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http://www.myexperiment.org/announcements/47

A live webinar on Taverna, myExperiment and BioCatalogue will be held by Paul Fisher on March 8th, 2011 at 16:00 GMT on BitesizeBio. For details see http://bitesizebio.com/webinars/the-taverna-project/.

http://www.myexperiment.org/announcements/7

myExperiment has been experiencing a lot of interest lately and thus a bigger load than usual. As a result we have introduced performance improvements on some areas of the site and working on more improvements.

Please contact us if you are experiencing major delays in loading up pages (please mention the pages affected).

We will also be moving to an external hosting service soon.

We are continually working on improving the performance and reliability of myExperiment.

Thanks,
The myExperiment Team

 

http://www.myexperiment.org/announcements/42
We're pleased to announce that myExperiment has joined the portofilio of projects in the e-Research South consortium. This means it is now part of two consortia funded by EPSRC, i.e. myGrid and e-Research South.
 
We welcome the new opportunities that this brings. We of course continue to develop myExperiment as part of our family of e-Laboratories projects which includes BioCatalogue, SysmoDB and methodbox.
 
For those attending the UK e-Science All Hands meeting in Cardiff (Sep 13-16) you'll find myExperiment on the e-Research South booth.  For this and other event announcements see the news page on the myExperiment Wiki.
 
-- Dave

 

 

 

http://www.myexperiment.org/announcements/56

A video is available of David De Roure's 10min myExperiment demo at the Microsoft 2011 eScience Workshop: Transforming Scholarly Communication held October 23–25, 2011 in Cambridge, Massachusetts, USA.

 

http://www.myexperiment.org/announcements/51

The Taverna team are pleased to announce that Taverna 2.3.0 Workbench and the Command Line Tool are now available for download.

Taverna 2.3.0 includes new service types, integration with service catalogues and experimental export of provenance information. Here are a few of the new features in the Workbench:

  • REST service allowing you to perform GET, POST, PUT and DELETE operations configured using a template
  • XPath service where you can create an XPath expression from an example XML document
  • Tool service that allows you to run commands or scripts as part of your workflow
  • Searching and browsing of service catalogues, such as the BioCatalogue, and addition of those services to your Workbench or workflow
  • Experimental export of provenance in the Open Provenance Model and Janus formats
  • Help via the online user manual

Taverna 2.3.0 also includes the Command Line Tool that allows you to execute workflows outside of the Workbench. The Command Line Tool is available either as a stand-alone download or bundled with the Workbench.

Tutorials and examples

Tutorials for Taverna are available under the Taverna 2.x documentation.

Example workflows can be found under the Starter pack tab in the myExperiment perspective of the Workbench. They can also be downloaded from the myExperiment Web site at http://www.myexperiment.org/packs/192.

Known issues

Although Taverna 2.3.0 contains many improvements there are some known issues with it. These are detailed in known-issues.txt in the download bundle. An updated and more detailed list can be found in our issue tracker Jira at:
http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10220.

System requirements

Details of Taverna’s system requirements are available on the Taverna website.

Note that Taverna 2.3.0 now requires separate installation of GraphViz on Mac OS X.

Licence and source code

Taverna is distributed under the LGPL 2.1 licence.

The source code for Taverna can be retrieved from our Subversion repository. We also recommend you to sign up to the taverna-hackers mailing list if you are a developer.

Reporting problems

If you find any problems that are not listed in known-issues.txt, then please send them to the taverna-users or taverna-hackers mailing lists. Our support team is monitoring the mailing lists and will try to respond to questions as soon as possible.

If you prefer not to subscribe to our mailing lists, you can send your questions directly to support@mygrid.org.uk and a member of our support team will respond to your inquiries.

Alan Williams

http://www.myexperiment.org/announcements/1

myExperiment now has a new Announcements feature that allows myExperiment admins to keep you informed on progress and other relevant news.

You can subscribe to the Announcements RSS feed (and soon we will have email notifications).

Don't forget to give us feedback!

http://www.myexperiment.org/announcements/79

Dear colleagues,

The Software Sustainability Institute (www.software.ac.uk) have started a petition to gather support to recognise the fundamental importance of software to research.

This is in response to the ever increasing reliance on well engineered and sustainable software practices, codes and systems to help support world leading research.

Please visit the change.org page where you can also sign the petition:

https://www.change.org/p/everyone-in-the-research-community-we-must-accept-that-software-is-fundamental-to-research-or-we-will-lose-our-ability-to-make-groundbreaking-discoveries

Please consider supporting this endeavour further by re-tweeting this tweet https://twitter.com/SoftwareSaved/status/522325490754154497
or by mentioning the petition on your social media account(s) e.g.LinkedIn with a status such as “Software is fundamental to research - if you agree, please show your support: http://lnkd.in/b2fea5F".

You could also send an email to any groups that you are a member of or directly contact anyone you know who has the ear of the research community and ask them to sign up.

