Virtual Laboratory for Development and Execution of Biomedical Collaborative Applications

Bubak, Marian; Gubała, Tomasz; Malawski, Maciej; Baliś, Bartosz; Funika, Włodzimierz; Bartyński, Tomasz; Ciepiela, Eryk; Harężlak, Daniel; Kasztelnik, Marek; Kocot, Joanna; Król, Dariusz; Nowakowski, Piotr; Pelczar, M.; Wach, Jakub; Assel, Matthias; Tirado-Ramos, Alfredo

doi:10.1109/cbms.2008.47

Cited by 16 publications

(11 citation statements)

References 8 publications

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“…Deforche et al 2007Deforche et al , 2008Bubak et al 2008;Sloot et al 2008a,b;Stoica et al 2008). The system we have described is still under development with new functionalities added frequently through extensive usability studies in a series of hospitals across Europe.…”

Section: Discussionmentioning

confidence: 98%

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HIV decision support: from molecule to man

Sloot

Coveney

Ertaylan

et al. 2009

Phil. Trans. R. Soc. A.

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Human immunodeficiency virus (HIV) is recognized to be one of the most destructive pandemics in recorded history. Effective highly active antiretroviral therapy and the availability of genetic screening of patient virus data have led to sustained viral suppression and higher life expectancy in patients who have been infected with HIV. The sheer complexity of the disease stems from the multiscale and highly dynamic nature of the system under study. The complete cascade from genome, proteome, metabolome and physiome to health forms a multidimensional system that crosses many orders of magnitude in temporal and spatial scales. Understanding, quantifying and handling this complexity is one of the biggest challenges of our time, which requires a highly multidisciplinary approach. In order to supply researchers with an interactive framework and to provide the medical professional with appropriate tools and information for making a balanced and reliable clinical decision, we have developed 'ViroLab', a collaborative decision-support system (http://www.virolab.org/). ViroLab contains computational models that cover various spatial and temporal scales from atomic-level interactions in nanoseconds up to sociological interactions on the epidemiological level, spanning years of disease progression. ViroLab allows for personalized drug ranking. It is on trial in six hospitals and various virology and epidemiology laboratories across Europe.

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Section: Discussionmentioning

confidence: 98%

“…It is integrated in a grid-based VL (Bubak et al 2008) that facilitates medical knowledge discovery and the interaction and integration of the wide variety of HIV modelling that is available. This offers the potential to provide medical doctors with a DSS to rank drugs targeted at individual patients.…”

Section: Discussionmentioning

confidence: 99%

HIV decision support: from molecule to man

Sloot

Coveney

Ertaylan

et al. 2009

Phil. Trans. R. Soc. A.

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“…Some other Grid portals take the approach of composing workflows from smaller building blocks, which are provided by rich libraries present in the portal. They include popular systems such as the Taverna workbench [10], MOTEUR [11], the Kepler system [12], and the ViroLab platform [13]. However, like other scientific Grid portals, they only allow a single user to edit a workflow.…”

Section: Related Workmentioning

confidence: 99%

A collaborative task planning and development environment on the Cloud/Grid

Hoang

Phung

Lawrence

2013

2013 19th IEEE International Conference on Networks (ICON)

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A Grid system is a promising solution for sharing distributed resources of registered participants to perform tasks whose demands may exceed the capacity of individual participating organization. However, the collaborative aspect of Grids is still underdeveloped as they lack features and mechanisms for human interaction and collaboration. This paper presents a prototype system for collaborative task planning and workflow development over a Grid implemented as a Rich Internet Application. It allows the participants to design their joint workflow interactively and collaboratively in a high level graphical notation. The resulting workflow can be automatically translated into Business Process Execution Language (BPEL) for testing and execution with a few clicks and forms the basis for further refinement and collaboration. This collaborative workflow design application is part of our larger Active Assistive Cloud/Grid infrastructure.

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“…Both are written in Ruby and can provide some interesting processing functionality. Experiments are stored in an application repository [8] which is based on the SVN version control system and can be shared between virtual laboratory users. Local gems, on the other hand, are stored in the Registry.…”

Section: Extending Goi With Local Gemsmentioning

confidence: 99%

“…convert output of one service to the format required by another one, or to perform some simple local processing which does not have to be delegated to an external service. Our experience with the virtual laboratory indicates [8,9] that such an approach is an interesting and convenient alternative to many existing scientific workflow systems which use graphical notation [10][11][12].…”

Section: Introductionmentioning

confidence: 99%