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From MyExperimentWiki

myExperiment makes it really easy for the next generation of scientists to contribute to a pool of scientific workflows, build communities and form relationships. It enables scientists to share, reuse and repurpose workflows and reduce time-to-experiment, share expertise and avoid reinvention.

Contents 1 What is myExperiment? 2 The myExperiment software 3 News and Events 4 How to get involved 5 Pages for Wiki users 6 Contact 7 FAQ 7.1 Which Workflow Systems are supported? 7.2 Can I execute workflows from myExperiment? 7.3 Can I share things other than workflows? 7.4 Do you support remote repositories? 7.5 Is the API available? 7.6 What are you working on at the moment? 7.7 What are others working on at the moment? 7.8 Why not use Facebook? 7.9 Why not use a portal solution? 7.10 Can I download the myExperiment software? 8 Contributors

[edit] What is myExperiment?

The myExperiment Virtual Research Environment enables you and your research community to share digital items associated with your research — in particular, it enables you to share and execute scientific workflows. It supports the individual scientist on their personal projects, forming a distributed community with scientists elsewhere who would otherwise be disconnected, enabling them to share, re-use and repurpose experiments, to reduce time-to-experiment, share expertise and avoid reinvention — and it does this in the context of the scholarly knowledge lifecycle. Hence myExperiment is a community social network, a market place, a platform for launching workflows and a gateway to other publishing environments. myExperiment is brought to you by a joint team from the universities of Southampton and Manchester in the UK, led by David De Roure and Carole Goble, and is funded by JISC under the Virtual Research Environments programme and by Microsoft's Technical Computing Initiative. myExperiment is part of the myGrid consortium, which develops the Taverna workbench for creating and executing scientific workflows, and also builds on CombeChem - two of the original UK e-Science Pilot Projects. The related Whip (Triana enactment) activity in Cardiff is supported by the OMII-UK Commissioned Software Programme. The latest myExperiment presentation is available in Powerpoint 97-2003 - see News and Events below for others. Download the A3 Poster, A4 Flyer or ANSI-D Poster. Papers on the design of myExperiment can be found here‎. (All PDF.)

[edit] The myExperiment software

We are developing the Web 2.0 open source Software that powers the myexperiment.org web site. The closed beta release of the site (myexperiment.org) was launched in July 2007 and the open beta in November, supporting communities sharing workflows. New features in the near future includes Taverna workflow execution as well as Experiment Objects – these enable you to group together the various digital items associated with an experiment and to handle their provenance. Ultimately the web site software will be downloadable so that you can run your own myExperiment instance — and connect it up with others if you wish.

Designed for maximum ease of reuse and for community development, all the myExperiment services are accessible through simple programming interfaces so that you can use your existing environment (such as a wiki) and augment it with myExperiment functionality – or build entirely new interfaces and functionality mashups which make use of myExperiment behind the scenes. We believe in bringing myExperiment to the user. Furthermore, myExperiment is designing to integrate with federated stores such as those used in scholarly publishing.

[edit] News and Events

David De Roure presented Six Principles of Software Design to Empower Scientists at the e-Science Project Management Symposium held at OeRC, Oxford, April 2008. David De Roure and Jiten Bhagat presented Towards Science Mashups in myExperiment at the at Microsoft Science All Hands Meeting in Seattle, March 2008. myExperiment mentioned in Nature Nature 451, 1024-1025 (20 February 2008). myExperiment featured in David De Roure's seminarThe New e-Science at the Oxford e-research Centre, Oxford, February 2008. myExperiment mentioned in Jim Hendler's article Reinventing Academic Publishing, Part 3 in in IEEE Intelligent Systems January/February 2008, page 2-3. myExperiment featured in Carole Goble's keynote Curating Services and Workflows: the Good, the Bad and the Ugly at the 3rd International Digital Curation Conference, Washington DC, December 2007. myExperiment featured in David De Roure's keynote The New e-Science at the IEEE e-Science Conference, Bangalore, December 2007. myExperiment.org is live! We are pleased to announce that we moved from closed to open beta on 12th November 2007. It was demoed at 9am PST by Savas Parastatidis at Supercomputing 07 in Reno and blogged.

myExperiment was presented by Carole Goble and David De Roure at the Microsoft e-Science Workshop at RENCI, North Carolina, 21-23 October, 2007. myExperiment was presented by David De Roure in the Web 2.0 workshop and the Workflow session (WFM-RG) at OGF21 in Seattle, 15 October, 2007. myExperiment was introduced by Katy Wolstencroft at the Joint OMII-UK & EBI Industry Programme Workshop, Hinxton, Cambridge UK, October 8-9 2007. myExperiment featured in talks by David De Roure at the Workshop on Scientific and Scholarly Workflow, Washington, October 2007. myExperiment featured in Carole Goble's keynotes at GRID2007 (Austin, Texas) and e-Social Science 2007 (Ann Arbor). The myExperiment fully-RESTful Developer's API is now available ( PDF) Members of the myExperiment team were present at the UK e-Science All Hands meeting in Nottingham, 10-13 September 2007 - with T shorts and mugs! myExperiment also featured in the VRE roundtable discussion on Wednesday 12th. Carole Goble gave a talk on myExperiment: A MySpace for the Self-serving Bioinformatician at the 4th Integrative Bioinformatics Workshop, Ghent, on September 11, 2007. myExperiment was introduced by Katy Wolstencroft at BOSC, Vienna on Saturday 21st July 2007 and opened for Beta testers at BOSC and ISMB myExperiment was demoed at the International Summer School on Grid Computing 2007, Sweden (ISSG07) on 20th July 2007 and opened for Beta testers on the myExperiment-discuss list. DDeR gave a position statement on Ending the Tyranny of the Grid - here are the slides.