Thanks in advance,
Aleksandra Nenadic
(On behalf of the Software Sustainability Institute)

 

http://www.myexperiment.org/announcements/65

We're very pleased to announce that myExperiment can now be accessed easily from Galaxy, the open, web-based platform for data intensive biomedical research. Galaxy users can export Galaxy workflows to myExperiment to store and share them, and import Galaxy workflows from the myExperiment site. This means Galaxy users can:

  • Share Galaxy workflows in a controlled way (e.g. within a project), publish them with a stable myExperiment reference for your papers (which is linked-data compatible), and use myExperiment's discovery facilities to find more Galaxy workflows as content grows.
  • Use the social website features directly to document, tag and discuss workflows, add licensing, credit and attribution, and to bundle your Galaxy workflows with associated data, documents, presentations etc into myExperiment "packs" for ease of reuse and preservation.
  • Benefit from a central workflow website with a broad community, which means you can manage workflows for multiple Galaxy installations, attract visitors to your workflows and research, and network with others.
  • Benefit from the evolving tooling and preservation capability of myExperiment through the Wf4Ever project. In addition to our Linked Data URLs, we have arranged for myExperiment to be publishing DOIs later in 2012.

 See the Galaxy Help page on the myExperiment Wiki for a step-by-step guide, but basically:

  1. When using Galaxy you can import Galaxy workflows from myExperiment by choosing "Upload or import workflow" in Galaxy's workflow menu, then the new "Visit myExperiment" link at the bottom of the page. Within the myExperiment interface you can then view a Galaxy workflow and select "Import this workflow into Galaxy". Some Galaxy tutorial workflows are currently available to help you try this out.
  2. To export Galaxy workflows to myExperiment you'll first need a myExperiment username and password, then you'll be able to upload Galaxy workflows and also make them visible to others if you wish.  To create a username and password go to http://www.myexperiment.org/ and register. Having a username and password enables you to benefit from all the features of the site.
  3. To export a Galaxy workflow to myExperiment select "Download or Export" from Galaxy's workflow menu, enter your myExperiment username and password in the "Export to myExperiment" section and click the "Export" button. Exported workflows are set to be "Private" by default but you can make them visible publicly or to friends, groups etc by clicking on "Click here to view the workflow on myExperiment" and changing the Sharing settings.
  4. Visit http://www.myexperiment.org/ at any time to change settings, add further description, tags, license etc, and to create "packs". You can also create and administer groups, link up with friends and network with other workflow users.

Contact Us if you have any questions. And please spread the word - we also have a flyer and slide.

Thanks to Finn Bacall, Don Cruickshank and Danius Michaelides in the myExperiment team for all their work with Jeremy Goecks and colleagues in the Galaxy team on the integration. 

-- Dave

 myExperiment-Galaxy slide image

http://www.myexperiment.org/announcements/60

The Taverna team are pleased to announce that Taverna 2.4.0 Workbench and the Command Line Tool are now available for download

Here are a number of new features in the Workbench:
 

  •     Text Constant service allowing easier entry of large textual values
  •     Greater control over what is return from REST service
  •     Ability to use all the example values for a workflow run with one button
  •     Easier annotation of services and control over their list handling


Taverna 2.4.0 also includes the Command Line Tool that allows you to execute workflows outside of the Workbench. The Command Line Tool is available either as a stand-alone download or bundled with the Workbench.

Tutorials and examples

Tutorials for Taverna are available under the Taverna 2.x documentation

Example workflows can be found under the Starter pack tab in the myExperiment perspective of the Workbench. They can also be downloaded from the myExperiment Web site at http://www.myexperiment.org/packs/254.

Known issues

Although Taverna 2.4.0 contains many improvements there are some known issues with it. These are detailed in known-issues.txt in the download bundle. An updated and more detailed list can be found in our issue tracker Jira

System requirements

Details of Taverna's system requirements are available at http://www.taverna.org.uk/download/workbench/system-requirements/

Note that Taverna 2.4.0 now requires separate installation of GraphViz on Mac OS X.

Licence and source code

Taverna is distributed under the LGPL 2.1 licence

The source code for Taverna can be retrieved from our Subversion repository . We also recommend you to sign up to the taverna-hackers mailing list if you are a developer

Reporting problems

If you find any problems that are not listed in known-issues.txt, then please send them to the taverna-users or taverna-hackers mailing lists. Our support team is monitoring the mailing lists and will try to respond to questions as soon as possible.

If you prefer not to subscribe to our mailing lists, you can send your questions directly to support@mygrid.org.uk and a member of our support team will respond to your inquiries.

http://www.myexperiment.org/announcements/74

We will be updating the implementation of the myExperiment service this week to make it better able to support everyone in the future: some aspects of the service may be at risk during this period, but please bear with us.

http://www.myexperiment.org/announcements/3

In true 'perpetual beta' fashion, we continue our updates and additions to myExperiment:

  • In the user profile page, you can now see how many times a user has been credited for Workflows and Files in myExperiment. You can also see these credited items directly in the new "Creditations" tab, when viewing a user's profile.
  • Clearer statistics in the Workflow, File and User pages.
  • Improved layout for the Workflow and File pages.

Feedback always welcome!

http://www.myexperiment.org/announcements/58

We are in the process of fixing the BioCatalogue synchronization.  We expect to resume the service by the end of Friday.

Don.

http://www.myexperiment.org/announcements/53

We are happy to announce the release of the Topics explorer tab, developed in collaboration with the Database Research Group at the University of Pennsylvania. Topics explorer uses tags and tag co-occurrence to organise workflows into categories.

