Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows.

Natay Aberra, Aswathy Sebastian, Aaron P Maloy, Christopher B Rees, Meredith L Bartron, Istvan Albert

Abstract read

In one paragraph

Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Natay AberraDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA.

Aswathy SebastianDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA.

Aaron P MaloyNortheast Fisheries Center, US Fish and Wildlife Service, Lamar, PA, 16848, USA.

Christopher B ReesNortheast Fisheries Center, US Fish and Wildlife Service, Lamar, PA, 16848, USA.

Meredith L BartronNortheast Fisheries Center, US Fish and Wildlife Service, Lamar, PA, 16848, USA.

Istvan AlbertDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, 201 Old Main, University Park, PA, 16802, USA. istvan.albert@gmail.com.ORCID http://orcid.org/0000-0001-8366-984X

Funding

U.S. Fish and Wildlife Service F16AC01007

6 · The paper itself

Abstract

backgroundBioinformaticians collaborating with life scientists need software that allows them to involve their collaborators in the process of data analysis.

resultsWe have developed a web application that allows researchers to publish and execute data analysis scripts. Within the platform bioinformaticians are able to deploy data analysis workflows (recipes) that their collaborators can execute via point and click interfaces. The results generated by the recipes are viewable via the web interface and consist of a snapshot of all the commands, printed messages and files that have been generated during the recipe run. A demonstration version of our software is available at https://www.bioinformatics.recipes/ . Detailed documentation for the software is available at: https://bioinformatics-recipes.readthedocs.io . The source code for the software is distributed through GitHub at https://github.com/ialbert/biostar-central .

conclusionsOur software platform supports collaborative interactions between bioinformaticians and life scientists. The software is presented via a web application that provides a high utility and user-friendly approach for conducting reproducible research. The recipes developed and shared through the web application are generic, with broad applicability and may be downloaded and executed on other computing platforms.

Indexed as

SoftwareComputational BiologyData AnalysisReproducibility of ResultsUser-Computer InterfaceWorkflowData analysisReproducibilityScientific workflows

Identifiers

PMID32640986

DOI10.1186/s12859-020-03602-6

PMCPMC7346607

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.