APE

A CLI, Java API and RESTful API for the automated generation of computational pipelines (scientific workflows) from large collections of computational tools.

25
mentions
5
contributors
Get started
477 commitsLast commit ≈ 2 months ago18 stars5 forks

Cite this software

What APE can do for you

Badges
Fairnessfair-software.eu OpenSSF Best Practices
Packages and ReleasesLatest release Maven Central
Build StatusBuild CodeQL Analysis
DocumentationDocumentation Status
DOIDOI
LicenseGitHub license

APE is a command line tool and Java API for the automated exploration of possible computational pipelines (scientific workflows) from large collections of computational tools.

APE relies on a semantic domain model that includes tool and type taxonomies as controlled vocabularies for the description of computational tools, and functional tool annotations (inputs, outputs, operations performed) using terms from these taxonomies. APE then computes possible workflows based on this domain model and a specification of the available workflow inputs, the intended workflow outputs and possibly additional constraints.

Internally, APE uses a component-based program synthesis approach. It translates the domain knowledge and workflow specification into logical formulas that are then fed to a SAT solver to compute satisfying instances. These solutions are then translated into the actual candidate workflows. For a detailed description, we refer to [1].

This video explains APE in 5 minutes.

Logo of APE
Keywords
Programming language
  • Java 100%
License
</>Source code
Packages
mvnrepository.com

Participating organisations

Utrecht University
Netherlands eScience Center
University of Potsdam

Reference papers

Mentions

Contributors

Anna-Lena Lamprecht
Anna-Lena Lamprecht
Principal investigator
University of Potsdam
Peter Kok
Peter Kok
RSE
Netherlands eScience Center
MV
Maurin Voshol
Software Engineer

Related projects

Facilitating the "Great Bake Off" of Bioinformatics Workflows

Workflomics: A platform for automated generation and workflow benchmarking in bioinformatics

Updated 7 months ago
In progress

Related software

RESTful APE

RE

RESTfull API for the APE (Automated Pipeline Explorer) library.

Updated 9 months ago
3

Workflomics

WO

Web platform for workflow exploration and benchmarking in bioinformatics

Updated 2 weeks ago
1 7