We encourage you to use Topics explorer, and to give feedback by clicking on the thumbs up / thumbs down icons inside each topic description. Your feedback will help evaluate the approach and ultimately improves your data exploration experience. Note that only logged in users can submit feedback. We also look forward to your written feedback, which should be addressed to Julia Stoyanovich (jstoy@cis.upenn.edu).

Topics explorer was developed by Julia Stoyanovich, Paramveer Dhillon, Brian Lyons and Susan B. Davidson at the University of Pennsylvania. This work was supported by the US National Science Foundation grant 0937060 to the Computing Research Association for the CIFellows Project and grant III-0803524.

Topics explorer is based on the latent Dirichlet allocation (LDA) topic model. For further info see "Exploring Repositories of Scientific Workflows" by Julia Stoyanovich, Ben Taskar, and Susan Davidson, WANDS 2010 pdf

This information is also available on the myExperiment wiki

http://www.myexperiment.org/announcements/9

The hardware upgrade is complete.  Please report any issues via the feedback page.

Thanks,
The myExperiment team.

http://www.myexperiment.org/announcements/50

Article 5(3) of the EU e-Privacy Directive requires that users have been informed about the use of cookies, the purpose that the cookie will be used for and the right to opt-out of the use of cookies. 

Like very many sites, myExperiment uses Google Analytics to monitor usage - we use this information to help deliver the service but for no other purposes.

Currently we do not have a mechanism for individuals to opt out of this monitoring.  Please contact us for further information and to express your views on this.  If appropriate we could turn off Google analytics.

Note we also set a session cookie on computers which is used to carry the “logged in” status from one page to the next, which is essential to the function of the site and not used for any other purpose.

-- Dave

 

http://www.myexperiment.org/announcements/19

Carole’s latest talk is now available on the myExperiment wiki – called "Curating Data? Curating Services!", it was delivered last week at the 21st International CODATA Conference, Ukraine, Kyiv and features myExperiment and Biocatalogue.

It’s available with all our myExperiment slideware on http://wiki.myexperiment.org/index.php/Presentations where you’ll also find the much talked-about presentation to the British Library on the future of research.

All Carole’s recent keynote talks are available in the pack http://www.myexperiment.org/packs/33

DDeR

http://www.myexperiment.org/announcements/16

We're pleased to announce that we've just reached the 1000 user mark!

The latest 50 users or so are down to our appearance last week at the 9th annual Bioinformatics Open Source Conference (BOSC)  and the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB) in Toronto.  This was a very useful community engagement where we met many users first hand and also got to see what other tools they're using.

Of course, the number of registered users is not the full measure of activity - many people access public content without accounts (navigating and searching the site, or direct from Google).  Another indicator on our dashboard is our site analysis, which recorded over 1400 unique IP visits in the month prior to these conferences.

Thanks all of you!

DDeR

http://www.myexperiment.org/announcements/67

Please be aware that The BioCatalogue will be undergoing maintenance on Tuesday August 14th 2012 between 08:30 and 15:00 BST. Searching and browsing services in myExperiment will work as normal but you'll be unable to click through to The BioCatalogue.

http://www.myexperiment.org/announcements/76

myExperiment may be down briefly sometime between Wednesday afternoon and Thursday morning whilst an update is performed.

Apologies for any inconvenience caused.

http://www.myexperiment.org/announcements/71


The next release of myExperiment is planned for the 22-04-2013. New features to be incorporated into the next release are:

  • A reorganisation of the side bar. Users have reported that the right hand side bar uses a lot of screen real estate for little value. User information will still be available via the user account page.
  • Additional support for news feeds. This is both in terms of the feeds available for new content, and an ability for groups to incorporate feed information into group pages. 

As part of our new release cycle process, we'd like to include a demo of new features and changes for any interested users. This will take place on 15-04-2013 at 14:00 (BST) and will be via a Skype call. If you are interested in participating, please contact Don Cruickshank <dgc@ecs.soton.ac.uk>.


Further overview information about release planning is available on the myExperiment wiki: <http://wiki.myexperiment.org/index.php/Developer:ReleaseSchedule>. For those interested in more details of current development status, please see the myExperiment JIRA: <http://dev.mygrid.org.uk/issues/browse/MYEXP>.

http://www.myexperiment.org/announcements/62

In announcement 50 on 25 May 2011, with Article 5(3) of the EU e-Privacy Directive in mind, we advised that myExperiment.org makes use of cookies for Google Analytics.  This is a followup announcement to say that, after advice and discussion, we have decided to cease our use of Google analytics. This will be effected prior to Friday 25 May 2012 in order to comply with the legislation.

-- Dave

http://www.myexperiment.org/announcements/48

Kostas Karasavvas has announced e-Galaxy, a new application that is a first step towards making Galaxy (http://galaxy.psu.edu/) and Taverna 2 more interoperable. It allows for the automatic generation of a Galaxy tool from a Taverna2 workflow. That tool can then be installed as usual in a Galaxy server. It will allow the Taverna workflow to become part of a Galaxy pipeline.

Users do not need to install e-Galaxy themselves. It is available as part of the myExperiment website. While browsing Taverna2 workflows the user will see an additional link "Download as Galaxy Tool" in the download section of the workflow. The next page provides instructions (and references) as well as an option to download the current workflow as a Galaxy tool.

