WebLab

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

Abstract WebLab is a data-centric, knowledge-sharing bioinformatic platform. It can be used by biologists to fetch, analyze, manipulate and share their data in an easy-to-use integrative environment.

Dedicated space is provided for users to store their input data and analysis results. Users can upload local data or fetch public data from remote databases, and then perform analysis using more than 260 integrated bioinformatic tools.

These bioinformatic tools can be further organized as customized 'analysis workflows' to accomplish complex tasks automatically.

In addition to conventional biological data, WebLab also provides rich support for ‘scientific literature’, such as searching against the full text of uploaded literature and exporting citations into various well-known citation managers such as EndNote and BibTex.

To facilitate team work among colleagues, WebLab provides an advanced and flexible sharing mechanism, which allows users to share input data, analysis results, scientific literature and ‘customized workflows’ for specified users or groups with sophisticated privilege settings.

WebLab was designed using a ‘modular approach’ and it includes three (3) main modules: Data management, Analysis service(s) and Team work.

Data management –

As a data-centric platform, WebLab provides an advanced data management system for users to store and manage their data and scientific literature online.

In their own data space (‘My Data’), users can create a new entry by uploading a file from a local disk or retrieving it from a remote database (s) through BioMart (see G6G Abstract Number 20517) and

The European Bioinformatics Institute (EBI) SRS - (SRS is a proven and scalable data integration platform that is used at over 300 commercial and academic sites delivering genomic data to thousands of users - SRS is licensed by EBI from BioWisdom Ltd).

After the data type for the newly created file is specified, WebLab can recognize the format and automatically detect available analysis tools using a context-sensitive approach.

The entries in My Data are presented in a hierarchical tree structure in the daily-used local file system. Users can create, rename and delete files, and directories (folders) in My Data by simple mouse clicks.

Moreover, users can also associate user-defined labels (Tags) or comments to entries in My Data, to classify and organize them in flexible and intuitive ways.

In addition to conventional operations supported by My Data, rich literature-specified functions are provided in ‘My Literature’. After uploading the literature, WebLab automatically generates an HTML preview, for a quick check of the paper's content in a browser without downloading the whole article.

Then, WebLab extracts and indexes the full text content of the uploaded articles. When the indexing is complete, users can do simple keyword or complex query search(s) against the full text of literature that exists in My Literature.

Moreover, citation information can also be fetched from NCBI based on PubMed ID or title.

Analysis service(s) –

As an integrative bioinformatic analysis platform, WebLab integrates numerous analysis tools within its uniform framework. In addition to command-line programs, Web-services and Grid-services are also integrated in WebLab.

By organizing different tools into a workflow, complex analysis tasks can be performed in one run.

In a workflow, several analysis tools are launched according to previously defined rules. Currently, two (2) ‘workflow models’, with different user interaction abilities are available in WebLab.

In the ‘Protocol model’, a workflow is executed stepwise, and the user can tune the parameters or options in each step, thus providing maximum flexibility.

On the other hand, in the ‘Macro model’, after mandatory parameters are first inputted by the user, each tool in this workflow model will be executed sequentially.

Thus, the Macro model is more suitable for routine analysis. Moreover, an existing Macro could be re-used and treated as a standard analysis tool to define a new workflow (recursive definition).

Besides defining their own workflows, users can also use several ‘pre- defined workflows’ for common analysis tasks such as ‘phylogenetic tree’ construction and protein function analysis.

A few popular client-side utilities including Sequence Manipulation Suite (SMS); WebMol (a Java-based PDB viewer) - [WebMol was designed to display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB)];

Dotlet (Dotlet is a program for comparing sequences by the diagonal plot method. It is designed to be platform-independent and to run in a Web browser); and

JalView (JalView is a Java alignment editor, which enables fast viewing and editing of large multiple sequence alignments) are also integrated into WebLab for the users to perform interactive work such as editing multiple sequence alignment(s) or visualizing structure.

While these utilities can Not be incorporated into a workflow like other standard analysis tools, due to their interactive nature, they have been proved to be quite useful in daily work.

Users can also keep their favorite analysis tools in their own ‘My Toolbox’ for quick access.

Team work –

To facilitate collaborative team work, WebLab provides a flexible sharing mechanism and group strategy for users to share their data and knowledge.

In WebLab, a user can share almost everything he owns with other users. For entries in ‘My Data’ and ‘My Literature’, both ‘read only’ and ‘read and write’ sharing privileges are provided.

By employing the ‘reference-count’ based sharing model, changes in these shared contents can be seen by all collaborators simultaneously to assure efficient cooperation among all partners.

On the other hand, once a user-defined workflow is shared out, a copy will be made which can be modified without altering the original one, to prevent a possible flaw caused by the recursive definition of the workflow.

Groups are designed for colleagues who work closely together. Any user can set up a new ‘virtual research group’ (VRG) and invite other users to join the new VRG.

A member of a VRG can also share with other members in the VRG, by employing similar operations used for sharing with a normal user.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site WebLab

Price Contact manufacturer.

G6G Abstract Number 20518

G6G Manufacturer Number 104134