_Model_Interpretability +Introduction_to_Molecular_Attention_Transformer +Large_Scale_Chemical_Screens +Learning_Unsupervised_Embeddings_for_Molecules +Modeling_Protein_Ligand_Interactions +Modeling_Protein_Ligand_Interactions_With_Atomic_Convolutions +Molecular_Fingerprints +Multisequence_Alignments +Physics_Informed_Neural_Networks +Protein_Deep_Learning +Putting_Multitask_Learning_to_Work +PytorchLightning_Integration +Scanpy +The_Basic_Tools_of_the_Deep_Life_Sciences +Training_a_Generative_Adversarial_Network_on_MNIST +Training_a_Normalizing_Flow_on_QM9 +Training_an_Exchange_Correlation_Functional_using_Deepchem +Transfer_Learning_With_ChemBERTa_Transformers +Uncertainty_In_Deep_Learning +Using_Reinforcement_Learning_to_Play_Pong +Working_With_Datasets +Working_With_Splitters \ No newline at end of file From 9da856ce72bea9d653008c2aa9e8e73e407c78a5 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Fri, 12 Jan 2024 16:13:35 +0000 Subject: [PATCH 05/11] minor fix --- new-website/utils/tutorials/contents.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index 89c2bed2..ee0f902b 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1,4 +1,4 @@ -# Con +# Conents About_nODE_Using_Torchdiffeq_in_Deepchem Advanced_Model_Training Advanced_model_training_using_hyperopt @@ -42,4 +42,4 @@ Transfer_Learning_With_ChemBERTa_Transformers Uncertainty_In_Deep_Learning Using_Reinforcement_Learning_to_Play_Pong Working_With_Datasets -Working_With_Splitters \ No newline at end of file +Working_With_Splitters From 3d2c8dccf356da842f39bb114848c21a357e81f3 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Fri, 12 Jan 2024 16:32:02 +0000 Subject: [PATCH 06/11] minor fixes --- new-website/utils/tutorials/build_pdf_book.py | 2 +- new-website/utils/tutorials/contents.md | 88 +++++++++---------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index 376d6e2e..1d45a176 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -73,7 +73,7 @@ def merge_pdf_pages(a: List[str]): command = "pdfunite " for i in a: command = command + i + ' ' - os.system(command, "merged.pdf") + os.system(command + "merged.pdf") def compile_information_pages(): """Converts the Acknowledgent page and content page from diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index ee0f902b..0f919105 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1,45 +1,45 @@ # Conents -About_nODE_Using_Torchdiffeq_in_Deepchem -Advanced_Model_Training -Advanced_model_training_using_hyperopt -An_Introduction_To_MoleculeNet -Atomic_Contributions_for_Molecules -Conditional_Generative_Adversarial_Networks -Creating_Models_with_TensorFlow_and_PyTorch -Creating_a_high_fidelity_model_from_experimental_data -DeepQMC_tutorial -Deep_probabilistic_analysis_of_single-cell_omics_data -Exploring_Quantum_Chemistry_with_GDB1k -Generating_molecules_with_MolGAN -Going_Deeper_on_Molecular_Featurizations -Hierarchial_Moelcular_Generation_with_HierVAE -Interactive_Model_Evaluation_with_Trident_Chemwidgets -Introducing_JaxModel_and_PINNModel -Introduction_To_Material_Science -Introduction_to_Bioinformatics -Introduction_to_Equivariance -Introduction_to_GROVER -Introduction_to_Gaussian_Processes -Introduction_to_Graph_Convolutions -Introduction_to_Model_Interpretability -Introduction_to_Molecular_Attention_Transformer -Large_Scale_Chemical_Screens -Learning_Unsupervised_Embeddings_for_Molecules -Modeling_Protein_Ligand_Interactions -Modeling_Protein_Ligand_Interactions_With_Atomic_Convolutions -Molecular_Fingerprints -Multisequence_Alignments -Physics_Informed_Neural_Networks -Protein_Deep_Learning -Putting_Multitask_Learning_to_Work -PytorchLightning_Integration -Scanpy -The_Basic_Tools_of_the_Deep_Life_Sciences -Training_a_Generative_Adversarial_Network_on_MNIST -Training_a_Normalizing_Flow_on_QM9 -Training_an_Exchange_Correlation_Functional_using_Deepchem -Transfer_Learning_With_ChemBERTa_Transformers -Uncertainty_In_Deep_Learning -Using_Reinforcement_Learning_to_Play_Pong -Working_With_Datasets -Working_With_Splitters +- About_nODE_Using_Torchdiffeq_in_Deepchem +- Advanced_Model_Training +- Advanced_model_training_using_hyperopt +- An_Introduction_To_MoleculeNet +- Atomic_Contributions_for_Molecules +- Conditional_Generative_Adversarial_Networks +- Creating_Models_with_TensorFlow_and_PyTorch +- Creating_a_high_fidelity_model_from_experimental_data +- DeepQMC_tutorial +- Deep_probabilistic_analysis_of_single-cell_omics_data +- Exploring_Quantum_Chemistry_with_GDB1k +- Generating_molecules_with_MolGAN +- Going_Deeper_on_Molecular_Featurizations +- Hierarchial_Moelcular_Generation_with_HierVAE +- Interactive_Model_Evaluation_with_Trident_Chemwidgets +- Introducing_JaxModel_and_PINNModel +- Introduction_To_Material_Science +- Introduction_to_Bioinformatics +- Introduction_to_Equivariance +- Introduction_to_GROVER +- Introduction_to_Gaussian_Processes +- Introduction_to_Graph_Convolutions +- Introduction_to_Model_Interpretability +- Introduction_to_Molecular_Attention_Transformer +- Large_Scale_Chemical_Screens +- Learning_Unsupervised_Embeddings_for_Molecules +- Modeling_Protein_Ligand_Interactions +- Modeling_Protein_Ligand_Interactions_With_Atomic_Convolutions +- Molecular_Fingerprints +- Multisequence_Alignments +- Physics_Informed_Neural_Networks +- Protein_Deep_Learning +- Putting_Multitask_Learning_to_Work +- PytorchLightning_Integration +- Scanpy +- The_Basic_Tools_of_the_Deep_Life_Sciences +- Training_a_Generative_Adversarial_Network_on_MNIST +- Training_a_Normalizing_Flow_on_QM9 +- Training_an_Exchange_Correlation_Functional_using_Deepchem +- Transfer_Learning_With_ChemBERTa_Transformers +- Uncertainty_In_Deep_Learning +- Using_Reinforcement_Learning_to_Play_Pong +- Working_With_Datasets +- Working_With_Splitters From c08f997de81f0b8d7df387274ed4bb8599062817 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Mon, 22 Jan 2024 15:58:41 +0000 Subject: [PATCH 07/11] content update --- new-website/utils/tutorials/contents.md | 86 ++++++++++++------------- 1 file changed, 43 insertions(+), 43 deletions(-) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index 0f919105..34cbd54a 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1,45 +1,45 @@ # Conents -- About_nODE_Using_Torchdiffeq_in_Deepchem -- Advanced_Model_Training -- Advanced_model_training_using_hyperopt -- An_Introduction_To_MoleculeNet -- Atomic_Contributions_for_Molecules -- Conditional_Generative_Adversarial_Networks -- Creating_Models_with_TensorFlow_and_PyTorch -- Creating_a_high_fidelity_model_from_experimental_data -- DeepQMC_tutorial -- Deep_probabilistic_analysis_of_single-cell_omics_data -- Exploring_Quantum_Chemistry_with_GDB1k -- Generating_molecules_with_MolGAN -- Going_Deeper_on_Molecular_Featurizations -- Hierarchial_Moelcular_Generation_with_HierVAE -- Interactive_Model_Evaluation_with_Trident_Chemwidgets -- Introducing_JaxModel_and_PINNModel -- Introduction_To_Material_Science -- Introduction_to_Bioinformatics -- Introduction_to_Equivariance -- Introduction_to_GROVER -- Introduction_to_Gaussian_Processes -- Introduction_to_Graph_Convolutions -- Introduction_to_Model_Interpretability -- Introduction_to_Molecular_Attention_Transformer -- Large_Scale_Chemical_Screens -- Learning_Unsupervised_Embeddings_for_Molecules -- Modeling_Protein_Ligand_Interactions -- Modeling_Protein_Ligand_Interactions_With_Atomic_Convolutions -- Molecular_Fingerprints -- Multisequence_Alignments -- Physics_Informed_Neural_Networks -- Protein_Deep_Learning -- Putting_Multitask_Learning_to_Work -- PytorchLightning_Integration +- About Neural ODE : Using Torchdiffeq with Deepchem +- Advanced Model Training +- Advanced model training using hyperopt +- An Introduction To MoleculeNet +- Atomic Contributions for Molecules +- Conditional Generative Adversarial Networks +- Creating Models with TensorFlow and PyTorch +- Creating a high fidelity model from experimental data +- DeepQMC tutorial +- Deep probabilistic analysis of single-cell omics data +- Exploring Quantum Chemistry with GDB1k +- Generating molecules with MolGAN +- Going Deeper on Molecular Featurizations +- Hierarchial Moelcular Generation with HierVAE +- Interactive Model Evaluation with Trident Chemwidgets +- Introducing JaxModel and PINNModel +- Introduction To Material Science +- Introduction to Bioinformatics +- Introduction to Equivariance +- Introduction to GROVER +- Introduction to Gaussian Processes +- Introduction to Graph Convolutions +- Introduction to Model Interpretability +- Introduction to Molecular Attention Transformer +- Large Scale Chemical Screens +- Learning Unsupervised Embeddings for Molecules +- Modeling Protein Ligand Interactions +- Modeling Protein Ligand Interactions With Atomic Convolutions +- Molecular Fingerprints +- Multisequence Alignments +- Physics Informed Neural Networks +- Protein Deep Learning +- Putting Multitask Learning to Work +- PytorchLightning Integration - Scanpy -- The_Basic_Tools_of_the_Deep_Life_Sciences -- Training_a_Generative_Adversarial_Network_on_MNIST -- Training_a_Normalizing_Flow_on_QM9 -- Training_an_Exchange_Correlation_Functional_using_Deepchem -- Transfer_Learning_With_ChemBERTa_Transformers -- Uncertainty_In_Deep_Learning -- Using_Reinforcement_Learning_to_Play_Pong -- Working_With_Datasets -- Working_With_Splitters +- The Basic Tools of the Deep Life Sciences +- Training a Generative Adversarial Network on MNIST +- Training a Normalizing Flow on QM9 +- Training an Exchange Correlation Functional using Deepchem +- Transfer Learning With ChemBERTa Transformers +- Uncertainty In Deep Learning +- Using Reinforcement Learning to Play Pong +- Working With Datasets +- Working With Splitters From 8cab565d2153b3c1c3d3ff8ed4f085bc8d2a66c0 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 23 Jan 2024 16:12:11 +0000 Subject: [PATCH 08/11] minor addition --- new-website/utils/tutorials/build_pdf_book.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index 1d45a176..173e50b4 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -73,7 +73,7 @@ def merge_pdf_pages(a: List[str]): command = "pdfunite " for i in a: command = command + i + ' ' - os.system(command + "merged.pdf") + os.system(command + "storage/merged.pdf") def compile_information_pages(): """Converts the Acknowledgent page and content page from @@ -89,3 +89,4 @@ def compile_information_pages(): html_to_pdf() merge_pdf() compile_information_pages() + merge_pdf_pages(['storage/title.pdf', 'storage/acknowledgement.pdf', 'storage/contents.pdf', 'storage/full_pdf.pdf']) From 4aebba1d324f3734dfb12c5889bd1acfa821d4a0 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 23 Jan 2024 16:50:12 +0000 Subject: [PATCH 09/11] content fix --- new-website/utils/tutorials/contents.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index 34cbd54a..61645866 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1,4 +1,4 @@ -# Conents +# Contents - About Neural ODE : Using Torchdiffeq with Deepchem - Advanced Model Training - Advanced model training using hyperopt From 5555f0fdae2c144a666f99c24a6fa874863801b8 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Wed, 24 Jan 2024 17:30:13 +0000 Subject: [PATCH 10/11] CONTENT UPDATE --- new-website/utils/tutorials/contents.md | 114 +++++++++++++++--------- 1 file changed, 70 insertions(+), 44 deletions(-) diff --git a/new-website/utils/tutorials/contents.md b/new-website/utils/tutorials/contents.md index 61645866..8513475f 100644 --- a/new-website/utils/tutorials/contents.md +++ b/new-website/utils/tutorials/contents.md @@ -1,45 +1,71 @@ # Contents -- About Neural ODE : Using Torchdiffeq with Deepchem -- Advanced Model Training -- Advanced model training using hyperopt -- An Introduction To MoleculeNet -- Atomic Contributions for Molecules -- Conditional Generative Adversarial Networks -- Creating Models with TensorFlow and PyTorch -- Creating a high fidelity model from experimental data -- DeepQMC tutorial -- Deep probabilistic analysis of single-cell omics data -- Exploring Quantum Chemistry with GDB1k -- Generating molecules with MolGAN -- Going Deeper on Molecular Featurizations -- Hierarchial Moelcular Generation with HierVAE -- Interactive Model Evaluation with Trident Chemwidgets -- Introducing JaxModel and PINNModel -- Introduction To Material Science -- Introduction to Bioinformatics -- Introduction to Equivariance -- Introduction to GROVER -- Introduction to Gaussian Processes -- Introduction to Graph Convolutions -- Introduction to Model Interpretability -- Introduction to Molecular Attention Transformer -- Large Scale Chemical Screens -- Learning Unsupervised Embeddings for Molecules -- Modeling Protein Ligand Interactions -- Modeling Protein Ligand Interactions With Atomic Convolutions -- Molecular Fingerprints -- Multisequence Alignments -- Physics Informed Neural Networks -- Protein Deep Learning -- Putting Multitask Learning to Work -- PytorchLightning Integration -- Scanpy -- The Basic Tools of the Deep Life Sciences -- Training a Generative Adversarial Network on MNIST -- Training a Normalizing Flow on QM9 -- Training an Exchange Correlation Functional using Deepchem -- Transfer Learning With ChemBERTa Transformers -- Uncertainty In Deep Learning -- Using Reinforcement Learning to Play Pong -- Working With Datasets -- Working With Splitters + +### 1. Introduction To Deepchem +1. The Basic Tools of the Deep Life Sciences +2. Working With Datasets +3. An Introduction To MoleculeNet +4. Molecular Fingerprints +5. Creating Models with TensorFlow and PyTorch +6. Introduction to Graph Convolutions +7. Going Deeper on Molecular Featurizations +8. Working With Splitters +9. Advanced Model Training +10. Creating a high fidelity model from experimental data +11. Putting Multitask Learning to Work +12. Modeling Protein Ligand Interactions +13. Modeling Protein Ligand Interactions With Atomic Convolutions +14. Conditional Generative Adversarial Networks +15. Training a Generative Adversarial Network on MNIST +16. Advanced model training using hyperopt +17. Introduction to Gaussian Processes +18. PytorchLightning Integration + +### 2. Molecular Machine Learning +1. Molecular Fingerprints +2. Going Deeper on Molecular Featurizations +3. Learning Unsupervised Embeddings for Molecules +4. Atomic Contributions for Molecules +5. Interactive Model Evaluation with Trident Chemwidgets +6. Transfer Learning With ChemBERTa Transformers +7. Training a Normalizing Flow on QM9 +8. Large Scale Chemical Screens +9. Introduction to Molecular Attention Transformer +10. Generating molecules with MolGAN +11. Introduction to GROVER + +### 3. Modeling Proteins +1. Protein Deep Learning + +### 4. Protein Ligand Modeling +1. Modeling Protein Ligand Interactions +2. Modeling Protein Ligand Interactions With Atomic Convolutions +3. DeepChemXAlphafold + +### 5. Quantum Chemistry +1. Exploring Quantum Chemistry with GDB1k +2. DeepQMC tutorial +3. Training an Exchange Correlation Functional using Deepchem + +### 6. Bioinformatics +1. Introduction to Bioinformatics +2. Multisequence Alignments +3. Deep probabilistic analysis of single-cell omics data + +### 7. Material Sciences +1. Introduction To Material Science + +### 8. Machine Learning Methods +1. Using Reinforcement Learning to Play Pong +2. Introduction to Model Interpretability +3. Uncertainty In Deep Learning + +### 9. Deep Differential Equations +1. Physics Informed Neural Networks +2. Introducing JaxModel and PINNModel +3. About Neural ODE : Using Torchdiffeq with Deepchem + +### 10. Equivariance +1. Introduction to Equivariance + +### 11. Olfaction +1. Predict Multi Label Odor Descriptors using OpenPOM \ No newline at end of file From 6b2ac4c2ef41d82f71f7267bd6328505333a2273 Mon Sep 17 00:00:00 2001 From: Rakshit Kumar Singh Date: Tue, 30 Jan 2024 16:24:09 +0000 Subject: [PATCH 11/11] markdown to html --- .../utils/tutorials/acknowledgement.html | 21 +++ new-website/utils/tutorials/build_pdf_book.py | 7 +- new-website/utils/tutorials/contents.html | 125 ++++++++++++++++++ new-website/utils/tutorials/title.html | 30 +++++ 4 files changed, 180 insertions(+), 3 deletions(-) create mode 100644 new-website/utils/tutorials/acknowledgement.html create mode 100644 new-website/utils/tutorials/contents.html create mode 100644 new-website/utils/tutorials/title.html diff --git a/new-website/utils/tutorials/acknowledgement.html b/new-website/utils/tutorials/acknowledgement.html new file mode 100644 index 00000000..4c82554a --- /dev/null +++ b/new-website/utils/tutorials/acknowledgement.html @@ -0,0 +1,21 @@ + + + +

