Mobyle

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

Abstract Mobyle is a full web bioinformatics framework and web portal specifically aimed at the integration of bioinformatics software and databanks.

Mobyle provides a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet advanced data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system.

Mobyle offers the invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software.

While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions.

Mobyle is a generic web-based framework –

While including advanced technologies such as web services, remote execution and dataflow mechanisms, Mobyle addresses major end- user concerns arising from the use of sophisticated bioinformatics systems.

A recent study shows how simple issues in the user interface can impede the use of a system by scientists, causing them to waste time and even preventing them from using it further.

To address this issue, the design of Mobyle's interface is user- centered, to provide a usable yet customizable access to a large panel of services, from 'genome analysis' to structural bioinformatics.

The description language it uses to generate user interfaces is sufficiently extensive and flexible for rich user interfaces to be generated.

Its core partly relies on concepts previously embedded in the Pasteur Institute Software Environment (PISE) - (PISE is a tool that can generate Web interfaces for Molecular Biology programs) and the Ressource Parisienne en Bioinformatique Structurale (RPBS) portal.

Moreover, different Mobyle servers can be federated to integrate services distributed over various sites. This functionality enables the federation of a network of curated portals, combining the skills of each of them.

The Mobyle program description language also enables you to define web services, as shown by the PlayMOBY Mobyle companion tool, which automates the publication of BioMOBY web services, and has monitoring capabilities that provide the bases for service quality monitoring.

Homogeneous user interfaces to heterogeneous programs –

Mobyle automates the generation of web interfaces using an abstract definition of a program's parameters. This solution provides a homogeneous interface to all the programs, minimizing the syntactic complexity. It is also helpful in file management issues and program chaining.

Persistent user workspaces –

Mobyle allows a fast and temporary guest access to the programs and also gives the users the possibility to create registered accounts, which allows user data and jobs to be maintained and managed across multiple work sessions.

XML description of interfaces –

All Mobyle data, including program descriptions, job definitions and user workspaces are stored in XML documents. The main element of the system, the program description, is inherited from the PISE system. It describes various aspects in a language that targets simplicity as much as possible.

Note: A formal description of the XML grammar used to describe Mobyle programs is available on the manufacturer's webpage.

Network-enabled bioinformatics tools –

The Mobyle system aims at acting as a ‘hub’ for a set of programs of interest. A program integrated in Mobyle can Not only be local but also remote, using the Mobyle Net functionality. Additionally, current and future developments aim at providing gateways to web-service-based systems such as BioMOBY.

User interface design –

Mobyle provides the scientist with a global and integrated view of all the elements needed to perform his or her analyses. At a glance, the user can see which programs are available and which analyses have already been run.

The portal is organized in three (3) main parts: a left navigation panel, a central panel displaying a selection of elements of the current work, such as forms and results, and horizontal tabs enabling the user to navigate between these elements.

Program search –

Available programs are classified so that they can be searched, using program and parameter names, prompts and documentation, or bibliographic references.

The page that displays the results of a given analysis also provides the user with the 'list of programs' that can be run for further analysis. This list guides users, restricting them to a view of programs that are compatible with a given result file.

User workspace –

At any time, the user can navigate between previously used forms and details of individual analyses, for instance to compare results. This view persists over separate uses of the portal during a given amount of time.

This navigation model gives a ‘flat’ multi-directional access to several forms. A list of bookmarked data is also available: this provides the user with reuse-based access and information on previously submitted data.

Forms and reusability –

The Program forms are classical HTML forms. They contain a specific control element - the databox - designed to facilitate data reuse by biologists.

This control allows users to set parameter values for biological data (e. g. DNA sequence or 3D protein structure) using various methods (pasting, file upload, databank entry retrieval, bookmark reuse).

Results and interactive chaining –

The job status and results page provides a preview of the job data and metadata. It also includes an advanced control element - the resultbox - which lets users access results in plain browser windows, download them to their workstation, bookmark them or ‘pipe’ them to a new form, i. e. display a new form that is preloaded with the user data.

This ability to pipe data into a new form, together with databox bookmark reuse, permits interactive program chaining within the portal.

Flexible layout design –

The portal, given a ‘program definition’, can automatically generate a form and a result page without any need for layout information.

However, this process can be overridden to generate program-specific forms and job result pages with particular layouts. This possibility can prove extremely useful, for instance to fulfill custom program requirements or to define a particular layout required for optimal use of a given program.

Data typing and helpers –

A major aspect of Mobyle is its capacity to facilitate 'automated data conversion' and formatting for service integration, thus saving the user from tedious and non-scientific data manipulation tasks.

The Mobyle typing system describes program parameters using a typing mechanism that aims to help users in such tasks. It modifies the interface display, the controls for user values (the input parameters), the possibility of chaining between programs and data reusability.

The Mobyle network –

The Mobyle network allows the execution of programs that are available on different Mobyle servers from a single portal. This feature facilitates user access to services physically distributed over different Mobyle servers, within an integrated environment enabling data reuse and program chaining.

Workflows and protocols –

Mobyle contains an embedded prototype dataflow-oriented ‘workflow engine’, enabling the chaining of successive or parallel tasks to be automated.

It runs on top of the Mobyle core library, exploiting the Mobyle network to execute tasks distributed between local and remote servers, and orchestrates the tasks to synchronize their execution with the availability of all their input data.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site Mobyle

Price Contact manufacturer.

G6G Abstract Number 20516

G6G Manufacturer Number 104135