The client applications below will allow you to discover and access data and analysis services provided through the BioMOBY framework. Some also allow the construction and execution of re-usable workflows and analytical pipelines.
Clients
- User Applications
- Web-based
Clients with embedded BioMOBY functionality
- Web-based
Web-based Clients
Jabba
The Java Arabidopsis BioMoby Aggregator (Jabba) is a collection of single applications, which all return for an AGI locus code, specific information retrieved from BioMoby Webservices (this information can be images, literature, etc).
Jabba searches several information spread around the internet for each AGI locus code. With Jabba you will be able to find publications, in which your AGI code appears, ontology terms like GO or MapManBins, your AGI code is assigned to, or images of mutants and phenotypes if available. It also returns more detail information about your AGI locus code. So you can get the sequence, crossreferences, insertions, information from GeneSwinger and so on.
Basically, Jabba is a one-stop-shop for information about an AGI locus code. For this we use so called aggregators, which are software thaat collects information from different places and integrates them into one simple and meaningful view.
By Andreas Groscurth
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BioMOBY Dashboard
The portal into all things Moby! Browse the registry, browse the ontologies, create/edit services or ontology nodes, even test your services… just about anything that can be done with Moby can be done through the Dashboard!
By Martin Senger; made into a Java Web Start app by Andreas Groscurth
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Moby Gadgets
A Google Gadget for every Moby Service that consumes a single identifier as its input. Now you can easily run BioMOBY services from within your iGoogle page!
By Mark Wilkinson
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Gbrowse moby
The first Moby client ever written; very simplistic and limited in power, but easy to understand and use for beginners.
This browser utilizes BioMoby as a data-driven Web Service discovery system – it discovers bioinformatics resources that can consume whatever data-type is currently displayed in your browser window. To begin your browsing session you must provide a starting point for your exploration – the piece of data you are interested in knowing something more about. This takes the form of a Namespace (the common abbreviation for a particular database), and an ID (the identifier itself). For example, the Genbank record for the Arabidopsis ubiquitin conjugating enzyme (gi|431260) is in the Namespace NCBI_gi with the ID 431260.
By Mark Wilkinson
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MOWserv
MOWServ is a versatile web client to access BioMOBY compatible services using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain.
By Instituto Nacional de Bioinformatica
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Remora
Remora, a web server implemented according to the BioMOBY web-service specifications, provides life science researchers with an easy-to-use workflow generator and launcher, a repository of predefined workflows and a survey system.
By Sebastien Carrere and Jerome Gouzy at Genopole Toulouse
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Ahab
Ahab allows parallel execution of multiple services simulteneously.
By Benjamin Good, Clarence Kwan, Wilkinson Laboratoy, University of B.C., B.C., Canada
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Magallanes
Magallanes is a Java library of algorithms to help in the discovery of services and datatypes and the workflows composition. The search engine aims to identify the set of resources that satisfy the user’s query (e.g. what services are available to process my sequence?) and has the ability of profile user behaviour to offer the best results for each user.
Magallanes also can compose workflows automatically. The user only need to specify the workflow’s input and output data types and Magallanes will find the shortest path from the input to the output. A minimal workflow edition is available, Magallanes will show to the user all the possible shortest paths and the user will be able to select the one that he wants. Once the workflow haven’t more alternative paths, it could be exported to Scufl format.
By Javier Rios and OswaldoTrelles, University of Málaga, Spain.
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use it now (JAVA Web Start)!
mAPI
mAPI is a framework for the developement of applications with the main characteristic of be modular and adaptable to different scenarios. The natural flexiblity of the framework allows the conecction to different data sources and combine their contents for showing all to the user with a easy to use and powerful interface.
By S. Ramirez, J. Rios, M. Garcia, J. Karlsson, O. Trelles, University of Malaga.
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MobyRegistrationPages
MobyRegistrationPages is an AJAX enabled web based tool that allows you to register nodes into the BioMoby ontologies. Additionally, you can remove nodes from the ontologies and even call the RDFAgent!
By Edward Kawas, University of British Columbia
Registry Browser
A web based Biomoby registry browser. Query registries for information on any node in a Biomoby ontology and get human readable descriptions that describe them. If you query for a service, then you can even test the service with one click.
By LIPM (Laboratoire Interactions Plantes Microorganismes)
BioExtract Server
The BioExtract Server is an open, Web-based system designed to aid researchers in the analysis of genomic data by providing a platform to facilitate the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and Web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI) non-redundant nucleotide and protein databases. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of Web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and KEGG. The system offers generic support for other SOAP-based Web services and also allows users to integrate local command line tools residing on their own CPUs through the use of a client-side Java applet.
By Brendel Group, Iowa State University and Lushbough Bioinformatics Group, University of South Dakota
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User Applications
Seahawk
Allows a user to load text or HTML data sources, then discover and execute MOBY Services through hyperlinks and text highlighting.
By Paul Gordon, SUN Centre of Excellence, University of Calgary, Alberta, Canada
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Taverna
The Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows.The BioMOBY plugin allows linking of inputs and outputs from both Moby and non-Moby services into extensive and complex workflows created in the Workbench..
Publication
BioMOBY Plugin Users Guide
Tutorial
Tutorial as PDF
By Tom Oinn and the team at myGrid. BioMOBY support added by Martin Senger and Edward Kawas
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jORCA
jORCA is a desktop client able to efficiently integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools. jORCA manages repositories heterogeneity supported by the Modular-API that provides a uniform view of metadata (e.g. GRID-based, pure WSDL–services, BioMoby and others), making the integration of bioinformatics Web-Services easier.
jORCA allows the execution of different web-services invocation protocols and includes features to cover a broad range of user skills:
drag-and-drop edition styles, easy incorporation of viewers for data types, custom favorite’s section that allows the user to freely define a customized environment, on-line updated documentation, etc and it is fully configurable by means of default parameters in text-files (e.g.
initial-links, look & feel, etc).
This work has been performed and financed in the context of INB developments (National Institute for Bioinformatics, a platform of Genoma-España), and it is also being used in the framework of the Advancing Clinic-Genomic Trials’ EU-project (ACGT; Contract Code 026996).
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Pitch Eye
Pitch Eye is a java web-start based application.
The application uses BioMoby services to collect diverse information about amino acid and nucleotide sequences and presents it in user-friendly, interactive graphical way.
By INB computational node (BSC)
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Web-based Embedded Clients
BioTrawler
Explore protein interaction networks by surfing MOBY!
By Frank Gibbons, Harvard University
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BlueJay
Explore genomes with MOBY out-linking functionality.
By Paul Gordon, University of Calgary, Alberta, Canada (Genome Canada/Genome Alberta)
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BioFloWeb
Arabidopsis ‘gene cards’ via PlaNet MOBY services.
By Sophie Durand, INRA, France & PlaNet Consortium
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AtiDB Client
Arabidopsis Locus Report via PlaNet MOBY services.
By Sean Walsh, John Innes Centre, UK
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