From 98b2a2e76c737d4b111bcf682157c0f01b04ad12 Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 09:31:20 -0500 Subject: [PATCH 01/10] Update README.md data links. --- README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index a935de5..a769332 100644 --- a/README.md +++ b/README.md @@ -20,18 +20,19 @@ python [SCRIPT] [OPTIONS] Options for any script may be listed using the `-h/--help` flag. -Pre-processed / pre-trained data and models may be downloaded from [figshare/doi:](figshare.com) and should be unpacked at `data/` in this directory. This directory may also be used as an example of how to structure input and output files / directories. +Pre-processed / pre-trained data and models may be downloaded from [(figshare doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552) and should be unpacked at `data/` in this directory. This directory may also be used as an example of how to structure input and output files / directories. An alternative use case would be to train / re-train a new model in the `train/` code and make new predictions using the `predict/` code. ## Data -As reported, domain-peptide and protein-protein interactions are available via [figshare/doi:](figshare.com). In addition, we provide pre-processed data for this repository and the website repository, +As reported, domain-peptide and protein-protein interactions are available via [figshare (doi:10.6084/m9.figshare.10084745)](https://figshare.com/articles/Predictions_-_Domain-Peptide_and_Protein-Protein_Interactions_-_HSM/10084745). In addition, we provide pre-processed data for this repository and the website repository, + +- Raw training data: [(figshare doi:10.6084/m9.figshare.11520297)](https://figshare.com/articles/Training_Data_-_Peptide-Binding_Domain-Peptide_Interactions/11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. +- Pre-processed data: [(figshare doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552). Needed to work with this repo. +- Data supporting the website at [proteinpeptide.io](proteinpeptide.io) -- Raw training data: [figshare/doi:](figshare.com). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. -- Website data: [figshare/doi:](figshare.com). Data supporting the website at [proteinpeptide.io](proteinpeptide.io) -The data used to the train the model is also provided at a separate data repository: [figshare/doi:](figshare.com). ## Requirements - Python (>= 3.5) From 371c50c38afd7888639f378f47e2e2225e56d989 Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 09:32:54 -0500 Subject: [PATCH 02/10] Update README.md parenthesis --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a769332..5419d71 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ python [SCRIPT] [OPTIONS] Options for any script may be listed using the `-h/--help` flag. -Pre-processed / pre-trained data and models may be downloaded from [(figshare doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552) and should be unpacked at `data/` in this directory. This directory may also be used as an example of how to structure input and output files / directories. +Pre-processed / pre-trained data and models may be downloaded from [figshare (doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552) and should be unpacked at `data/` in this directory. This directory may also be used as an example of how to structure input and output files / directories. An alternative use case would be to train / re-train a new model in the `train/` code and make new predictions using the `predict/` code. @@ -28,8 +28,8 @@ An alternative use case would be to train / re-train a new model in the `train/` As reported, domain-peptide and protein-protein interactions are available via [figshare (doi:10.6084/m9.figshare.10084745)](https://figshare.com/articles/Predictions_-_Domain-Peptide_and_Protein-Protein_Interactions_-_HSM/10084745). In addition, we provide pre-processed data for this repository and the website repository, -- Raw training data: [(figshare doi:10.6084/m9.figshare.11520297)](https://figshare.com/articles/Training_Data_-_Peptide-Binding_Domain-Peptide_Interactions/11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. -- Pre-processed data: [(figshare doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552). Needed to work with this repo. +- Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://figshare.com/articles/Training_Data_-_Peptide-Binding_Domain-Peptide_Interactions/11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. +- Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552). Needed to work with this repo. - Data supporting the website at [proteinpeptide.io](proteinpeptide.io) From e6a7d043bcf5def899bd636fc4b80cdc72644fba Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 09:35:46 -0500 Subject: [PATCH 03/10] Update README.md, minor changes to links. --- README.