For more information and contact details: https://trac.nbic.nl/elabfactory/wiki/eGalaxy

http://www.myexperiment.org/announcements/39

 We are pleased to announce that myExperiment has been updated to comply with Linked Data guidelines and is now accessible to Linked Data tools.

For further information see http://rdf.myexperiment.org/

There will be a presentation about the myExperiment view of Repositories and Linked Data at the Open Repositories Conference in Madrid next week - see http://wiki.myexperiment.org/index.php/News for more info about the event.

Please let us know how you get on using this new service.

 

 

http://www.myexperiment.org/announcements/8

The myExperiment server will be down at 9-11am GMT on 28th March for hardware upgrade.

http://www.myexperiment.org/announcements/57

The myExperiment wiki is hosted at University of Southampton where electrical works taking place in the University Data Centre will affect IT services between January 3rd and 6th 2012 - however we have been advised that the wiki should not be affected by these works.  The myexperiment.org servers are hosted separately at a commercial provider.

-- Dave

http://www.myexperiment.org/announcements/43

myExperiment was exhibited on the e-Research South booth at this year's UK e-Science All Hands meeting in Cardiff, UK, September 13-16, where members of the team and many of our "friends and family" were in attendence.

 
Carole Goble gave a plenary talk on Thursday 16th September on The Long Tail Scientist, and myExperiment was featured in two talks co-presented by David De Roure:
 
Shaping Ramps for Data-Intensive Research by Malcolm Atkinson, David De Roure, Jano van Hemert and Danius Michaelides on Tuesday 14th September
 
SALAMI: Structural Analysis of Large Amounts of Music Information by David De Roure, J. Stephen Downie and Ichiro Fujinaga on Wednesday 15th September
 
There was also a MethodBox talk by Shoaib Sufi on Wednesday 14th and demos on the Digital Social Research booth. Our Southampton chemistry colleagues also had several presentations - congratulations to Steve Wilson for winning the best student paper award!
 
See the News page for links to the slides etc.
 
-- Dave

 

http://www.myexperiment.org/announcements/34

 Welcome to Marcus Ramsden who has recently joined the myExperiment team.  Marcus has a background in EPrints - see  http://www.ecs.soton.ac.uk/people/mmr or he is also known as http://id.ecs.soton.ac.uk/person/11331  

 

http://www.myexperiment.org/announcements/52

Thousands of pounds are available for UK-based researchers who want to travel.

If you use software in your research and you have a good understanding of what’s happening in your field (and an idea about what will be happening soon) then the Software Sustainability Institute want to hear from you. The institute will pay researchers from any discipline up to £3000 a year to attend conferences and report on the latest developments in their field.

If you are interested visit www.software.ac.uk/agents to find out how to apply - closing date is 8th August 2011.

The Software Sustainability Institute (SSI) is funded by the research councils to help researchers use and develop software for their research. To better understand the fields that most need our help, the institute are setting up a network of Agents. Working as an Agent, you will receive travelling expenses in return for a short report about the conference you attended, the people you met and your views on the topics that look most promising in the future.

The benefits:

• Up to £3000 a year to attend the conferences and events that you want to attend
• Your advocacy will ensure that your field benefits from the best support for software development
• Add world-leading researchers to your professional network
• Free attendance at training events for new tools and technologies
• If you develop code, improve your knowledge of effective techniques for developing sustainable software
• A great addition to your CV

You don’t have to be a professor or a Principal Investigator. We are looking for UK-based researchers with a good knowledge of their field, who are keen to travel and to meet new people, and have experience of national and international collaborations. We are looking for applicants from all disciplines and especially from the fields that have been flagged as strategically important to UK research: the ageing population, environment and climate change, the digital economy, energy and food security.

After a three-month trial period, Agents will be recruited for an initial term of one year, which is renewable each year. We expect to recruit around ten Agents every year.

By becoming an SSI Agent, you will attend more of the conferences that you want to attend, meet influential researchers from across all disciplines and ensure that your field receives the best support for software development. If
you’re interested, or you’d like to nominate someone, please visit www.software.ac.uk/agents. If you would like more information, email Agents@software.ac.uk.

http://www.myexperiment.org/announcements/25

Our paper "Software Design for Empowering Scientists", which discusses the design principles of Taverna and myExperiment, has appeared in the January/February 2009 issue of IEEE Software ("Developing Scientific Software, Part 2"). The article is available to subscribers on http://www2.computer.org/portal/web/csdl/doi/10.1109/MS.2009.22 and the preprint is available on http://eprints.ecs.soton.ac.uk/15032/  The full reference is

De Roure, D. and Goble, C. Software Design for Empowering Scientists, IEEE Software, Volume 26, Issue 1, Jan-Feb 2009, pages 88-95. Digital Object Identifier 10.1109/MS.2009.22

Also, myExperiment, along with OpenWetWare and nanoHub, feature in the article "Research intelligence - Log on to a global laboratory" in the January 1st issue of THE (Times Higher Education) , written by Sarah Collinson and Zoe Corbyn.  You can find the article on http://www.timeshighereducation.co.uk/story.asp?sectioncode=26&storycode=404834

...and Happy New Year to all our users!

-- Dave

http://www.myexperiment.org/announcements/66

We suffered a hardware failure this morning and have had to move the entire service onto one machine. As a result myExperiment will be alittle slower than usual. We dont believe anything was lost as the database server was not effected.

We are also investigating an ongoing problem with uploading workflows.