Acknowledgement

+

+ We acknowledge the DeepChem community for their contributions and support. +

+ + \ No newline at end of file diff --git a/new-website/utils/tutorials/build_pdf_book.py b/new-website/utils/tutorials/build_pdf_book.py index 173e50b4..e289939f 100644 --- a/new-website/utils/tutorials/build_pdf_book.py +++ b/new-website/utils/tutorials/build_pdf_book.py @@ -77,12 +77,13 @@ def merge_pdf_pages(a: List[str]): def compile_information_pages(): """Converts the Acknowledgent page and content page from - Markdowns to pdf, then they can be merged with the content + Html to pdf, then they can be merged with the content pdf using `merge_pdf_pages` function. """ - os.system('mdpdf -o storage/acknowledgement.pdf acknowledgement.md') - os.system('mdpdf -o storage/contents.pdf contents.md') + pdfkit.from_file('title.html', 'storage/title.pdf') + pdfkit.from_file('contents.html', 'storage/contents.pdf') + pdfkit.from_file('acknowledgement.html', 'storage/acknowledgement.pdf') if __name__ == "__main__": os.system("mkdir " + PDF_PATH) diff --git a/new-website/utils/tutorials/contents.html b/new-website/utils/tutorials/contents.html new file mode 100644 index 00000000..ffccb884 --- /dev/null +++ b/new-website/utils/tutorials/contents.html @@ -0,0 +1,125 @@ + + + +