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 5419d71..2a576eb 100644 --- a/README.md +++ b/README.md @@ -4,13 +4,13 @@ This repository implements the hierarchical statistical mechanical (HSM) model described in the paper [Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.](nature.com) -An **associated website** is available at [proteinpeptide.io](proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). +An **associated website** is available at [proteinpeptide.io](htttps://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). This file documents how this package might be [used](#usage), the [location of associated data](#data), and [other metadata](#reference). ## Usage -The model was implemented in Python (>= 3.5) primarily using TensorFlow (>= 1.4) ([Software Requirements](#requirements)). To work with this repository, we recommend downloading pre-processed data available at [doi:](figshare.com) into "data/". Alternatively, it is possible to either re-process raw data ([doi:](figshare.com)) or include new data. The folder contains two major directories: `train/` and `predict/`. Each directory is accompanied by a `README.md` file detailing usage. +The model was implemented in Python (>= 3.5) primarily using TensorFlow (>= 1.4) ([Software Requirements](#requirements)). To work with this repository, either download pre-processed data (see below) or include new data. The folder contains two major directories: `train/` and `predict/`. Each directory is accompanied by a `README.md` file detailing usage. To train / re-train new models, use the `train.py` script in `train/`. To make predictions using a model, use one of two scripts, `predict_domains.py` and `predict_proteins.py`, for predicting either domain-peptide interactions or protein-protein interactions. Scripts are designed with a CLI and should be used from the command line: @@ -30,9 +30,7 @@ As reported, domain-peptide and protein-protein interactions are available via [ - Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://figshare.com/articles/Training_Data_-_Peptide-Binding_Domain-Peptide_Interactions/11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. - Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552). Needed to work with this repo. -- Data supporting the website at [proteinpeptide.io](proteinpeptide.io) - - +- Data supporting the website at [proteinpeptide.io](https://proteinpeptide.io) ## Requirements - Python (>= 3.5) @@ -47,7 +45,7 @@ Please reference the associated publication: Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:](https://doi.org/). ([citation.bib](https://raw.githubusercontent.com/aqlaboratory/hsm/misc/citation.bib)) -See also, a **website** at [proteinpeptide.io](proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). +See also, a **website** at [proteinpeptide.io](https://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). ## Funding From 6c759c186f7a7f32219cca4142984b6d51f56775 Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 09:40:31 -0500 Subject: [PATCH 04/10] Update data links in predict/README.md --- predict/README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/predict/README.md b/predict/README.md index c6ecd83..5c553ae 100644 --- a/predict/README.md +++ b/predict/README.md @@ -8,7 +8,7 @@ Predictions are run through one of two scripts, `predict_domains.py` and `predic ## Domain-Peptide Interaction Predictions -Code used for predicting domain-peptide interactions is located in the predict/ directory in this repository. The functionality should primarily be accessed via the predict\_domains.py script. +Code used for predicting domain-peptide interactions is located in the predict/ directory in this repository. The functionality should primarily be accessed via the `predict_domains.py` script. ```python python predict_domains.py [INPUT DOMAINS METADATA] [INPUT PEPTIDES METADATA] [OPTIONS] @@ -18,7 +18,7 @@ Additional options for using either script may be listed using the `-h/--help` f The basic steps for predicting a new interaction is: ### 0. Pre-process data and models. -By default, the code assumes that models are located at `predict/models/` and pre-processed data, which can be downloaded (see [Data section](#data)), are available at `data/metadata`. New data must be passed explicitly to the code (see the next section). Output model files should be the same as formatted by `output_models.py` in the `train/` directory. +By default, the code assumes that models are located at `predict/models/` and pre-processed data, which can be downloaded from [figshare (doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552), should be available at `data/predict`. New data must be passed explicitly to the code (see the next section). Output model files should be the same as formatted by `output_models.py` in the `train/` directory. Input domains files should have the format: ``` @@ -50,7 +50,7 @@ The domain and peptide alignment lengths refer to the domain / peptide alignment ## Protein-Protein Interaction Predictions -Code used for predicting protein-protein interactions is located in the predict/ directory in this repository. The functionality should primarily be accessed via the predict\_proteins.py script. +Code used for predicting protein-protein interactions is located in the predict/ directory in this repository. The functionality should primarily be accessed via the `predict_proteins.py` script. ```python python predict_proteins.py [-p [INPUT PPI PAIRS]] [OPTIONS] @@ -59,13 +59,13 @@ Additional options for using either script may be listed using the `-h/--help` f ## 0. Pre-process data and models. -By default, the `predict_proteins.py` script also assumes models are located at `predict/models/` and pre-processed data, which can be downloaded (see [Data section](#data)), are available at `data/metadata`. New data must be passed explicitly to the code (see the next section). The same models files may be used in both domain-peptide and protein-protein interaction prediction. To use new models, the same steps to specify the new models must be passed to `predict_proteins.py`. In addition, the models requiire metadata files (by