[Update 2012/08/09: problem with uploading workflows has been fixed]

http://www.myexperiment.org/announcements/11

 

You can now see more information about the internals of a Taverna workflow.  On the workflow page, scroll down to the bottom of the version box and you will see a new section "Workflow Components".  Here you can see what inputs/processors/outputs and so on are in that specific workflow version together with any metadata that is stored for those.

http://www.myexperiment.org/announcements/20

The myExperiment team is very pleased to announce that myExperiment can now store any type of workflow, not just Taverna ones.  This means that you can upload any file as a workflow which can then be shared, discovered, downloaded, tagged, rated, commented on, added to packs and so on.
 
We already have some Trident workflows, and some experimental plans from chemistry. You can upload your own types of workflows by going to the upload workflow page (you may be asked to log in). If we can't automatically detect the type of workflow and infer data from it (like title and description) you can provide this by selecting the "Enter custom metadata" option in step 2.
 
Note that we currently provide extended support for Taverna 1 workflows only - we can automatically detect the type, parse title/description metadata, generate preview images, view the internals and enact these workflows all directly in myExperiment. In the coming months we aim to work with our user communties to provide extended support for other types of workflows.
 
If you would like to get involved in providing extended support for other types of workflows then please contact us. We are keen to work with you in getting myExperiment to support as many other workflows types as possible.
 
Thanks again for all your support!
 
The myExperiment Team
 

http://www.myexperiment.org/announcements/36

 A new feature has just gone live - when people click on the workflow type in a workflow display (e.g. clicking on "Taverna 2" ), a page is displayed describing the system(s) that use that workflow type.   We are building up the descriptions by working with the system providers. Also, there is a new Wiki page describing how to add new workflow systems to myExperiment. This is on http://wiki.myexperiment.org/index.php/Workflow_systems

-- Dave

http://www.myexperiment.org/announcements/59

The synchronization process is now working again.  If there are any issues then please report them to bugs@myexperiment.org.

Many thanks,

Don.

http://www.myexperiment.org/announcements/45

Hi - You'll see something new on the Workflows tab...  we now have filters down the left hand side to help you navigate myExperiment's growing content (this is also on the files and packs tabs). We welcome feedback on what you think of this new feature and also how you'd like it to be developed further.

-- Dave

http://www.myexperiment.org/announcements/54

We are pleased to announce the new Services Tab.  This new tab provides a searchable interface to information about Web Services, to assist myExperiment users with workflow design and execution.

The Services Tab is populated with information from the BioCatalogue, which provides a curated catalogue of over 2000 Life Science Web Services from around 150 service providers.  The status of the services is actively monitored.

We are releasing this tab now to invite feedback which will help us to prioritise the devlopment of extensions to this functionality, such as other sources of service information and further integration with workflow discovery.  

Please send feedback to bugs@myexperiment.org

http://www.myexperiment.org/announcements/40

The Taverna team are pleased to announce that Taverna 2.2.0 Workbench and the Command Line Tool are now available for download.

Taverna 2.2.0 includes improvements to the Workbench user interface and gives users greater control over the workflow engine. Here are a few of the new features in the Workbench:

  • Loading and sharing of service sets
  • Ability to load and edit workflows that contain services that are offline
  • Reporting on the state of the workflow
  • Tabular representation of a workflow run
  • Retrying and parallelization of service calls
  • Consistent representation of the intermediate and workflow results
  • Pause/resume/cancel of a running workflow

Taverna 2.2.0 also includes the Command Line Tool that allows you to execute workflows outside of the Workbench. The Command Line Tool is available either as a stand-alone download or bundled with the Workbench.

Tutorials and examples

Tutorials for Taverna are available under the Taverna 2.x documentation.

Example workflows can be found under the Starter pack tab in the myExperiment perspective of the Workbench. They can also be downloaded from the myExperiment Web site at http://www.myexperiment.org/packs/122.

Known issues

Although Taverna 2.2.0 contains many improvements there are some known issues with it. These are detailed in known-issues.txt in the download bundle. An updated and more detailed list can be found in our issue tracker Jira at:
http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10171.

Taverna and Java

Taverna requires the Java Runtime Environment (JRE) version 5 or 6 from Sun. No other versions of Java have been tested.

Java on Linux

Some Operating Systems, such as Ubuntu, come with the Gnu GCJ version of Java that cannot be used to run Taverna due to bugs in GCJ.

To download Sun Java 6 for Ubuntu, start a Terminal and type the following:

sudo apt-get install sun-java6-jre

and follow the instructions. You might also have to switch the default Java installation by running something like

sudo update-java-alternatives -s java-6-sun

Read more details about Taverna’s system requirements, in particular how to set the location of the Graphviz binary dot if needed.

Licence and source code

Taverna is distributed under the LGPL 2.1 licence.

The source code for Taverna can be retrieved from our Subversion repository. We also recommend you to sign up to the taverna-hackers mailing list if you are a developer.

Reporting problems

If you find any problems that are not listed in known-issues.txt, then please send them to the taverna-users or taverna-hackers mailing lists. Our support team is monitoring the mailing lists and will try to respond to questions as soon as possible.

