Slivka and Slivka-bio: a lightweight framework for presenting executables as web services and its application in bioinformatics
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Motivation
Execution of code is critical for computational biology, but technical requirements can prevent others from running it. Public web-apps and services thus remain the most effective way to make code accessible, but no fully reusable infrastructure exists to help researchers do this.
Results
We developed Slivka to enable easy provision of robust HTTP-based execution services backed by local or distributed hardware; accessible via curl and dedicated clients. We demonstrate it with Slivka-bio, which provides semantically annotated services for Jalview 2.12 ( https://www.jalview.org/development/jalview_develop/ ) and includes 15+ tools for protein and RNA analysis. Slivka has been in production in academic and industry environments for 5 years and ran more than 1.5M jobs.
Availability and Implementation
Slivka and Slivka-bio are released under the Apache 2.0 License. Slivka-bio public instance at https://www.compbio.dundee.ac.uk/slivka with links to documentation, docker containers, and github repositories for Slivka-bio and Slivka.
Contact
j.procter@dundee.ac.uk and g.j.barton@dundee.ac.uk .