Contents

+
    +
  • +

    1. Introduction To Deepchem

    +
      +
    1. The Basic Tools of the Deep Life Sciences
      2. +
    2. Working With Datasets
      3. +
    3. An Introduction To MoleculeNet
      4. +
    4. Molecular Fingerprints
      5. +
    5. Creating Models with TensorFlow and PyTorch
      6. +
    6. Introduction to Graph Convolutions
      7. +
    7. Going Deeper on Molecular Featurizations
      8. +
    8. Working With Splitters
      9. +
    9. Advanced Model Training
      10. +
    10. Creating a high fidelity model from experimental data
      11. +
    11. Putting Multitask Learning to Work
      12. +
    12. Modeling Protein Ligand Interactions
      13. +
    13. Modeling Protein Ligand Interactions With Atomic Convolutions
      14. +
    14. Conditional Generative Adversarial Networks
      15. +
    15. Training a Generative Adversarial Network on MNIST
      16. +
    16. Advanced model training using hyperopt
      17. +
    17. Introduction to Gaussian Processes
      18. +
    18. PytorchLightning Integration
      19. +
    +
    • +
  • +

    2. Molecular Machine Learning

    +
      +
    1. Molecular Fingerprints +
    2. Going Deeper on Molecular Featurizations +
    3. Learning Unsupervised Embeddings for Molecules +
    4. Atomic Contributions for Molecules +
    5. Interactive Model Evaluation with Trident Chemwidgets +
    6. Transfer Learning With ChemBERTa Transformers +
    7. Training a Normalizing Flow on QM9 +
    8. Large Scale Chemical Screens +
    9. Introduction to Molecular Attention Transformer +
    10. Generating molecules with MolGAN +
    11. Introduction to GROVER +
    +
    • +
  • +

    3. Modeling Proteins

    +
      +
    1. Protein Deep Learning +
    +
    • +
  • +

    4. Protein Ligand Modeling

    +
      +
    1. Modeling Protein Ligand Interactions +
    2. Modeling Protein Ligand Interactions With Atomic Convolutions +
    3. DeepChemXAlphafold +
    +
    • +
  • +

    5. Quantum Chemistry

    +
      +
    1. Exploring Quantum Chemistry with GDB1k +
    2. DeepQMC tutorial +
    3. Training an Exchange Correlation Functional using Deepchem +
    +
    • +
  • +

    6. Bioinformatics

    +
      +
    1. Introduction to Bioinformatics +
    2. Multisequence Alignments +
    3. Deep probabilistic analysis of single-cell omics data +
    +
    • +
  • +

    7. Material Sciences

    +
      +
    1. Introduction To Material Science +
    +
    • +
  • +

    8. Machine Learning Methods

    +
      +
    1. Using Reinforcement Learning to Play Pong +
    2. Introduction to Model Interpretability +
    3. Uncertainty In Deep Learning +
    +
    • +
  • +

    9. Deep Differential Equations

    +
      +
    1. Physics Informed Neural Networks +
    2. Introducing JaxModel and PINNModel +
    3. About Neural ODE : Using Torchdiffeq with Deepchem +
    +
    • +
  • +

    10. Equivariance

    +
      +
    1. Introduction to Equivariance +
    2. Modeling Protein Ligand Interactions With Atomic Convolutions +
    3. DeepChemXAlphafold +
    +
    • +
  • +

    11. Olfaction

    +
      +
    1. Predict Multi Label Odor Descriptors using OpenPOM +
    +
    • +
+ + + + \ No newline at end of file diff --git a/new-website/utils/tutorials/title.html b/new-website/utils/tutorials/title.html new file mode 100644 index 00000000..74910a53 --- /dev/null +++ b/new-website/utils/tutorials/title.html @@ -0,0 +1,30 @@ + + + +

The DeepChem Book

+

+ Democratizing Deep-Learning for Drug Discovery Quantum Chemistry, Materials Science and Biology +

+

+ Bharath Ramsundar +

+ + \ No newline at end of file