Github Repository
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06:55
Inverse Probability of Treatment Weighting (Propensity Score) using the Military Health System Data Repository and National Death Index
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Cited by 14 •
2020
When randomized controlled trials are not feasible, a comprehensive health care data source like the Military Health System Data Repository provides an attractive alternative for retrospective analyses. Incorporating mortality data from the national death index and balancing differences between groups using propensity weighting helps reduce biases inherent in retrospective designs.
05:37
Rapid in-silico Battery Electrolyte Electrochemical Reaction Generation using 3T-VASP Multi-Scale Energy Minimization
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2025
The 3T-VASP framework combines hierarchical structure transformation with ab initio multi-scale gradients to significantly reduce the number of steps needed to escape local energy minima and model electrochemical reactions. This protocol presents a method for generating electrochemical reaction byproducts for various electrolyte component combinations using only 100-150 static DFT calculations.
09:10
Measuring Single-Cell Aging with an Imaging-based Biomarker of Chromatin and Epigenetic Aging
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2026
The protocol presents the imaging and computational workflow to extract and validate imaging-based chromatin and epigenetic age (ImAge).
06:04
Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis
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Cited by 36 •
2021
The aqueous humor is a high-yield liquid biopsy for retinoblastoma, intraocular cancer that cannot be biopsied in vivo due to the risk of extraocular spread. Herein, a method for safely extracting aqueous humor via clear corneal paracentesis and steps for genomic analysis to identify prognostic biomarkers are presented.
08:35
Mapping Microglial Parameters Software (MMPS): An Open-Source, User-Friendly Tool for Quantitative Microglia Morphology Analysis
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2026
Mapping Microglial Parameters Software (MMPS) is a user-friendly analysis pipeline that requires no coding expertise and semi-automates single-cell microglial morphology analysis from immunofluorescence images. Validated in a rodent lipopolysaccharide-induced neuroinflammation model, MMPS reproducibly detects activation-associated morphological changes and enables standardized, scalable microglial phenotyping.
FAQs
Commits create a dated record of project updates, allowing contributors to connect a script, protocol, or analysis change with the evolving work. This history helps a team identify what changed, when changes occurred, and maintain a transparent account of development. In biological projects, it can clarify how analytical materials were revised over time.
Branches let contributors develop features or analyses separately from the shared project, reducing disruption while work is in progress. A pull request then provides the route for presenting those updates for review and possible merging. Keeping these functions distinct supports organized collaboration and makes decisions about changes easier to inspect.
Version control supports reproducibility by preserving the project's evolving analytical materials rather than treating each revision as an isolated file. When scripts, documentation, or related resources change, the recorded history helps collaborators identify those differences and inspect the methods behind an analysis. That visibility makes materials easier to reuse or adapt.
A team can begin by placing its computational workflow, analysis scripts, laboratory protocols, and documentation in one organized project space. Contributors can then develop separate updates on branches, record completed changes in commits, and submit pull requests for review before merging them into the shared project. This workflow coordinates work while preserving its history.
Repository contents can extend beyond code. Biology researchers may use the space for computational workflows, data-analysis scripts, laboratory protocols, documentation, and other reproducible research materials. Keeping these related resources together helps readers inspect how an analysis or procedure is supported, while allowing teams to preserve and share the materials as projects evolve.
Maintaining project history helps researchers identify changes across an evolving biological project and coordinate contributions from different team members. Shared, inspectable materials also make analytical methods easier for others to reuse or adapt. These benefits are especially relevant when a project combines computational workflows with protocols, documentation, and analysis resources.