If you prefer not to subscribe to our mailing lists, you can send your questions directly to support@mygrid.org.uk and a member of our support team will respond to your inquiries.

http://www.myexperiment.org/announcements/68

Yesterday (12th September 2012) we experienced a hardware failure on the myExperiment service resulting in the downtime for much of the working day. We've reinstated the service from backup on a different server in a different location. The backup was from early in the morning and we are currently working through some issues with restoring the backup. Please report any issues to bugs@myexperiment.org or via the feedback link.

http://www.myexperiment.org/announcements/77

Taverna 2.5.0 Workbench and Command Line Tool are now available to download from http://www.taverna.org.uk

http://www.myexperiment.org/announcements/22

Taverna 2 beta 1 the public beta for Taverna 2 is now available for download from http://www.mygrid.org.uk. Taverna 2 itself is scheduled for release in December 2008.

Taverna 2 workflows have new capabilities but you can still run existing Taverna 1 workflows in Taverna 2.

Issue Reporting

If you notice any problems with Taverna 2 beta 1 that are not included in the issues then please report them on the taverna-users mailing list (see http://www.mygrid.org.uk/tools/taverna/taverna-mailing-lists/)

Increased Functionality

Taverna 2 beta 1 (http://www.mygrid.org.uk/tools/taverna/taverna-2/taverna-2b1-documentation) has greatly improved functionality over Taverna 1. It includes:

   * An improved user interface
   * A configurable flexible activity (service) palette
   * A new graphical workflow editor including
         o Drag and drop of activities into the workflow
         o Graphical creation/deletion of input and output ports
         o Graphical creation/deletion of links
         o Activity selection by clicking
         o Expansion of ports on individual activities
         o Expansion of individual nested workflows
         o Zooming
         o Unlimited undo and redo of edits
   * A greatly improved enactor offering
         o Pipelining of data from iterative calls of an activity so
           that subsequent activities are started as soon as possible
         o Streaming of data from individual calls of activities so
           subsequent activities can start
         o Production of output results as soon as possible
         o Support for WSRF services
         o Error reporting to allow traceback and debugging of problems
         o Error resilience so that one faulty piece of data does not
           stop a workflow run
   * A contextual view to show and edit information about an activity
   * A graphical interface for user preferences - including the
     default set of activities
   * Improved monitoring of workflow enactment
         o Monitoring of iterations of activities
         o Progress viewing within nested workflows
   * Support for URLs in local workers
   * Customization of local workers as workflow-specific beanshells
   * Saving/closing of all workflows
   * Opening of multiple workflows in one go
   * Cyclic dependency detection within workflows
   * Expansion into nested workflows using the Workflow Explorer

Installation

For details on how to install and run Taverna 2 beta 1 please see the download documentation at http://www.mygrid.org.uk/tools/taverna/taverna-2/download-taverna-2b1

License

Taverna 2 beta 1 is licensed under the the Lesser General Public License (LGPL) Version 2.1.

Issues and Future Roadmap

There are some known issues (http://www.mygrid.org.uk/tools/taverna/taverna-2/taverna-2b1-documentation/taverna-2b1-issues/) with Taverna 2 beta 1. A roadmap (http://www.mygrid.org.uk/tools/taverna/taverna-2/taverna-2b1-documentation/taverna-2b1-roadmap/) describes our plans to solve them and, also, to increase Taverna 2's functionality.

 

http://www.myexperiment.org/announcements/63

We have been advised that many of the WSDL web services hosted by the DNA Databank of Japan (DDBJ) will be unavailable until further notice. Details can be found on the DDBJ website.

http://www.myexperiment.org/announcements/31

This is an update and “call for interest”

 
After experiments on our test servers, and consultation with some of the experts in the linked data and repositories communities, we have now sorted out what we’ll do to bring myExperiment into the world of Linked Data.
 
Note that what we’re referring to here is the www.myexperiment.org site and making sure that it behaves correctly with respect to HTTP accept headers and response codes in order to be Linked Data compliant. This is in addition to the SPARQL endpoint for myExperiment which David Newman has been supporting for some time rdf.myexperiment.org
 
The Linked Data world seems to be supplying the linked data and then seeing what people will do with it, rather than working from specific use cases.  Now we’ve sorted out supply we’ll soon be really interested in use cases!  If you are working in this area and would like to work with myExperiment and Linked Data we’d be really pleased to hear from you – mail the myexperiment-discuss list or contact me personally.
 
We’ll let you know when this service is going to go live – probably in the Easter period depending how testing goes.
 
Thanks
 
-- Dave
 
http://www.myexperiment.org/announcements/49

The myExperiment SPARQL endpoint has been upgraded to support RDFS reasoning - if you go to the SPARQL endpoint web page you'll find a checkbox to enable reasoning, and there's also a link to show how your results might differ when reasoning is enabled. This is a beta service and we welcome feedback.  Thanks to David Newman for his work with the 4store reasoner team to provide this support in myExperiment.

http://www.myexperiment.org/announcements/4

The Group sharing functionality on myExperiment has just been revamped!

When you upload a new Workflow or File, in the Sharing box you will get the option to explicitly share the item to Groups, as well as setting regular view/download/update permissions.

Once shared with a Group, the item will show in the Group's main page, within the "Shared Items" tab.

Also, when you then view the Workflow/File page, it will show you which Groups that item has been shared with.

We hope you find this explicit Group sharing useful.

