BioMOBY

Category Cross-Omics>Workflow Knowledge Bases/Systems/Tools

Abstract BioMOBY is a biological Web Service interoperability initiative that began as a retreat of representatives from the ‘model organism’ database community in September, 2001.

Its long-term goal is to provide a simple, extensible platform through which the myriad of ‘on-line biological databases’ and analytical tools can offer their information and analytical services in a fully automated and interoperable way.

End user BioMOBY Applications –

The client applications listed 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 –

1) Seahawk - Seahawk allows a user to load text or HTML data sources, then discover and execute MOBY Services through hyperlinks and text highlighting. Seahawk is a Java applet (or application component) that allows a user to:

Seahawk is Not a ‘visual programming environment’ for workflows, but rather allows ‘workflow construction’ by example. It is Not for deploying services or seeing the guts of MOBY Objects and service calls.

2) Taverna - (see G6G Abstract Number 20514) - The Taverna Workbench provides a desktop authoring environment and enactment engine for ‘scientific workflows’. The BioMOBY plug-in allows linking of inputs and outputs from both Moby and non-Moby services into extensive and complex workflows created in the Taverna Workbench.

3) jORCA - jORCA is a desktop client able to efficiently integrate different types 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 a 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).

4) Pitch Eye - Pitch Eye is a Java application that can be used to visualize ‘amino acid’ and ‘nucleotide sequences’ along with available information about them found through BioMoby services.

The sequence can be retrieved through available BioMoby services or introduced manually (typed, pasted or dragged). The user is offered to execute various BioMoby services from an available list. Where possible, results are aligned with the original sequence.

Clients - Web-based –

1) Jabba - The Java Arabidopsis BioMoby Aggregator (Jabba) is a collection of single applications, which all return specific info retrieved from ‘BioMoby Webservices’ (this information can be images, literature, etc.) for an Arabidopsis Genome Initiative (AGI) locus code.

Jabba searches information spread across 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, which 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 that you can get the sequence, cross-references, insertions, info from GeneSwinger, etc.

2) BioMOBY Dashboard - the Dashboard is a Graphical User Interface (GUI) helping Biomoby service providers to develop and deploy their Biomoby services. Because of its extensibility, however, it may also contain panels that are useful even for pure Biomoby end-users, when they wish to call Biomoby services.

3) Moby Gadgets - Contains 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!

4) 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.

5) MOWserv - MOWServ is a versatile web client that can be used to access BioMOBY compatible services using the service description stored in the BioMOBY catalogue.

This automatic ‘interface generator’ significantly reduces development 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 at the National Institute for Bioinformatics in Spain.

6) REMORA - (see G6G Abstract Number 20521) - REMORA is a web server that is implemented according to BioMoby web-service specifications, providing life science researchers with an easy-to-use ‘workflow generator’ and launcher, a repository of ‘predefined workflows’ and a survey system.

7) Magallanes - (see G6G Abstract Number 20511) - Magallanes (Magellan) (Multi-Architecture Resources Discovering) is a versatile, platform-independent Java library of algorithms aimed at discovering bioinformatics Web Services and associated data types.

The Magallanes software library supplies an integrated framework to develop advanced ‘discovery engines’ that help researchers find web- services and associated data-types.

8) mAPI - mAPI is a flexible and expandable framework for the development of ‘distributed architectures’ which enable the discovery and exploitation of knowledge based (KB) resources.

The framework provides modular functionality for sharing and discovering different resources, metadata related to tools, users, and data types registered in central repositories, including the ability for handling data storage and tool invocation.

9) MobyRegistrationPages - MobyRegistrationPages is an AJAX enabled Web Based tool that allows you to register nodes into the BioMoby ontologies. Additionally, you can also remove nodes from the ontologies.

10) Registry Browser - A Web Based Biomoby Registry browser. Users can 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, you can then test the service with one click.

Clients with embedded BioMOBY functionality - Web-Based –

1) Bluejay - Bluejay is a set of Java™ objects for the processing, display and querying of XML encoded linear scale data. The main subject for analysis in the manufacturer's implementation are ‘genetic and protein sequences’, where features fall somewhere on the ‘linear molecules’.

2) BioFloWeb - With this tool, you can search for information about an Arabidopsis thaliana gene. BioFloWeb displays a ‘gene report’ containing data provided by PlaNet BioMoby web services.

3) AtiDB Client - Produces the Arabidopsis Locus Report via PlaNet MOBY services which includes synonyms, GO terms, insertions, InterProScan results and other information.

System Requirements

Web-based.

Manufacturer

Multiple manufacturers and contributors - myGrid has donated significant developer’s time and goodwill to implementing support for MOBY-S services into their architecture;

Open Bioinformatics Foundation - the OBF has donated server space, bandwidth, and extensive administrative support to the BioMOBY project. The OBF hosts the BioMoby website, and the CVS repository;

YourKit is supporting open source projects with its full- featured Java Profiler. YourKit, LLC is the creator of innovative and intelligent tools for profiling Java and .NET applications and others.

Manufacturer Web Site BioMOBY

Price Contact manufacturer.

G6G Abstract Number 20520

G6G Manufacturer Number 104137