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

Abstract biowep (a ‘Web Enactment Portal’ for Bioinformatics) is a web based client application, that allows the selection and execution of a set of predefined workflows.

The biowep architecture includes a Workflow Manager (WM), a User Interface (UI) and a Workflow Executor (WE).

The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench (see G6G Abstract Number 20514) or BioWMS (see G6G Abstract Number 20526).

Enactment of workflows is carried out by FreeFluo for Taverna workflows and by Hermes, a mobile agent-based middleware, for BioWMS workflows.

The main workflow processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks.

The interface supports user authentication and profiling. Workflows can be selected on the basis of user profiles and can be searched through their annotations. Results can be saved.

The manufacturers developed a web system that supports the selection and execution of pre-defined workflows, thus simplifying access for all researchers.

The implementation of ‘Web Services’ allowing specialized software to interact with an exhaustive set of ‘biomedical databases’ and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis.

biowep is available for interested researchers as a reference portal. Researchers are invited to submit their workflows to this workflow repository.

Selection of a workflow --

In biowep, users are authenticated. The system stores information on workflows executed by each user and it is therefore able to list these executed workflows. The last executed workflows are listed first and for each workflow executed in the past, its version number and the execution date are also shown.

The system also supports the retrieval of lists of available workflows on the basis of the role of the user in their organization (e.g., researcher, clinician, computer scientist) and the domains of interest (e.g., mutation analysis, gene prediction…).

In the latter case, workflows are listed by date (last executed first), while, in the former, they can also be listed by number of executions carried out by all users (i.e., by popularity among users of the system).

biowep - Search of a workflow through its annotation --

Search and identification of workflows of interest can also be achieved by means of the annotation of the workflows. Conditions can be defined on the application domain of the workflow, as well as on its type (the kind of elaboration or analysis that it performs) and the type of its input and output fields.

Conditions can be set on each column and they are then combined by using a logical AND. When multiple conditions are placed on the same column, they are combined by using a logical OR.

An example query could be: find all workflows in the molecular biology domain (application domain) including at least one elaboration step that retrieves (retrieval task) DNA sequences (output) on the basis of a GenBank accession number (input).

Of course, end users are Not obliged to put conditions on every field: these can be left undetermined. A search that does Not impose any condition(s) on any field will result in a list of all annotated steps and workflows.

Results are listed on the same page and include the annotation. Also included is a note that specifies whether the retrieved data refers to the overall task performed by a workflow or to the task performed by a single step in a workflow.

In the former case, the workflow can be enacted, while, in the latter, a list of all workflows including that step can be requested.

biowep - Workflow enactment --

The enactment of workflows created with Taverna is carried out, as already mentioned, by using Freefluo. In this case, the execution is performed on the server and results are stored in the system and made available to the user as soon as they are available.

If the execution takes more time than a pre-defined period (usually 30 seconds, but this time can be changed by modifying a parameter in the configuration file), the workflow is executed in the background and the user is invited to retrieve results later in the results section.

In this case, results are also returned via e-mail.

Alternately, workflows created with BioWMS, are executed by issuing a request to the Hermes server that is available at the University of Camerino. In this case, results are only returned via e-mail.

biowep - Visualization and management of results --

In biowep, workflow executions and related results can be saved, either temporarily or in definitively, stored and later retrieved, analyzed and used for further analyses.

Results can be displayed on the user’s computer by using a Java library, which must be downloaded from the portal and installed locally. A version of the Java virtual machine must also be available and running on the user's side.

The visualization library is derived from the Taverna Workbench which includes some extra Java classes.

Biowep - Available workflows --

biowep currently includes a set of workflows that are devoted to the retrieval of data from the IARC TP53 Mutation Database and from the CABRI catalogues of biological resources. Some of these workflows were first created in the sphere of the Oncology over Internet - O2I project.

Some of the workflows have been made available both in Scufl and in XPDL formats. More workflows are being created and tested in various application domains.

biowep - Support for users and developers --

Support for users and developers is available on the manufacturer's web-site, from where researchers can retrieve all available documentation (user and installation manuals, presentations, and papers) and download software, database structure and workflows. Archives of mailing lists are also available at the support portion of the manufacturer's web site.

Three mailing lists have been created: biowep-announce, biowep- forum and biowep-dev. The first is an announcements list to inform users about the availability of new versions of biowep and new workflows.

The second is an open discussion list on biowep features, also aimed to answer user questions. The third list is restricted to developers and it is the depute list for discussions about improvements, new features, and bug fixes.

Biowep - Comparison with workflow engines --

Biowep is Not a workflow management system (WMS) itself. It does Not allow researchers to create their own workflows.

Instead, it allows all researchers to enact pre-defined workflows. Biowep significantly simplifies access for non-skilled researchers to access automated in-silico procedures implemented by using external workflow management systems.

This allows them to avoid undergoing a deep and continuous training process on the best WMS, available Web Services and their specific features and requirements.

Such training, indeed, would be needed in order to use either a WMS or Web Service(s) directly.

Also, since the portal is able to enact workflows defined by different standards (currently, Scufl and XPDL) and created by different workflow management systems (currently, Taverna and BioWMS), it offers researchers the possibility of taking full advantage of the best features and inter-operational capabilities included in workflow management systems.

Biowep is currently being further developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics - LITBIO.

Foreseen extensions of biowep include, apart from the addition of new workflows, integration with more workflow management systems and engines.

System Requirements



Manufacturer Web Site biowep

Price Contact manufacturer.

G6G Abstract Number 20525

G6G Manufacturer Number 104142