matteogalgo-ph/MaligPx: MaligPx-Initial-Release
Year: 2026
Type: software
Abstract: MaligPx v0.1.0 — Reproducible Infrastructure Baseline Release Date: July 19, 2026 MaligPx v0.1.0 establishes the project's first reproducible computational baseline. This release completes the infrastructure required for subsequent biological data acquisition and analysis while ensuring that the software environment, repository architecture, and project documentation are fully version-controlled and reproducible. This release contains no biological analyses or experimental results. Instead, it defines the stable computational foundation upon which all future stages of the project will be built. Highlights Established the canonical Miniforge-based Python environment. Standardized the project environment (maligpx, Python 3.10). Implemented a Conda-first dependency management strategy. Installed and verified the complete scientific computing stack, including Scanpy, AnnData, scVelo, CellRank, and Scrublet. Generated reproducible environment specifications through environment.yml, environment.lock.yml, and requirements.txt. Standardized the repository architecture for reproducible computational biology research. Established comprehensive project documentation, including decision logs, project logs, research logs, dataset documentation, and acquisition tracking. Added an MIT License. Synchronized the repository with GitHub. Dataset Preparation The primary discovery dataset has been identified and audited. Dataset: Peng et al. (2019) Repository: Genome Sequence Archive (CRA001160) Repository inspection confirmed that only raw paired-end FASTQ files are publicly distributed. Consequently, MaligPx will reconstruct gene-expression count matrices directly from raw sequencing reads as part of the official computational workflow. This preprocessing strategy has been formally adopted as a project decision and will precede all downstream analyses. No biological data are included in this release. Reproducibility The computational environment has been frozen through the following files: environment.yml environment.lock.yml requirements.txt These files collectively define the software environment required to reproduce future analyses. Repository Status The repository now contains: standardized project architecture reproducible software environment scientific documentation framework dataset provenance documentation decision history Git version control open-source licensing The repository is considered infrastructure-complete and ready to begin biological data acquisition. Next Milestone The next release will initiate MD-3 and will include: acquisition of the Peng et al. (2019) metadata package staged download of raw sequencing data checksum verification preprocessing pipeline initialization preparation for expression matrix reconstruction This release represents the completion of the computational infrastructure phase of MaligPx and marks the transition from repository engineering to experimental data acquisition.
Author: Matteo Gabriel Galgo
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: green
OpenAlex ID: W7169714410