Workflomics: A Web Platform for Generating and Benchmarking Bioinformatics Workflows

Presenter: Vedran Kasalica, Netherland eScienceCenter
Co-authors: Nauman Ahmed, Peter Kok, Rob Marissen, Anna-Lena Lamprecht, Magnus Palmblad (@magnuspalmblad)

Schedule: Session 4 (Amsterdam / Online hybrid) Wednesday 15 May, EMEA Friendly time

We present Workflomics, a web platform designed to aid bioinformatics analysis, with an initial focus on proteomics. It leverages the Automated Pipeline Explorer (APE) library to generate workflows in Common Workflow Language (CWL), tailored to user specifications. These workflows undergo a benchmarking process, enabling users to identify the most efficient analysis strategies tailored to their needs. Benchmarking is segmented into two distinct phases: the design-time phase evaluates workflows using pre-execution metrics such as licensing compliance, citation frequency, and compatibility with various operating systems. The run-time phase, in contrast, assesses execution-based performance indicators like memory consumption, processing duration, and error management. To ensure workflows can be executed automatically through cwltool, we include CWL tool descriptions and reference datasets. This approach ensures users can make well-informed decisions, selecting workflows that meet their technical requirements and maximize efficiency. (live-demo)

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