myExperiment Virtual Research Environment

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

Abstract myExperiment Virtual Research Environment is a collaborative environment where scientists can safely publish their workflows and experiment plans, share them with groups and find those of others.

The myExperiment Virtual Research Environment enables you and your colleagues to share ‘digital items’ associated with your research - in particular it enables you to share and execute ‘scientific workflows’.

Workflows, other digital objects and bundles (called Packs) can now be swapped, sorted and searched like photos and videos on the Web.

Unlike Facebook or MySpace, myExperiment fully understands the needs of the researcher and makes it easy for the next generation of scientists to contribute to a pool of scientific methods, build communities and form relationships - reducing time-to-experiment, sharing expertise and avoiding reinvention.

The social web site, launched in November 2007, contains one of the largest public collections of workflows across multiple ‘workflow systems’ including Taverna (over 800 workflows) and Trident and is used by thousands of users ranging from life sciences and chemistry to social statistics and music information retrieval.

Note: myExperiment has over 2,300 users, 160 groups, 800 workflows, 200 files and 70 packs.

All the myExperiment services are accessible through simple RESTful programming interfaces and a SPARQL endpoint so that you can use your existing environment and augment it with myExperiment functionality - or build entirely new interfaces and functionality ‘mashups’.

myExperiment Workflow Systems supported --

You can use myExperiment to share workflows for use in any workflow system.

The manufacturer provides extra support (such as metadata handling, service extraction, visualization, enactment) for particular systems.

At this stage the manufacturers are working foremost with the Taverna Workflow Workbench (T1 and T2) and with Microsoft's Trident, and the manufacturers are planning support for Meandre during 2009/10


myExperiment features/capabilities include:

1) User Profiles - myExperiment allows scientists to create profiles, containing different kinds of personal information: contact details, location, details about work and professional life.

The profiles help to identify contributors who are to be credited for a particular piece of work and also to search for people based in the same location, having similar interests or working on related projects.

2) Groups - Groups are designed to enhance collaboration among scientists who work closely together.

Anyone can create new groups and invite other users to join them; it is also possible to browse existing groups and request membership in them.

3) Resource Sharing - Users can share various kinds of resources with each other - these include workflows, files and packs.

myExperiment makes every effort to provide very flexible and robust ways for the uploader to set up permissions for viewing, downloading and updating of the shared resources.

Options vary from marking contributions as personal and invisible for anyone else to giving permission to anyone to have full control over the resource.

Registered users can then view resources (if permitted), rate them, leave comments and write reviews on them.

4) Tags - myExperiment provides an option to add keywords (also known as “tags”) to each resource, group and pack - thus annotating all available resources.

Search of the latter based on the use of tags overcomes problems associated with simple textual searching. It narrows down the search area and helps to provide more precise results.

5) Workflows - Scientific workflows in various formats can be uploaded to myExperiment.

Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files.

Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded.

This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

6) Files - Any kind of file can be shared with the help of myExperiment.

7) Packs - Packs are used to create collections of related resources - these can include both internal myExperiment resources (like workflows, files and other packs) and links to externally available items.

Descriptions can be set up for the pack in general and for each item independently, helping users to find resources that are relevant to them.

8) Credits and Attributions - It is very important to give credit to people and make reference to resources that have been used in the creation of new resources.

myExperiment provides an easy way to do this - when a contributor is about to upload a new piece of work, along with the description, access permissions and tags, they can also record credits and attributions.

This process has been made easy, intuitive and quick as possible.

9) Messaging - A messaging system is available to enable communication among the users of myExperiment.

It resembles a conventional e-mail system but is dedicated for delivering internal messages directly to the users.

10) News Feeds - The system logs actions that are taken by users - a record is taken, when new users join myExperiment, when someone joins a particular group, uploads new or updates existing resources.

These are then displayed in a comprehensible manner to every other user, thus enabling them to keep track of the latest events on myExperiment.

System Requirements

Contact manufacturer.


Manufacturer Web Site myExperiment

Price Contact manufacturer.

G6G Abstract Number 20513

G6G Manufacturer Number 104132