From e5832e48d10f0fe99a1cc21bf383ee929487c7b9 Mon Sep 17 00:00:00 2001 From: Hossam Mahmoud Date: Sat, 26 Sep 2026 06:31:51 +0300 Subject: [PATCH] Release metadata for 0.3.0: citation, Zenodo title and description Co-Authored-By: Claude Opus 5.5 --- .zenodo.json | 45 ++++++++++++++++++++++++++------------------- CHANGELOG.md | 2 +- CITATION.cff | 9 ++++++--- 3 files changed, 33 insertions(+), 23 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 8dc871b..b0dbc0d 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,20 +1,27 @@ { - "title": "MolDynX Tools (formerly mdforge): a reusable, reproducible analysis framework for GROMACS molecular dynamics simulations", - "description": "MolDynX Tools (formerly mdforge) turns a GROMACS simulation directory into a complete, publication-quality, fully reproducible analysis. It discovers files, detects the biomolecular system (protein / ligand / DNA / RNA / membrane / ions / multi-chain), auto-selects the appropriate analyses, runs them with streaming-friendly performance, and produces 300-dpi figures, a reproducibility manifest, and Markdown/HTML/PDF reports. Extensible via a plugin architecture and drivable from a single YAML config.", - "upload_type": "software", - "license": "MIT", - "access_right": "open", - "creators": [ - { "name": "Mahmoud, Hossam", "orcid": "0009-0004-7804-4174" } - ], - "keywords": [ - "molecular dynamics", - "GROMACS", - "MDAnalysis", - "mdtraj", - "trajectory analysis", - "bioinformatics", - "computational biology", - "reproducibility" - ] -} + "title": "MolDynX Tools: a reusable, reproducible analysis framework for GROMACS molecular dynamics simulations", + "description": "MolDynX Tools (formerly mdforge) turns a GROMACS simulation directory into an audited, reproducible analysis. It selects the production run from evidence (atom counts, time span, log completion) rather than file size, diagnoses and proves its periodic-boundary treatment, audits minimisation and equilibration, runs structural, dynamic and interface analyses, computes MM-GBSA/MM-PBSA binding free energies with gmx_MMPBSA, and writes data-driven Markdown/HTML documents and self-verifying datasets. Extensible via a plugin architecture and drivable from a single YAML config.", + "upload_type": "software", + "license": "MIT", + "access_right": "open", + "creators": [ + { + "name": "Mahmoud, Hossam", + "orcid": "0009-0004-7804-4174" + } + ], + "keywords": [ + "molecular dynamics", + "GROMACS", + "MDAnalysis", + "mdtraj", + "trajectory analysis", + "bioinformatics", + "computational biology", + "reproducibility", + "MM-GBSA", + "MM-PBSA", + "protein-protein interactions" + ], + "version": "0.3.0" +} \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 15b5870..f08bfa2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## 0.3.0 — unreleased +## 0.3.0 — 2026-09-26 ### Renamed: mdforge → **MolDynX Tools** diff --git a/CITATION.cff b/CITATION.cff index 94a0efb..4590b22 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,6 +1,6 @@ cff-version: 1.2.0 message: "If you use this software, please cite it as below." -title: "MolDynX Tools (formerly mdforge): a reusable, reproducible analysis framework for GROMACS molecular dynamics simulations" +title: "MolDynX Tools: a reusable, reproducible analysis framework for GROMACS molecular dynamics simulations" abstract: >- MolDynX Tools analyses GROMACS MD simulations of arbitrary biomolecular systems from a single simulation directory: it detects the system, auto-selects analyses, @@ -14,8 +14,8 @@ authors: repository-code: "https://github.com/SamDozer/MolDynX-Tools" url: "https://github.com/SamDozer/MolDynX-Tools" license: MIT -version: 0.2.1 -date-released: "2026-07-08" +version: 0.3.0 +date-released: "2026-09-26" doi: 10.5281/zenodo.21265946 keywords: - molecular dynamics @@ -24,3 +24,6 @@ keywords: - trajectory analysis - bioinformatics - reproducibility + - MM-GBSA + - MM-PBSA + - protein-protein interactions