Discovery Net

Discovery Net is one of the earliest examples of a scientific workflow system allowing users to coordinate the execution of remote services based on Web service and Grid Services (OGSA and Open Grid Services Architecture) standards. The system was designed and implemented at Imperial College London as part of the Discovery Net pilot project funded by the UK e-Science Programme (E-Science#The UK e-Science programme). Many of the concepts pioneered by Discovery Net have been later incorporated into a variety of other scientific workflow systems.

History: The Discovery Net e-Science Pilot Project

The Discovery Net system was developed as part of the Discovery Net pilot project (2001–2005), a £2m research project funded by the EPSRC under the UK e-Science Programme (E-Science#The UK e-Science programme). The research on the project was conducted at Imperial College London as a collaboration between the Departments of Computing, Physics, Biochemistry and Earth Science & Engineering. Being a single institution project, the project was unique compared to the other 10 pilot projects funded by the EPSRC which were all multi-institutional.

The aims of the Discovery Net project were to investigate and address the key issues in developing of an e-Science platform for scientific discovery from the data generated by a wide variety of high throughput devices. It originally considered requirements from applications in life science, geo-hazard monitoring, environmental modelling and renewable energy. The project successfully delivered on all its objectives including the development of the Discovery Net workflow platform and workflow system. Over the years the system evolved to address applications in many other areas including bioinformatics, cheminformatics, health informatics, text mining and financial and business applications.

Discovery Net Scientific Workflow System

The Discovery Net system developed within the project is one of the earliest examples of scientific workflow systems. It is an e-Science platform based on a workflow model supporting the integration of distributed data sources and analytical tools thus enabling the end-users to derive new knowledge from devices, sensors, databases, analysis components and computational resources that reside across the Internet or grid.

Architecture and Workflow Server

The system is based on a multi-tier architecture, with a workflow server providing a number of supporting functions needed for workflow authoring and execution, such as integration and access to remote computational and data resources, collaboration tools, visualisers and publishing mechanisms. The architecture itself evolved over the years focusing on the internals of the workflow server (Ghanem et al. 2009) to support extensibility over multiple application domains as well as different execution environments.

Visual Workflow Authoring

Discovery Net workflows are represented and stored using DPML (Discovery Process Markup Language), an XML-based representation language for workflow graphs supporting both a data flow model of computation (for analytical workflows) and a control flow model (for orchestrating multiple disjoint workflows).

As with most modern workflow systems, the system supported a drag-and-drop visual interface enabling users to easily construct their applications by connecting nodes together.

Within DPML, each node in a workflow graph represents an executable component (e.g. a computational tool or a wrapper that can extract data from a particular data source). Each component has a number of parameters that can be set by the user and also a number of input and output ports for receiving and transmitting data.

Each directed edge in the graph represents a connection from an output port, namely the tail of the edge, to an input port, namely the head of the edge. A port is connected if there is one or more connections from/to that port. In addition, each node in the graph provides metadata describing the input and output ports of the component, including the type of data that can be passed to the component and parameters of the service that a user might want to change. Such information is used for the verification of workflows and to ensure meaningful chaining of components. A connection between an input and an output port is valid only if the types are compatible, which is strictly enforced.

Separation between Data and Control Flows

A key contribution of the system is its clean separation between the data flow and control flow models of computations within a scientific workflows. This is achieved through the concept of embedding enabling complete data flow fragments to be embedded with a block-structured fragments of control flow constructs. This results both in simpler workflow graphs compared to other scientific workflow systems, e.g. Taverna workbench and the Kepler scientific workflow system and also provides the opportunity to apply formal methods for the analysis of their properties.

Data Management and Multiple Data Models

A key feature of the design of the system has been its support for data management within the workflow engine itself. This is an important feature since scientific experiments typically generate and use large amounts of heteregeneous and distributed data sets. The system was thus designed to support persistence and caching of intermediate data products and also to support scalable workflow execution over potentially large data sets using remote compute resources.

A second important aspect of the Discovery Net system is based on a typed workflow language and its extensibility to support arbitrary data types defined by the user. Data typing simplifies workflow scientific workflow development, enhances optimization of workflows and enhances error checking for workflow validation . The system included a number of default data types for the purpose of supporting data mining in a variety if scientific applications. These included a Relational model for tabular data, a bioinformatics data model (FASTA) for representing gene sequences and a stand-off markup model for text mining based on the Tipster architecture.

Each model has an associated set of data import and export components, as well as specific visualizers, which integrate with the generic import, export and visualization tools already present in the system. As an example, chemical compounds represented in the widely used SMILES (Simplified molecular input line entry specification) format can be imported inside data tables, where they can be rendered adequately using either a three-dimensional representation or its structural formula. The relational model also serves as the base data model for data integration, and is used for the majority of generic data cleaning and transformation tasks.

