REMORA

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

Abstract REMORA is a pilot in the ocean of BioMoby web-services.

This ‘web server’ is implemented according to the BioMoby web-service specification, providing ‘life science researchers’ with an easy-to-use ‘workflow generator’ and launcher, a repository of pre-defined workflows and a survey system.

REMORA main features/capabilities –

REMORA has been designed to create and launch BioMoby (see G6G Abstract Number 20520) workflows.

This means that, in accordance with BioMoby specifications, REMORA manages parameters via ‘secondary articles’ as well as namespaces and services with incoming or outgoing collections.

From an ergonomic point of view the manufacturer has simplified the interface by using the standard scheme of road crossing color codes.

Thus, the color ‘red’ represents blocking steps and running problems, while the color ‘green’ represents ready to go services and achieved computations and the ‘orange’ code represents a punctual warning such as removal confirmation or a settings edition.

In addition, ‘color blind’ people can run REMORA using a grey-scale based layout.

REMORA Workflow design and submission –

The user starts the workflow design by adding a type or a namespace to the data he/she wants to analyze, then, depending on this information, REMORA displays a list of applicable web-services from which the user can select one or several services to be run.

After submission, rectangular icons representing services will appear in the ‘workflow graph’ as well as octagons representing output data.

Thus, the user can progress step-by-step in the workflow building process by ‘clicking’ on a data icon to get the list of applicable services and then adding more web-services to the workflow.

In this way, REMORA acts Not only as a discovery tool but also as a step-by-step generator of consistent workflows (in the limit of web- service semantic consistency).

Once the graph has been designed, the user enters into the configuration mode, to first enter the ‘query data’ (e.g. a string, a Fasta file, etc.) and next to set the web-service parameters.

These two actions can simply be performed by clicking on the service icon in order to get the appropriate ‘web form’.

The ‘design step’ ends with a submission form composed of two (2) fields, one for a short ‘workflow description’ and the other one to enter the users ‘E-mail address’ to send the URL of the ‘result web page’ after workflow completion.

REMORA Visualization –

The same graphical representation is used for data visualization.

In the same way that any service can be configured by clicking on its icon, one can click on a ‘data node’ to access the web-service results.

The REMORA graph can be saved to and reloaded from the user's computer either to see the results or to run the workflow again after editing, if needed.

REMORA Survey mode –

For many database searches, it is relevant to run the same workflow regularly. For this feature, the user receives, in the result e-mail, an additional internet address from which he/she can access a form to program (schedule) the workflow to run weekly or monthly.

REMORA Frequently Asked Workflow (FAW) section –

By analogy with ‘Frequently Asked Questions’, a repository of the most ‘common workflows’ is available on the server.

Compared with saving a workflow on the hard drive, registration in the FAW has the advantage that the ‘workflow development’ effort can be shared, as well as the possibility to see the workflow itself as a potential analysis resource, after the initial step of ‘user data typing’.

Furthermore, the FAW repository enables any visitor to quickly make use of a set of validated workflows.

REMORA Hook mode –

This feature does Not target end-users. Its purpose is to enable the remote control of REMORA from any other web server.

Typically, this function provides access to web-services or REMORA workflows from any web server on condition that data to be analyzed are reachable via the web.

The full description of the ‘hook’ command is available in the ‘Help’ section (on the manufacturer's web-site). This section also provides several links to ‘movie files’ that dynamically present all REMORA features.

REMORA technical and future –

REMORA is a Perl-CGI web server that uses the BioMoby Perl API 0.8.2a.

In creating REMORA, the ‘CommonSubs’ library has been largely rewritten using the ‘xsltproc processor’, in order to speed up the processing of large sized XML files.

The GraphViz Perl module is used for both ‘graphic workflow’ representations and navigation.

Some 'Gbrowse moby' renderers (see G6G Abstract Number 20520 under ‘Clients - Web-based’) have been adapted to REMORA.

In the future, the manufacturer will integrate further BioMoby specifications with the aim of establishing a compatibility link with Taverna (see G6G Abstract Number 20514) workflows, as soon as it is possible to do this without any functional loss.

In addition, the manufacturer will improve REMORA by integrating relevant evolutions that are expected to occur in the semantic MOBY project.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site REMORA

Price Contact manufacturer.

G6G Abstract Number 20521

G6G Manufacturer Number 104137