Your feedback is always welcome!

http://www.myexperiment.org/announcements/35

 

BioCatalogue is a sister project of myExperiment - it provides a curated catalogue of Life Science Web Services. If you've not used it, check out http://www.biocatalogue.org/ and http://www.biocatalogue.org/wiki/

We're just commencing the first part of an integration between myExperiment and Biocatalogue - this will make it easy for myExperiment users to access service information, navigating to BioCatalogue for further details (documentation etc) .  In turn, BioCatalogue will benefit from information about the services used in the public workflows of myExperiment.

The first step has been to extend the myExperiment codebase to harvest information over BioCatalogue's RESTful API.  In due course we'll be trialling a new "services tab" on our myExperiment test servers.  Watch this space!

-- Dave

 

 

 

  

 

 

 

http://www.myexperiment.org/announcements/44

Several of our "e-Laboratories" projects are featured at this year's  Microsoft eScience Workshop in Berkeley, California, October 11-13. These include the following talks, the first two of which feature myExperiment:

  • A.J. Milstead, J.G. Frey, D. Michaelides and D. De Roure. MyExperimentalScience, extending the "workflow"
  • David De Roure, J. Stephen Downie and Ichiro Fujinaga. Data Intensive Research in Computational Musicology
  • Simon Jupp, James Eales, Simon Fischer, Jörg Uwe-Kietz, Rishi Ramgolam, Alan Williams, Robert Stevens and Carole Goble. e-LICO: Delivering Data Mining to the Life Science Community
  • Nathan Green, Matt Sperrin, Richard Williams, Philip Couch, Emma Carruthers, Eleanora Fichera, John Ainsworth, Martin O’Flaherty, Simon Capewell and Iain Buchan. A Framework for Large-Scale Modelling of Population Health
  • Katy Wolstencroft, Stuart Owen, Matthew Horridge, Olga Krebs, Wolfgang Mueller and Carole Goble. RightField: Rich Annotation of Experimental Biology Through Stealth Using Spreadsheets

Slides will be put on the presentations page of the wiki as they become available.

-- Dave

 

 

 

 

http://www.myexperiment.org/announcements/26

We've made some changes to the statistics that myExperiment captures about your content:

  • View and download statistics are now split into those made directly from myExperiment website and those made externally. For myExperiment accesses we also give an indication whether the access was from a member (ie someone logged in) or annoymous. These details are available on the 'see breakdown' link in the statistics sidebar.
  • We do not count viewings or downloads of your own items (based on whether you are logged into the site or not)
  • We do not count accesses made by search engine crawlers.

We've gone through our log files and where possible adjusted existing statistics to reflect the above changes. As a result, you'll likely see a drop in the counts for your content.

http://www.myexperiment.org/announcements/17

There have been changes to existing attributes and filters in Biomart release 50.

The complete list is below.

If your Biomart query uses any of the changes below please update your workflow accordingly.

 

Key

-  means GONE

+  means REPLACEMENT

 

Attributes

- 3utr_end

- 3utr_start

- 5utr_end

- 5utr_start

- cdna_length

-cds_length

- constitutive

- gene_chrom_end

+ end_position

- gene_chrom_start

+ start_position

- gene_stable_id

+ ensembl_gene_id

- ensembl_cdna_length

- ensembl_cds_length

- ensembl_peptide_length

- exon_cdna_end

- exon_cdna_start

- exon_cds_end

- exon_cds_start

- exon_chrom_strand

+ strand

- exon_coding_end

- exon_coding_start

- family

- family_description

- feat_chr_end

-  feat_chr_name

- feat_chr_start

- feature_set

-  feature_type

- feature_value

- str_chrom_name

- chromosome_name

- struct_biotype

- biotype

-  struct_description

+ description

- struct_external_gene_id

- struct_family

- struct_transcript_count

- transcript_count

- transcript_chrom_end

- transcript_chrom_start

- transcript_chrom_strand

- transcript_display_id

 + ensembl_transcript_id

+ ensembl_peptide_id

- type

- unified_uniprot

- unified_uniprot_accession

- uniprot_varsplic_id

- evidence_code

- go

+ go_biological_process_id

+ go_cellular_component_id

+ go_molecular_function_id

- go_description

+ go_bilogical_process_linkage_type

+ go_cellular_component_linkage_type

+ go_molecular_functions_linkage_type

- *species*_external_db

- *species*_external_id

- *species*_dn_ds

 

FILTERS

- with_3utr

- with_5utr

- biol_process

+ go_biol_process_filters

- cell_component

+ go_cell_location_filters (fix this name in 51) < evidence_code

+ go_mol_function_filters

- evidence_code_biol_process

+ go_biol_process_evidence_code

- evidence_code_cell_component

+ go_cell_location_evidence_code (fix this name in 51)

- constitutive

- exon_stable_id

+ ensembl_exon_id

 - external_db_name

- transcript_stable_id

- translation_stable_id

http://www.myexperiment.org/announcements/21

We're very pleased to announce a number of new features in response to feedback from myExperiment users:

  • Group announcements - group admins can now make public or private announcements within their group. This is a great way to keep people notified of events.
  • Pack downloads - you can now download a snapshot of a pack to your desktop. This will include any workflows and files in the pack as well as a manifest describing the whole pack.
  • Sent messages - you can now see all the messages you have sent via the internal messaging system in myExperiment. You can access this by going to your inbox.
  • Better tracking of version uploads and editors - you can now easily see who uploaded versions of workflows as well as who last edited metadata.
  • Various UI improvements- e.g: better "invite to your groups" box on other user's profile pages (to easily invite them to your groups).
  • Search enhancements - e.g. search for a service used in a workflow.

