SnakeMaker A Preview of A User-Friendly Tool For Biomedical Data Processing

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21460%2F24%3A00380551" target="_blank" >RIV/68407700:21460/24:00380551 - isvavai.cz</a>

Result on the web

<a href="https://ieeexplore.ieee.org/document/10805593" target="_blank" >https://ieeexplore.ieee.org/document/10805593</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/EHB64556.2024.10805593" target="_blank" >10.1109/EHB64556.2024.10805593</a>

Result language

angličtina

Original language name

SnakeMaker A Preview of A User-Friendly Tool For Biomedical Data Processing

Original language description

Biomedical data analysis often relies on complex computational steps, leading to pipelines that are challenging to reproduce and share. These scripts, while powerful, can be difficult to understand and modify, especially for researchers with limited programming experience. This lack of transparency deteriorates collaboration and impedes the verification of scientific findings. To address this, we introduce SnakeMaker, a novel tool that simplifies the creation of reproducible and shareable workflows using the Snakemake workflow management system. SnakeMaker parses a set of user-friendly configuration files that specify inputs, outputs, parameters, and shell commands (or custom Python functions), automatically generating a complete Snakemake workflow. This approach significantly reduces the complexity of workflow definition, while enhancing transparency and reproducibility. By enabling easier workflow creation, sharing, and execution, SnakeMaker aims to foster collaboration and improve the reliability of neuroimaging research. The tool's modular design also allows for the creation and sharing of specialized ”forks” tailored to specific analysis pipelines, promoting a community-driven approach to workflow development. SnakeMaker has the potential to be a valuable resource for the scientific community, facilitating robust and reproducible research practices.

Czech name

—

Czech description

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Type

D - Article in proceedings

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2024

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

2024 E-Health and Bioengineering Conference (EHB)

ISBN

979-8-3315-3214-7

ISSN

2575-5137

e-ISSN

2575-5145

Number of pages

4

Pages from-to

373-376

Publisher name

IEEE Xplore

Place of publication

—

Event location

Iasi

Event date

Nov 14, 2024

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

001413708800091