GPFlow: An Intuitive Environment for Web Based Scientific Workflow

Abstract

Increasingly scientists are using collections of software tools in their research. These tools are typically used in concert, often necessitating laborious and error prone manual data reformatting and transfer. We present an intuitive workflow environment to support scientists with their research. The workflow, GPFlow, wraps legacy tools, presenting a high level, interactive web based frontend to scientists. The workflow backend is realized by a commercial grade workflow engine (BizTalk). The workflow model is inspired by spreadsheets and is novel in its support for an intuitive method of interaction as required by many scientists e.g. bioinformaticians. We apply GPFlow to two bioinformatics experiments and demonstrate its flexibility and simplicity.

WorkWays: Interacting with Scientific Workflows

“…Kepler Meta-genomics BioWep [16] Taverna, BioWMS Bioinformatics CrowdLab [56] VisTrail Visualisation GridFlow portal [57] GridFlow General purpose Pegasus portal [15] Pegasus General purpose OOPS [58] Swift Bioinformatics GTLab [59] DAGMan, Taverna General purpose LEAD [3] BPEL Weather forecast SciencePipes [60] Kepler Zoology GPFlow [25] Windows Workflow Foundation Bioinformatics Ergatis [61] Ergatis Bioinformatics Galaxy [62] Galaxy Bioinformatics VisIVO [63] Zen, Taverna Astrophysics HELIO [64] Zen, Taverna Heliophysics MoSGrid [65] Zen Computational Chemistry e-BioInfra Gateway [66] MOTEUR Neuro-science HubZero + Pegasus [67] Pegasus General purpose MediGrid [24] Grid Workflow Execution System Biomedical DIRAC portal [68] DIRAC Workflow management system General purpose Atmospherics Data Processing Portal [69] Kepler Atmospherics [70] √ √ JSON mincviewer [47] × √ MINC file/file path paraviewWeb [71] × √ File path loop however does not attract much attention. To the best of our knowledge, MediGrid [24] and GPFlow [25] are two workflow-based gateways that support interactive workflows. GPFlow workflows are state-based; each component of the workflow can be in either 'running' or 'suspended' state, and user inputs are processed at 'suspended' state [25].…”

“…To the best of our knowledge, MediGrid [24] and GPFlow [25] are two workflow-based gateways that support interactive workflows. GPFlow workflows are state-based; each component of the workflow can be in either 'running' or 'suspended' state, and user inputs are processed at 'suspended' state [25]. GPFlow supports interactions between running workflows and users by associating a Web interface with each component.…”

Go-Smart: Web-based computational modeling of minimally invasive cancer treatments

“…While many such bioengineering, bioinformatics and biomedical workflow systems now exist, it is less common to see such systems with an integrated web-based interface for dynamic inclusion of third-party workflows. Certain projects have based extended existing workflow packages to improve cloud functionality or user-friendly web support, such as the Tavaxy project [2], combining the Galaxy system with the Taverna suite, WorkWays providing a web gateway for Kepler [52], or GPFlow wrapping Microsoft BizTalk and Human Workflow Services in a user-friendly scientific web interface [65]. In an offline setting, the GIMIAS open source framework provides a set of offline analysis and visualization tools that may be used inconjunction with Taverna to build complete research workflows, or preliminary clinical workflows [47].…”