Applications

The system won the “Most Innovative Data Intensive Application Award” at the ACM SC02 (Supercomputing 2002) conference and exhibition, based on a demonstration of a fully interactive distributed genome annotation pipeline for a Malaria genome case study. Many of the features of the system (architecture features, visual front-end, simplified access to remote Web and Grid Services and inclusion of a workflow store) were considered novel at the time, and have since found their way into other academic and commercial systems, and especially features found in Bioinformatics workflow management systems.

Beyond the original Discovery Net project, the system has been used in a large number of scientific applications, for example the BAIR: Biological Atlas of Insulin Resistance project funded by the Welcome Trust and also in a large number of projects funded by both the EPSRC and BBSRC in the UK. The Discovery Net technology and system have also evolved into commercial products though the Imperial College spinout company InforSense Ltd, which further extended and applied the system in a wide variety of commercial applications as well as through further research projects, including SIMDAT, TOPCOMBI, BRIDGE and ARGUGRID.

References

Moustafa Ghanem, Yike Guo, Anthony Rowe, Patrick Wendel. Grid-Based Knowledge Discovery Services for High Throughput Informatics. HPDC '02: Proceedings of the 11th IEEE International Symposium on High Performance Distributed Computing. July, 2002. "http://doi.ieeecomputersociety.org/10.1109/HPDC.2002.1029946"
Vasa Curcin, Moustafa Ghanem, Yike Guo, Martin Kohler, Anthony Rowe, Jameel Syed, Patrick Wendel. Discovery Net: towards a grid of knowledge discovery. KDD'02: Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining. August, 2002. "http://doi.acm.org/10.1145/775047.775145"
Jameel Syed, Moustafa Ghanem, Yike Guo. Discovery processes: representation and re-use. Proceedings of the First UK e-Science All-hands Conference, Sheffield, UK. September, 2002.
Nikolaos Giannadakis, Moustafa Ghanem, Yike Guo. Information integration for e-Science. Proceedings of the First UK e-Science All-hands Conference, Sheffield, UK. September, 2002.
Moustafa Ghanem, Yike Guo, Huma Lodhi, Yong Zhang. Automatic scientific text classification using local patterns: KDD CUP 2002 (task 1). ACM SIGKDD Explorations Newsletter. Volume 4, Issue 2, pp. 95–96. ACM Press. December, 2002. "http://www.sigkdd.org/explorations/issues/4-2-2002-12/ghanem.pdf"
Anthony Rowe, Dimitrios Kalaitzopolous, Michelle Osmond, Moustafa Ghanem, Yike Guo. The Discovery Net system for high throughput bioinformatics. Bioinformatics. Volume 19, pp.225–231. Oxford Journals. 2003. PMID 12855463
Salman Alsairafi, Fillippia-Sofia Emmanouil, Moustafa Ghanem, Nikolaos Giannadakis, Yike Guo, Dimitrios Kalaitzopolous, Michelle Osmond, Anthony Rowe, Patrick Wendel. The Design of Discovery Net: Towards Open Grid Services for Knowledge Discovery. Int. J. High Perfm. Computing. Special Issue on Grid Computing Infrastructure and Applications. pp. 297–315. Sage Publications, Inc. August, 2003 "http://hpc.sagepub.com/cgi/content/short/17/3/297".
Nikolaos Giannadakis, Anthony Rowe, Moustafa Ghanem, Yike Guo. InfoGrid: providing information integration for knowledge discovery. Information Sciences -- Informatics and Computer Science. Special Issue on Knowledge Discovery from Distributed Information Sources. Volume 155, Issues 3–4, pp.199–226. Elsevier Science Bv. October, 2003. "http://portal.acm.org/citation.cfm?id=966314".
Moustafa Ghanem, Yike Guo, Anthony Rowe. Integrated data and text mining in support of bioinformatics. Proceedings of the 3rd UK e-Science All-hands Conference AHM 2004, Nottingham, UK. September, 2004.
Vasa Curcin, Moustafa Ghanem, Yike Guo. SARS analysis on the Grid. Proceedings of the 3rd UK e-Science All-hands Conference AHM 2004, Nottingham, UK. September, 2004
Peter Au, Vasa Curcin, Moustafa Ghanem, Nikolaos Giannadakis, Yike Guo, Mohammad Jafri, Michelle Osmond, Anthony Rowe, Jameel Syed, Patrick Wendel, Yong Zhang. Why Grid-based data mining matters? Fighting natural disasters on the Grid: From SARS to land slides. Proceedings of the 3rd UK e-Science All-hands Conference AHM 2004. September, 2004