See News for further information and past events.

[edit] How to get involved

We welcome all forms of participation – whether you would like to take part in trials, deploy the software, integrate it with other systems, or contribute code or content. We are currently conducting trials in the life sciences domain; other disciplines, including chemistry, social science and music, are in the pipeline – as are other workflow systems including Triana.

If you are interested in finding out more please join the myexperiment-discuss mailing list and request an account for this Wiki by emailing bugs@myexperiment.org (this will enable you to access pages beyond this public main page). We're very keen to hear from people who would like to take part in the current trials, especially existing Taverna users. Contact details are below.

[edit] Pages for Wiki users

You need a myExperiment Wiki account to get at the following pages — to request a Wiki account please email bugs@myexperiment.org

Talks Papers Videos

Marketing Images

Documentation Management pages (limited access)

[edit] Contact

Bugs, feedback, feature requests, mailing list, Wiki accounts etc please send email to bugs@myexperiment.org (we'll be providing separate emails in due course - for now everything is going into FogBugz for routing - you will receive a tracking ticket).

Investigators:

David De Roure dder@ecs.soton.ac.uk +44 23 8059 2418

Carole Goble carole.goble@manchester.ac.uk +44 161 275 6195

[edit] FAQ

[edit] Which Workflow Systems are supported?

You can use myExperiment to share workflows for use in any workflow system. We provide extra support (such as metadata handling, service extraction, visualisation, enactment) for particular systems. At this stage we are working foremost with the Taverna Workflow Workbench, we are beginning to provide support for Triana and we have recently started talking with our Kepler colleagues. Please contact us about your favourite workflow system.

[edit] Can I execute workflows from myExperiment?

As well as sharing workflows, our goal is that myExperiment will be integrated with remote execution services for supported workflow systems, so that users can run workflows from myExperiment and from other interfaces which use myExperiment functionality. Taverna execution support is currently under test and will be available soon; Triana execution is under development at University of Cardiff. Please contact us about your favourite workflow system. We anticipate that web-based interfaces and functionality mashups will become the predominant interfaces to workflow systems, especially in a multiworkflow environment.

[edit] Can I share things other than workflows?

Yes. You can share any files or blobs, within reasonable storage constraints. Support for sharing collections of things will be provided soon through Encapsulated myExperiment Objects (EMOs) which are designed to interoperate with the emerging OAI-ORE standard.

[edit] Do you support remote repositories?

We support remote objects that can be access via a URI. We are specifically looking at repositories supporting the OAI harvesting protocol, and will be working with ePrints. We have also conducted feasibility studies with S3 and SRB. Please contact us about your favourite repository.

[edit] Is the API available?

myExperiment has a simple RESTful API and we encourage you to use it. Our development team and developer community warmly welcomes new API users. Contact the team for documentation.

[edit] What are you working on at the moment?

The Development team is working on: attachments and packs, Taverna enactment, blogging the lab, Triana support and enactment, Kepler support, remote hosting, tagging of groups, support for Encapsulated myExperiment Objects (EMOs), interfaces and mashups using SilverLight 2, analysing trials data, myExperiment data model, extensions to the API.

[edit] What are others working on at the moment?

(Why not tell us what you are doing to add to this list...?) WHIP project at Cardiff. Google gadgets. Integration with "blogging the lab" work. Looking at integration with Research Information Centre (RIC), a virtual research environment being jointly developed by the Technical Computing Group at Microsoft and The British Library.

[edit] Why not use Facebook?

The myExperiment project is producing software that anyone can download and use, and it especially caters for the attribution, licensing and sharing models required by our science users, together with integration with their work and publishing environments. This makes it quite different to Facebook. We are very keen to see tools that bring myExperiment and Facebook together - for example we would like to work with people on Facebook apps that bring through myExperiment functionality. Contact us if you're interested!

[edit] Why not use a portal solution?

The first principal of the myExperiment design is "bring myExperiment to the user". Firstly, we have deliberately aimed our human interface at the next generation of scientists. Secondly, we have deliberately aimed our programmatic interface (API) so that our functionality can be made available through other interfaces - such as portals. That said, myExperiment could have been built using portal techniques and we deliberately chose not to do so (as part of "our experiment"!) We hope that myExperiment encourages and informs a debate about portal approaches.

[edit] Can I download the myExperiment software?

Yes. myExperiment is Open Source software written in Ruby on Rails, and is available on RubyForge under the BSD Licence. Please let us know if you are installing myExperiment as we can provide advice on installation.

[edit] Contributors

Thanks to the myExperiment team, family and friends:

Jiten Bhagat	Mark Borkum	Andy Brass	Simon Coles	Don Cruickshank	Cat De Roure
June Finch	Paul Fisher	Jeremy Frey	Antoon Goderis	Andrew Harrison	Duncan Hull
Matt Lee	Yuwei Lin	Bertram Ludaescher	Danius Michaelides	Kurt Mueller	David Newman
Cameron Neylon	Savas Parastatidis	Meik Poschen	Rob Procter	Marco Roos	Stian Soiland
Ian Taylor	Frederique Van Till	Alexander Voss	David Withers	Katy Wolstencroft	Ed Zaluska