From 2c996279a2c9f74defe4a5c187ccbc1cefe5ecd4 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 7 Sep 2026 16:27:37 +0100 Subject: [PATCH 1/2] docs: add SIST logo and refresh README metadata --- README.md | 5 +++++ docs/source/_static/logos/SIST-logo-black-text.svg | 1 + docs/source/_static/logos/SIST-logo-white-text.svg | 1 + docs/source/conf.py | 7 ++++++- 4 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 docs/source/_static/logos/SIST-logo-black-text.svg create mode 100644 docs/source/_static/logos/SIST-logo-white-text.svg diff --git a/README.md b/README.md index 3bb6af9..41d3956 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,11 @@ The codes in this repository are for analyzing three types of structural transitions in superhelical DNA molecules of specified base sequences and kilobase lengths. These are strand separation, BZ transitions and cruciform extrusion. More types of transitions may be added as their energetics become known. The statistical mechanical methods and algorithms used in these analyses are described in the papers cited below. +

+ SIST logo + SIST logo +

+ ## Citations When using these algorithms you must cite the first paper below, and some or all of the others, depending on which types of analyses you perform: diff --git a/docs/source/_static/logos/SIST-logo-black-text.svg b/docs/source/_static/logos/SIST-logo-black-text.svg new file mode 100644 index 0000000..9974caa --- /dev/null +++ b/docs/source/_static/logos/SIST-logo-black-text.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/source/_static/logos/SIST-logo-white-text.svg b/docs/source/_static/logos/SIST-logo-white-text.svg new file mode 100644 index 0000000..66ae614 --- /dev/null +++ b/docs/source/_static/logos/SIST-logo-white-text.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py index e7e7ccb..0d04b6b 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -38,4 +38,9 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output html_theme = 'furo' -# html_static_path = ['_static'] +html_theme_options = { + "dark_logo": "logos/SIST-logo-white-text.svg", + "light_logo": "logos/SIST-logo-black-text.svg", +} + +html_static_path = ['_static'] From 0a7115e662913f0887ca12f939a38f58fcc58ce1 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Mon, 7 Sep 2026 16:42:33 +0100 Subject: [PATCH 2/2] docs(readme): add status badges, update contact email --- README.md | 27 +++++++++++++++++++-------- 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 41d3956..f167f24 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,13 @@ -# SIST: Stress-Induced Structural Transitions in superhelical DNA +SIST: Stress-Induced Structural Transitions in superhelical DNA +============================== + +| Category | Badges | +|----------------|--------| +| **Build** | [![PR Checks](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml) | +| **Documentation** | [![Docs - Status](https://app.readthedocs.org/projects/sist/badge/?version=latest)](https://sist.readthedocs.io/en/latest/?badge=latest) | +| **Citation** | | +| **Anaconda** | [![Anaconda.org](https://anaconda.org/CCPBioSim/sist/badges/version.svg)](https://anaconda.org/CCPBioSim/sist/) [![Last Updated](https://anaconda.org/CCPBioSim/sist/badges/latest_release_date.svg)](https://anaconda.org/CCPBioSim/sist) [![Platforms](https://anaconda.org/CCPBioSim/sist/badges/platforms.svg)](https://anaconda.org/CCPBioSim/sist) [![License](https://anaconda.org/CCPBioSim/sist/badges/license.svg)](https://anaconda.org/CCPBioSim/sist) [![Downloads](https://anaconda.org/CCPBioSim/sist/badges/downloads.svg)](https://anaconda.org/CCPBioSim/sist)| +| **Quality** | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/SIST/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/SIST?branch=main) | ## Purpose of SIST @@ -11,16 +20,18 @@ The codes in this repository are for analyzing three types of structural transit ## Citations -When using these algorithms you must cite the first paper below, and some or all of the others, depending on which types of analyses you perform: - -Zhabinskaya, D., Madden, S., & Benham, C. J. (2015). SIST: stress-induced structural transitions in superhelical DNA. Bioinformatics, 31(3), 421-422. +If you use SIST, please cite the software itself (see [`CITATION.cff`](CITATION.cff)) along with the paper below, which is required for any use of these algorithms: -Fye, R. M. and Benham, C. J. (1999), “Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA”, Phys Rev E, 59, 3408-3426. +> Zhabinskaya, D., Madden, S., & Benham, C. J. (2015). SIST: stress-induced structural transitions in superhelical DNA. *Bioinformatics*, 31(3), 421-422. -Zhabinskaya, D. and Benham, C. J. (2011), “Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA”, PLoS Comput Biol, 7, 1-14. +Additionally, cite whichever of the following apply to the type(s) of transition you analyze: -Zhabinskaya, D. and Benham, C. J. (2013), “Competitive superhelical transitions involving cruciform extrusion”, Nucleic Acids Res, 41(21), 9610-9621. +| Transition type | Reference | +|---|---| +| Strand separation | Fye, R. M. and Benham, C. J. (1999), "Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA", *Phys Rev E*, 59, 3408-3426. | +| BZ transition | Zhabinskaya, D. and Benham, C. J. (2011), "Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA", *PLoS Comput Biol*, 7, 1-14. | +| Cruciform extrusion | Zhabinskaya, D. and Benham, C. J. (2013), "Competitive superhelical transitions involving cruciform extrusion", *Nucleic Acids Res*, 41(21), 9610-9621. | ## Contact Information -For questions or problems, please contact either Dina Zhabinskaya (dzhabinskaya@ucdavis.edu), Craig Benham (cjbenham@ucdavis.edu), or Sally Madden (sallymadden@gmail.com). +For questions or problems, please contact CCPBIOSIM@stfc.ac.uk.