Vasa Curcin, Moustafa Ghanem, Yike Guo, Anthony Rowe, Wayne He, Qiang Lu, Hao Pei, Yuanyuan Li. IT Service Infrastructure for Integrative Systems Biology. SCC '04: Proceedings of the 2004 IEEE International Conference on Services Computing. IEEE Computer Society. September, 2004. "http://doi.ieeecomputersociety.org/10.1109/SCC.2004.1357998".
Moustafa Ghanem, Vasa Curcin, Yike Guo, Neil Davis, Rob Gaizauskas, Yikun Guo, Henk Harkema, Ian Roberts, Jonathan Ratcliffe. GoTag: A case study in using a shared UK e-Science infrastructure. 4th UK e-Science All Hands Meeting 2005. September, 2005
Neil Davis, Henk Harkema, Rob Gaizauskas, Yikun Guo, Moustafa Ghanem, Tom Barnwell, Yike Guo, Jonathan Ratcliffe. Three Approaches to GO-Tagging Biomedical Abstracts. CEUR Workshop Proceedings. April, 2006.
Moustafa Ghanem, Nabeel Azam, Mike Boniface, Justin Ferris. Grid-Enabled Workflows for Industrial Product Design. 2nd IEEE International Conference on e-Science and Grid Computing (e-Science'06). IEEE Computer Society. December, 2006. "portal.acm.org/citation.cfm?id=1192547".
Moustafa Ghanem, Nabeel Azam, Mike Boniface. Workflow Interoperability in Grid-based Systems. Cracow Grid Workshop 2006. October, 2006
Vasa Curcin, Moustafa Ghanem, Yike Guo, Kostas Stathis, Francesca Toni. Building next generation Service-Oriented Architectures using argumentation agents. 3rd International Conference on Grid Services Engineering and Management (GSEM 2006). Springer Verlag. September, 2006.
Patrick Wendel, Arnold Fung, Moustafa Ghanem, Yike Guo. Designing a Java-based Grid scheduler using commodity services. Proceedings of the UK e-Science All Hands Meeting 2006. Nottingham, UK, September 2006.
Qiang Lu, Xinzhong Li, Moustafa Ghanem, Yike Guo, Haiyan Pan. Integrating R into Discovery Net. Proceedings of the UK e-Science All Hands Meeting 2006. September, 2006.
Jian Guo Liu, Moustafa Ghanem, Vasa Curcin, Christian Haselwimmer, Yike Guo, Gareth Morgan, Kyran Mish. Achievements and Experiences from a Grid-Based Earthquake Analysis and Modelling Study. E-SCIENCE '06: Proceedings of the Second IEEE International Conference on e-Science and Grid Computing. IEEE Computer Society Press. December, 2006. "http://doi.ieeecomputersociety.org/10.1109/E-SCIENCE.2006.17".
Mark Richards, Moustafa Ghanem, Michelle Osmond, Yike Guo, John Hassard. Grid based analysis of air pollution data. Ecological Modelling. Volume 194, Issues 1–3, pp.274–286. Elsevier. March, 2006. "http://linkinghub.elsevier.com/retrieve/pii/S0304380005005259".
Jameel Syed, Moustafa Ghanem, Yike Guo. Supporting scientific discovery processes in Discovery Net. Concurrency and Computation: Practice and Experience. Volume 19, Issue 2, pp. 167–179. Wiley InterScience, 2006.
Vasa Curcin, Moustafa Ghanem, Yike Guo, John Darlington. Mining adverse drug reactions with e-science workflows. Proceedings of the 4th Cairo International Biomedical Engineering Conference, 2008. CIBEC 2008. December, 2008.
Vasa Curcin, Moustafa Ghanem. Scientific workflow systems - can one size fit all? Proceedings of the 4th Cairo International Biomedical Engineering Conference, 2008. CIBEC 2008. December, 2008. "www.doc.ic.ac.uk/~vc100/papers/Scientific_workflow_systems.pdf".
Moustafa Ghanem, Vasa Curcin, Patrick Wendel, Yike Guo. Building and using analytical workflows in Discovery Net. Data Mining Techniques in Grid Environments. Dubitzky, Werner (Ed). pp. 119–140. Wiley-Blackwell. November, 2008.
Vasa Curcin, Moustafa Ghanem, Yike Guo. Analysing scientific workflows with Computational Tree Logic. Journal of Cluster Computing Special Issue of Recent Advances in e-Science. 2009. "http://www.springerlink.com/index/83640077M2347783.pdf"
Antje Wolf, Martin Hofmann-Apitius, Moustafa Ghanem, Nabeel Azam, Dimitrios Kalaitzopoulos, Kunqian Yu, Vinod Kasam. DockFlow - A prototypic PharmaGrid for virtual screening integrating four different docking tools. In Proceedings of HealthGrid 2009 Volume 147, pp.3–12 Studies in Health Technology and Informatics May, 2009