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A scientific workflow framework for 13C metabolic flux analysis

Paper ID Volume ID Publish Year Pages File Format Full-Text
22532 43366 2016 13 PDF Available
Title
A scientific workflow framework for 13C metabolic flux analysis
Abstract

•13C metabolic flux analysis is a high-precision technique to quantify metabolic fluxes.•Computational 13C MFA evaluation workflows are interactive and iterative.•Service orientation puts the scientist in the center of analysis activities.•Cloud computing leverages access to large computational resource pools.•Provenance collection combined with version control is the key to reproducibility.

Metabolic flux analysis (MFA) with 13C labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of 13C MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision-making is context dependent and requires expertise, rendering an automated evaluation process hardly possible.Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand 13C MFA workflows. 13C MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by 13C MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases.

Keywords
API, application programming interface; BPEL, Business Process Execution Language; CLE, carbon labeling experiment; CSV, comma separated values; EMR, elastic map reduce; (LC-)MS, (liquid chromatography) mass spectrometry; HDF5, hierarchical data format (v
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A scientific workflow framework for 13C metabolic flux analysis
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 232, 20 August 2016, Pages 12–24
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us