default, stored in `data/metadata`) that describe either the domain or peptide composition of proteins. Metadata are formatted as Python dictionaries (stored as pickle'd files) with the format: +By default, the `predict_proteins.py` script also assumes models are located at `predict/models/` and pre-processed data, which can be downloaded via [figshare (doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552), are available at `data/metadata`. New data must be passed explicitly to the code (see the next section). The same models files may be used in both domain-peptide and protein-protein interaction prediction. To use new models, the same steps to specify the new models must be passed to `predict_proteins.py`. In addition, the models requiire metadata files (by default, stored in `data/metadata`) that describe either the domain or peptide composition of proteins. Metadata are formatted as Python dictionaries (stored as pickle'd files) with the format: ## 1. Run predictions Predictions can be computed using the described script: ```python -python predict_proteins.py [-p [INPUT PPI PAIRS]] [OPTIONS] +python predict_proteins.py [--ppi_pairs [INPUT PPI PAIRS]] [OPTIONS] ``` -The `INPUT PPI PAIRS` option (passed using `-p / --ppi_pairs`) passed to the code denotes a csv file containing the proteins to predict. These pairs should be formatted as a csv file where each line contains a pair of protein IDs (`,`). These IDs should reference IDs in the metadata files. If no pairs are passed, all valid pairs are returned. Different metadata files may be passed in using the `--domain_metadata` and `--peptide_metadata` options. +The `INPUT PPI PAIRS` option (passed using `--ppi_pairs`) passed to the code denotes a csv file containing the proteins to predict. These pairs should be formatted as a csv file where each line contains a pair of protein IDs (`,`). These IDs should reference IDs in the metadata files. If no pairs are passed, all valid pairs are returned. Different metadata files may be passed in using the `--domain_metadata` and `--peptide_metadata` options. From ac8aee8d95f3d1d7b51bcf8be0c152a89cab94ab Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 12:38:02 -0500 Subject: [PATCH 05/10] Update links Paper went live, updated associated links. --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 2a576eb..5a6b223 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,9 @@ -This repository implements the hierarchical statistical mechanical (HSM) model described in the paper [Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.](nature.com) +This repository implements the hierarchical statistical mechanical (HSM) model described in the paper [Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.](https://doi.org/10.1038/s41592-019-0687-1) -An **associated website** is available at [proteinpeptide.io](htttps://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). +An **associated website** is available at [proteinpeptide.io](https://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). This file documents how this package might be [used](#usage), the [location of associated data](#data), and [other metadata](#reference). @@ -20,16 +20,16 @@ python [SCRIPT] [OPTIONS] Options for any script may be listed using the `-h/--help` flag. -Pre-processed / pre-trained data and models may be downloaded from [figshare (doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552) and should be unpacked at `data/` in this directory. This directory may also be used as an example of how to structure input and output files / directories. +Pre-processed / pre-trained data and models may be downloaded from [figshare (doi:10.6084/m9.figshare.11520552)](https://doi.org/10.6084/m9.figshare.11520552) and should be unpacked at `data/` in this directory. This directory may also be used as an example of how to structure input and output files / directories. An alternative use case would be to train / re-train a new model in the `train/` code and make new predictions using the `predict/` code. ## Data -As reported, domain-peptide and protein-protein interactions are available via [figshare (doi:10.6084/m9.figshare.10084745)](https://figshare.com/articles/Predictions_-_Domain-Peptide_and_Protein-Protein_Interactions_-_HSM/10084745). In addition, we provide pre-processed data for this repository and the website repository, +As reported, domain-peptide and protein-protein interactions are available via [figshare (doi:10.6084/m9.figshare.10084745)](https://doi.org/10.6084/m9.figshare.10084745). In addition, we provide pre-processed data for this repository and the website repository, -- Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://figshare.com/articles/Training_Data_-_Peptide-Binding_Domain-Peptide_Interactions/11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. -- Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552). Needed to work with this repo. +- Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://doi.org/10.6084/m9.figshare.11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. +- Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://doi.org/10.6084/m9.figshare.11520552). Needed to work with this repo. - Data supporting the website at [proteinpeptide.io](https://proteinpeptide.io) ## Requirements @@ -43,7 +43,7 @@ As reported, domain-peptide and protein-protein interactions are available via [ ## Reference Please reference the associated publication: -Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:](https://doi.org/). ([citation.bib](https://raw.githubusercontent.com/aqlaboratory/hsm/misc/citation.bib)) +Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:10.1038/s41592-019-0687-1](https://doi.org/10.1038/s41592-019-0687-1). ([citation.bib](https://raw.githubusercontent.com/aqlaboratory/hsm/misc/citation.bib)) See also, a **website** at [proteinpeptide.io](https://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). From abcf0f5beba6f938fcb3884bff450fd5103773c4 Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 12:40:18 -0500 Subject: [PATCH 06/10] Update figshare links to resolve via doi --- predict/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/predict/README.md b/predict/README.md index 5c553ae..7d583bf 100644 --- a/predict/README.md +++ b/predict/README.md @@ -18,7 +18,7 @@ Additional options for using either script may be listed using the `-h/--help` f The basic steps for predicting a new interaction is: ### 0. Pre-process data and models. -By default, the code assumes that models are located at `predict/models/` and pre-processed data, which can be downloaded from [figshare (doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552), should be available at `data/predict`. New data must be passed explicitly to the code (see the next section). Output model files should be the same as formatted by `output_models.py` in the `train/` directory. +By default, the code assumes that models are located at `predict/models/` and pre-processed data, which can be downloaded from [figshare (doi:10.6084/m9.figshare.11520552)](https://doi.org/10.6084/m9.figshare.11520552), should be available at `data/predict`. New data must be passed explicitly to the code (see the next section). Output model files should be the same as formatted by `output_models.py` in the `train/` directory. Input domains files should have the format: ``` @@ -59,7 +59,7 @@ Additional options for using either script may be listed using the `-h/--help` f ## 0. Pre-process data and models. -By default, the `predict_proteins.py` script also assumes models are located at `predict/models/` and pre-processed data, which can be downloaded via [figshare (doi:10.6084/m9.figshare.11520552)](https://figshare.com/articles/Pre-processed_data_-_Git_Repo_-_HSM/11520552), are available at `data/metadata`. New data must be passed explicitly to the code (see the next section). The same models files may be used in both domain-peptide and protein-protein interaction prediction. To use new models, the same steps to specify the new models must be passed to `predict_proteins.py`. In addition, the models requiire metadata files (by default, stored in `data/metadata`) that describe either the domain or peptide composition of proteins. Metadata are formatted as Python dictionaries (stored as pickle'd files) with the format: +By default, the `predict_proteins.py` script also assumes models are located at `predict/models/` and pre-processed data, which can be downloaded via [figshare (doi:10.6084/m9.figshare.11520552)](https://doi.org/10.6084/m9.figshare.11520552), are available at `data/metadata`. New data must be passed explicitly to the code (see the next section). The same models files may be used in both domain-peptide and protein-protein interaction prediction. To use new models, the same steps to specify the new models must be passed to `predict_proteins.py`. In addition, the models requiire metadata files (by default, stored in `data/metadata`) that describe either the domain or peptide composition of proteins. Metadata are formatted as Python dictionaries (stored as pickle'd files) with the format: ## 1. Run predictions From ba99aecfff1263bd60da8e586e30a244f1a3837c Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Mon, 6 Jan 2020 12:43:33 -0500 Subject: [PATCH 07/10] Fixed link to citation.bib --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5a6b223..1a45a90 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ As reported, domain-peptide and protein-protein interactions are available via [ ## Reference Please reference the associated publication: -Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:10.1038/s41592-019-0687-1](https://doi.org/10.1038/s41592-019-0687-1). ([citation.bib](https://raw.githubusercontent.com/aqlaboratory/hsm/misc/citation.bib)) +Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:10.1038/s41592-019-0687-1](https://doi.org/10.1038/s41592-019-0687-1). ([citation.bib](misc/citation.bib)) See also, a **website** at [proteinpeptide.io](https://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). From 279b01c0cbf81a1bb2cea5fb841ecb01c254fbf2 Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Tue, 7 Jan 2020 11:46:54 -0500 Subject: [PATCH 08/10] Update web links Need to update SSL certs to enable https:// access to website. Switching to proteinpeptide.io for now. Will switch back when updated. