Computational protocol: mORCA: ubiquitous access to life science web services

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Protocol publication

[…] The presented application (mORCA) significantly extends the functionality of the initial mobile client prototype described in our previous work [] In this new development we have included important new features such as asynchronous calls with monitoring capabilities, the evolution from web-app to hybrid app, or the development of new modules to list and execute third-party services. Additionally, minor changes have been done including a new fuzzy search mechanism, a user accounting module, and a complete restyling of the application after performing a usability study with users of the BIBM application domains.In this section the design and implementation of a mobile client satisfying such requirements is outlined. The current capabilities of mobile devices have been considered during the whole life cycle. [...] Our design consists of a server-side in which MAPI and its Web Service are in charge of communicating with both the repositories and the client. The client-side deals with the information provided by the server through different modules and also it manages how this information is shown to the user.MAPI [] is a tool for the standardization of the metadata contained in different Web Service repositories. It permits the use of different formats of services using a standard interface in a transparent way since the data type module manages these different formats. In addition, MAPI enables the execution of services responding to diverse communication protocols (e.g. SOAP, REST, and BioMOBY []). To perform this task, it implements a set of execution workers (i.e. service invocation modules), which are specifically designed to execute a given type of service. Further functionality includes user management, and file system operations (see the MAPI modules represented as boxes in the right part of Fig. ).Fig. 1The modules of the client-side are in charge of the main functionality described before:User authenticationBrowsing the repositoryDiscovering servicesService parameter compositionService invocationFile management, including data uploading and downloadingService execution monitoringUser authenticationBrowsing the repositoryDiscovering servicesService parameter compositionService invocationFile management, including data uploading and downloadingService execution monitoring [...] Access to Web Service repositories is delegated to the server-side. The server-side is able to work with multiple repositories by implementing different accesses for each of the configured catalogues, decoupling the client-side from this task. The client- side just requests a hierarchical list of services from the server-side. To display the retrieved service tree, whatever the catalogue, a nested “Listview” was used to represent it as a list of folders and services (see Fig. ). This representation enables users to do a fast examination of the Web Services tree. Later on users can look for a specific service by navigating through the categories. During the navigation process, new panels with the services and subcategories of the selected category appear from the right-hand side.Fig. 2Using this implementation, the developed mobile client is able to browse all the service catalogues that the MAPI server-side is able to handle. This includes the traditional BioMOBY repositories of the Spanish National Institute of Bioinformatics, and other catalogues such as Bio.tools and BioCatalogue. New catalogues can be easily added to the system by mapping its service metadata to our data structure.Since a given catalogue can potentially contain a huge number of services, a textbox component (see Fig. ) provides users the possibility to filter the services tree according to a user-defined search criteria. The search engine developed, which lists just the corresponding services and categories, is a simplification of the service discovery function of the Magallanes tool []. It is important to note that the implemented search works in a fuzzy way, meaning that it produces results even if the search criteria lead to some mismatches. […]

Pipeline specifications

Software tools mORCA, MAPI, Magallanes
Application Miscellaneous
Organisms Malus domestica