From d79a0dd8bbb59ed0e271def065da633bc46ef562 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Mon, 10 Aug 2026 10:55:50 -0500 Subject: [PATCH 1/2] docs: add preprint citation and cleanup readme --- README.md | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 5e88616f..4210008d 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,13 @@ # Signaling Pathway Reconstruction Analysis Streamliner (SPRAS) [![Test SPRAS](https://github.com/Reed-CompBio/spras/actions/workflows/test-spras.yml/badge.svg)](https://github.com/Reed-CompBio/spras/actions/workflows/test-spras.yml) [![Documentation](https://readthedocs.org/projects/spras/badge/?version=latest)](https://spras.readthedocs.io) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13366795.svg)](https://doi.org/10.5281/zenodo.13366795) -SPRAS is a work-in-progress dockerized library of pathway reconstruction enhancement tools. -The framework will contain different pathway reconstruction algorithms that connect genes and proteins of interest in the context of a general protein-protein interaction network, allowing users to run multiple algorithms on their inputs. -See the GLBIO 2021 [slides](https://doi.org/10.6084/m9.figshare.14551476) or [video](https://www.youtube.com/watch?v=nU8EARwMqdM&list=PLmX8XnLr6zeHlqhhxDy4fA5o65Q6m76KX&index=19) for more information. -To read more about the specific pathway reconstruction algorithms that may be supported in the future, refer to [our list of algorithms](https://spras.readthedocs.io/en/latest/prms/prms.html). +SPRAS is a containerized library of pathway reconstruction tools. +The framework contains different pathway reconstruction algorithms that connect genes and proteins of interest in the context of a general protein-protein interaction network, allowing users to run multiple algorithms on their inputs. +See the SPRAS [manuscript](https://doi.org/10.64898/2026.08.04.742550) or the GLBIO 2021 [slides](https://doi.org/10.6084/m9.figshare.14551476) or [video](https://www.youtube.com/watch?v=nU8EARwMqdM&list=PLmX8XnLr6zeHlqhhxDy4fA5o65Q6m76KX&index=19) for more information. -This repository is very much a work in progress and is not yet stable enough for real data analysis. -The latest features can be found on various development branches. +This repository is a work in progress and may undergo breaking changes. The instructions below support running SPRAS with a fixed configuration on example data to demonstrate its functionality. Open a [GitHub issue](https://github.com/Reed-CompBio/spras/issues) or contact [Anthony Gitter](https://gitterlab.org/) or [Anna Ritz](https://www.reed.edu/biology/ritz/) to provide feedback on this early version of SPRAS. @@ -69,8 +68,7 @@ Large SPRAS workflows may benefit from execution with HTCondor, a scheduler/mana **Snakemake file**: Defines a workflow to run all pathway reconstruction algorithms on all datasets with all specified hyperparameters. -**Dockerized pathway reconstruction algorithms**: Pathway reconstruction algorithms are run via Docker images using the docker-py Python package. -[PathLinker](https://github.com/Murali-group/PathLinker), [Omics Integrator](https://github.com/fraenkel-lab/OmicsIntegrator), [Omics Integrator 2](https://github.com/fraenkel-lab/OmicsIntegrator2), and [Maximum Edge Orientation](https://github.com/agitter/meo/) are the first supported algorithms. +**Containerized pathway reconstruction algorithms**: Pathway reconstruction algorithms are run via Docker images using the docker-py Python package. The files to create these Docker images are in the `docker-wrappers` subdirectory along with links to algorithms' original repositories. The Docker images are available on [DockerHub](https://hub.docker.com/orgs/reedcompbio). @@ -82,7 +80,7 @@ The tests require the conda environment in `environment.yml` and Docker. Run the tests with `pytest -s`. ## Singularity -Some computing environments are unable to run Docker and prefer Singularity as the container runtime. +Some computing environments are unable to run Docker and prefer Singularity (or Apptainer) as the container runtime. SPRAS has limited experimental support for Singularity instead of Docker, and only for some pathway reconstruction algorithms. SPRAS uses the spython package to interface with Singularity, which only supports Linux. @@ -92,3 +90,9 @@ If you use SPRAS in a research project, please cite the original datasets and al Part of `ml.py` is taken from the [scikit-learn example code](https://scikit-learn.org/stable/auto_examples/cluster/plot_agglomerative_dendrogram.html). The original third-party code is available under the BSD 3-Clause License, Copyright © 2007 - 2023, scikit-learn developers. + +## Citation +[A framework for benchmarking pathway reconstruction algorithms](https://doi.org/10.64898/2026.08.04.742550) +Neha Talluri, Tristan Figueroa-Reid, Justin Hiemstra, Chris S Magnano, Adam Shedivy, Nistha Panda, Yancheng Liu, Sumedha Sanjeev, Oliver Faulkner Anderson, Altaf Barelvi, Aden O'Brien, Olivia T Johnson, James A Haddad, Spencer A Halberg-Spencer, Akniyet Nurbol, Iris Jan, Mahunan Degbelo, Daniel Nachreiner, Canek Llera-Magord, Gabriel Howland, Grace H Li, Anna Ritz+, Anthony Gitter+. +*bioRxiv*, 2026. doi:10.64898/2026.08.04.742550 ++ denotes equal contribution. From ae1ef1ca98858df8702c029db639db5ca918487e Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Mon, 10 Aug 2026 11:06:41 -0500 Subject: [PATCH 2/2] docs: remove construction and add citatation --- docs/about.rst | 22 ++++++++++++++++++++-- docs/index.rst | 7 ------- 2 files changed, 20 insertions(+), 9 deletions(-) diff --git a/docs/about.rst b/docs/about.rst index 4ec5d14a..ecba71c5 100644 --- a/docs/about.rst +++ b/docs/about.rst @@ -7,8 +7,26 @@ is a work-in-progress dockerized library of pathway reconstruction enhancement tools. The framework will contain different pathway reconstruction algorithms that connect genes and proteins of interest in the context of a general protein-protein interaction network, allowing -users to run multiple algorithms on their inputs. See the GLBIO 2021 -slides_ or video_ for more information. +users to run multiple algorithms on their inputs. See the registered +report_ or GLBIO 2021 slides_ or video_ for more information. + +********** + Citation +********** + +| `A framework for benchmarking pathway reconstruction algorithms + `_ +| Neha Talluri, Tristan Figueroa-Reid, Justin Hiemstra, Chris S + Magnano, Adam Shedivy, Nistha Panda, Yancheng Liu, Sumedha Sanjeev, + Oliver Faulkner Anderson, Altaf Barelvi, Aden O'Brien, Olivia T + Johnson, James A Haddad, Spencer A Halberg-Spencer, Akniyet Nurbol, + Iris Jan, Mahunan Degbelo, Daniel Nachreiner, Canek Llera-Magord, + Gabriel Howland, Grace H Li, Anna Ritz\ :sup:`+`, Anthony + Gitter\ :sup:`+`. +| *bioRxiv*, 2026. doi:10.64898/2026.08.04.742550 +| :sup:`+` denotes equal contribution. + +.. _report: https://doi.org/10.64898/2026.08.04.742550 .. _slides: https://doi.org/10.6084/m9.figshare.14551476 diff --git a/docs/index.rst b/docs/index.rst index c8aae5e6..f6a26457 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -4,13 +4,6 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. raw:: html - -
- 🚧 Under Construction 🚧 -

This documentation is currently under construction. Some sections may be incomplete or subject to change.

-
- ################################### Welcome to SPRAS's documentation! ###################################