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1a45a90..8600c37 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ This repository implements the hierarchical statistical mechanical (HSM) model described in the paper [Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.](https://doi.org/10.1038/s41592-019-0687-1) -An **associated website** is available at [proteinpeptide.io](https://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). +An **associated website** is available at [proteinpeptide.io](proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). This file documents how this package might be [used](#usage), the [location of associated data](#data), and [other metadata](#reference). @@ -30,7 +30,7 @@ As reported, domain-peptide and protein-protein interactions are available via [ - Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://doi.org/10.6084/m9.figshare.11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. - Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://doi.org/10.6084/m9.figshare.11520552). Needed to work with this repo. -- Data supporting the website at [proteinpeptide.io](https://proteinpeptide.io) +- Data supporting the website at [proteinpeptide.io](proteinpeptide.io) ## Requirements - Python (>= 3.5) @@ -45,7 +45,7 @@ Please reference the associated publication: Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:10.1038/s41592-019-0687-1](https://doi.org/10.1038/s41592-019-0687-1). ([citation.bib](misc/citation.bib)) -See also, a **website** at [proteinpeptide.io](https://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). +See also, a **website** at [proteinpeptide.io](proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). ## Funding From 55bb0bb7f7dc361a67142ffd3c348ba08e21eb44 Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Tue, 7 Jan 2020 11:47:47 -0500 Subject: [PATCH 09/10] Make link work for previous commit --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 8600c37..b7a156f 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ This repository implements the hierarchical statistical mechanical (HSM) model described in the paper [Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.](https://doi.org/10.1038/s41592-019-0687-1) -An **associated website** is available at [proteinpeptide.io](proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). +An **associated website** is available at [proteinpeptide.io](http://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). This file documents how this package might be [used](#usage), the [location of associated data](#data), and [other metadata](#reference). @@ -30,7 +30,7 @@ As reported, domain-peptide and protein-protein interactions are available via [ - Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://doi.org/10.6084/m9.figshare.11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. - Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://doi.org/10.6084/m9.figshare.11520552). Needed to work with this repo. -- Data supporting the website at [proteinpeptide.io](proteinpeptide.io) +- Data supporting the website at [proteinpeptide.io](http://proteinpeptide.io) ## Requirements - Python (>= 3.5) @@ -45,7 +45,7 @@ Please reference the associated publication: Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:10.1038/s41592-019-0687-1](https://doi.org/10.1038/s41592-019-0687-1). ([citation.bib](misc/citation.bib)) -See also, a **website** at [proteinpeptide.io](proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). +See also, a **website** at [proteinpeptide.io](http://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). ## Funding From e6200287e4c761c3161a08d0661093a24f17939b Mon Sep 17 00:00:00 2001 From: Joe Cunningham Date: Wed, 8 Jan 2020 14:10:11 -0500 Subject: [PATCH 10/10] Update README.md - website works w/ https. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index b7a156f..1a45a90 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ This repository implements the hierarchical statistical mechanical (HSM) model described in the paper [Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.](https://doi.org/10.1038/s41592-019-0687-1) -An **associated website** is available at [proteinpeptide.io](http://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). +An **associated website** is available at [proteinpeptide.io](https://proteinpeptide.io). The website is built to facilitate interactions with results from the model including: (1) specific domain-peptide and protein-protein predictions, (2) the resulting networks, and (3) structures colored using the inferred energy functions from the model. Code for the website is available via the parallel repo: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web). This file documents how this package might be [used](#usage), the [location of associated data](#data), and [other metadata](#reference). @@ -30,7 +30,7 @@ As reported, domain-peptide and protein-protein interactions are available via [ - Raw training data: [figshare - doi:10.6084/m9.figshare.11520297](https://doi.org/10.6084/m9.figshare.11520297). Raw domain-peptide training data used to train the core HSM models. Unpack to `data/` in this directory. - Pre-processed data: [figshare - doi:10.6084/m9.figshare.11520552](https://doi.org/10.6084/m9.figshare.11520552). Needed to work with this repo. -- Data supporting the website at [proteinpeptide.io](http://proteinpeptide.io) +- Data supporting the website at [proteinpeptide.io](https://proteinpeptide.io) ## Requirements - Python (>= 3.5) @@ -45,7 +45,7 @@ Please reference the associated publication: Cunningham, J.M., Koytiger, G., Sorger, P.K., & AlQuraishi, M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." *Nature Methods* (2020). [doi:10.1038/s41592-019-0687-1](https://doi.org/10.1038/s41592-019-0687-1). ([citation.bib](misc/citation.bib)) -See also, a **website** at [proteinpeptide.io](http://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). +See also, a **website** at [proteinpeptide.io](https://proteinpeptide.io) for exploring the associated analyses (code: [aqlaboratory/hsm-web](https://github.com/aqlaboratory/hsm-web)). ## Funding