From ad43e34ece5f31f5b8245e14d261a86c7ba7b092 Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Mon, 6 Nov 2023 13:22:55 +0100 Subject: [PATCH 1/3] Update README.md with DeepRank2 link --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 405e2d2..859b5d9 100644 --- a/README.md +++ b/README.md @@ -23,6 +23,8 @@ DeepRank is a general, configurable deep learning framework for data mining prot DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models. +We recently developed [DeepRank2](https://github.com/DeepRank/deeprank2), an upgraded package that includes all the functionalities of DeepRank and more. + #### Features: - Predefined atom-level and residue-level PPI feature types From 849514d4501d7af99043c742277b0c7a81d1e6bc Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Wed, 22 Nov 2023 16:53:34 +0100 Subject: [PATCH 2/3] Update README.md Add more details about the new repo --- README.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/README.md b/README.md index 859b5d9..542f4ac 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,17 @@ +# :warning: Archiving Note + +This repository is no longer being maintained and has been archived for historical purposes. + +We have now developed [DeepRank2](https://github.com/DeepRank/deeprank2), an improved and unified version of DeepRank, [DeepRank-GNN](https://github.com/DeepRank/Deeprank-GNN), and [DeepRank-Mut](https://github.com/DeepRank/DeepRank-Mut). + +:sparkles: DeepRank2 allows for transformation and storage of 3D representations of both protein-protein interfaces (PPIs) and protein single-residue variants (SRVs) into either graphs or volumetric grids containing structural and physico-chemical information. These can be used for training neural networks for a variety of patterns of interest, using either our pre-implemented training pipeline for graph neural networks (GNNs) or convolutional neural networks (CNNs) or external pipelines. + +- :wrench: **Pull Requests** at github.com/DeepRank/deeprank2 +- :bug: **Bugs**: Reports of bugs can be filed agains our new repo github.com/DeepRank/deeprank2 +- :star: **Feature Requests**: Add your request or discuss the project w/ the community at github.com/DeepRank/deeprank2 + +We look forward to seeing you in our new spaces! + # DeepRank [![PyPI](https://img.shields.io/pypi/v/deeprank)](https://pypi.org/project/deeprank/) [![Documentation Status](https://readthedocs.org/projects/deeprank/badge/?version=latest)](http://deeprank.readthedocs.io/?badge=latest) From 7db6f1cf6b1418d8329b57ce715068619b7c722c Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Tue, 28 Nov 2023 20:26:29 +0100 Subject: [PATCH 3/3] Update README.md after Cunliang's review --- README.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 542f4ac..1ac03e4 100644 --- a/README.md +++ b/README.md @@ -6,11 +6,11 @@ We have now developed [DeepRank2](https://github.com/DeepRank/deeprank2), an imp :sparkles: DeepRank2 allows for transformation and storage of 3D representations of both protein-protein interfaces (PPIs) and protein single-residue variants (SRVs) into either graphs or volumetric grids containing structural and physico-chemical information. These can be used for training neural networks for a variety of patterns of interest, using either our pre-implemented training pipeline for graph neural networks (GNNs) or convolutional neural networks (CNNs) or external pipelines. -- :wrench: **Pull Requests** at github.com/DeepRank/deeprank2 -- :bug: **Bugs**: Reports of bugs can be filed agains our new repo github.com/DeepRank/deeprank2 -- :star: **Feature Requests**: Add your request or discuss the project w/ the community at github.com/DeepRank/deeprank2 +- :wrench: **Pull Requests** at [github.com/DeepRank/deeprank2/pulls](https://github.com/DeepRank/deeprank2/pulls) +- :bug: **Bugs**: Reports of bugs can be filed agains our new repo [github.com/DeepRank/deeprank2/issues](https://github.com/DeepRank/deeprank2/issues) +- :star: **Feature Requests**: Add your request or discuss the project w/ the community at [github.com/DeepRank/deeprank2/issues](https://github.com/DeepRank/deeprank2/issues) -We look forward to seeing you in our new spaces! +We look forward to seeing you in our new space - [DeepRank2](https://github.com/DeepRank/deeprank2)! # DeepRank [![PyPI](https://img.shields.io/pypi/v/deeprank)](https://pypi.org/project/deeprank/) @@ -37,8 +37,6 @@ DeepRank is a general, configurable deep learning framework for data mining prot DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models. -We recently developed [DeepRank2](https://github.com/DeepRank/deeprank2), an upgraded package that includes all the functionalities of DeepRank and more. - #### Features: - Predefined atom-level and residue-level PPI feature types