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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

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

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2024

Kód důvěrnosti údajů

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

Název statě ve sborníku

2024 E-Health and Bioengineering Conference (EHB)

ISBN

979-8-3315-3214-7

ISSN

2575-5137

e-ISSN

2575-5145

Počet stran výsledku

4

Strana od-do

373-376

Název nakladatele

IEEE Xplore

Místo vydání

—

Místo konání akce

Iasi

Datum konání akce

14. 11. 2024

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

001413708800091