 We hope you find these new features useful. Please do give us feedback!
 
The myExperiment Team

http://www.myexperiment.org/announcements/12

We’ve been listening to you and are continually improving the user experience in myExperiment.

We’ve made numerous style and layout changes to enhance the look and feel. For example, in the search and tags results pages, you can now see items grouped in tabs based on their type (eg. user, group, workflow and so on).

Thanks!

The myExperiment Team

http://www.myexperiment.org/announcements/83

SSL is now enabled on myExperiment.org

To maintain compatibility with clients using our API, we are still running the HTTP version of the site in parallel, and only certain pages (the home page and log-in page) will automatically redirect to HTTPS.

As always, if you encounter any problems please report them to bugs@myexperiment.org

http://www.myexperiment.org/announcements/30

The Taverna team are happy to announce that Taverna 2.1 is now
available for download at
http://www.taverna.org.uk/download/taverna-2-1/

It includes many new features and bug fixes based on extensive
usability reviews and hours of testing.

2.1 truly is the next release up from the 1.7.x line.

2.1 features:

   * Copy/paste, shortcuts, undo/redo, drag and drop
   * An Animated workflow diagram
   * Remembers added/removed services
   * Secure Web services support
   * Up-to-date R support
   * Enhanced Provenance (allows viewing Intermediate values during
workflow runs)
   * myExperiment integration
   * Excel and csv spreadsheet support

Release notes -
http://www.taverna.org.uk/documentation/taverna-2-1/release-notes/

Migration guide -
http://www.taverna.org.uk/documentation/taverna-2-1/migrating-from-taverna-1/

These links and example workflows are available in the Starter pack

http://www.myexperiment.org/announcements/37

We're pleased to announce that an article on myExperiment has just been published online for the 2010 Web Server issue of Nucleic Acids Research.

The abstract is onhttp://nar.oxfordjournals.org/cgi/content/abstract/gkq429 with links to the full text,

The citation for this paper is

Goble, C.A., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., and De Roure, D.: myExperiment: a repository and social network for the sharing of bioinformatics workflows, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq429

This paper accompanies a BioCatalogue paper in the same issue - see http://nar.oxfordjournals.org/cgi/content/abstract/gkq394

See the papers page of the myExperiment wiki http://wiki.myexperiment.org/index.php/Papers for all myExperiment papers.

Thanks to the team for help with this paper, and especially to Peter Li who led the submission.

-- Dave

Abstract

myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to bugs@myexperiment.org.

http://www.myexperiment.org/announcements/46

We're pleased to announce the launch of the new wf4ever project, which will be providing methods and tools required to ensure the long-term preservation of scientific workflows in order to support the scientific discovery process and the development of new scientific assets.  Planned wf4ever developments include Research Objects, Provenance support and Recommender Systems - important new functionality for myExperiment users!

wf4ever builds in particular on myExperiment and the dlibra Digital Library Framework, and is driven by workflow-intensive use cases in the domains of Astronomy and Genomics. The project is led by Intelligent Software Components (iSOCO) in Madrid, with University of Manchester, Universidad Politécnica de Madrid, University of Oxford, Poznan Supercomputing and Networking Center, Instituto de Astrofísica de Andalucía, and Leiden University Medical Centre.

See the News page of the myExperiment Wiki for a photo of the wf4ever team!

-- Dave

http://www.myexperiment.org/announcements/55

Sean Bechhofer presented Scientific Social Objects at the 1st International Workshop on Social Object Networks held in conjunction with 3rd IEEE Conference on Social Computing (SocialCom 2011), 9th-11th October 2011 in Boston, MA, USA.

Scientific research is increasingly conducted digitally and online, and consequently we are seeing the emergence of new digital objects shared as part of the conduct and discourse of science. These Scientific Social Objects are more than lumps of domain-specific data: they may comprise multiple components which can also be shared separately and independently, and some contain descriptions of scientific processes from which new objects will be generated. Using the myExperiment social website as a case study we explore Scientific Social Objects and discuss their evolution.

Slides are available on the wiki and on SlideShare.

http://www.myexperiment.org/announcements/41

 This is a heads-up that we'll be announcing support for the Galaxy and Meandre systems in coming weeks...

 
Galaxy is aimed at experimental biologists and developers (http://galaxy.psu.edu/).  The Galaxy team kindly hosted our lead developer, Don Cruickshank, to commence the integration earlier this month and we already have the first stage of the support on myexperiment.org
 
Meandre is a semantic-web-driven data-intensive flow execution environment (http://seasr.org/meandre) which is used in digital humanities - coding is complete and support will go live at the end of the month. This integration has been supported by the NEMA project funded by the Andrew W Mellon Foundation, who also fund Meandre as part of the SEASR project. 
 
We're also looking at Kepler (https://kepler-project.org/).  Preliminary work has been conducted by our colleagues at Monash e-Research Centre and we're now working on the implementation plan for Kepler support on myExperiment.org
 
Watch this space!
 
-- Dave
 
http://www.myexperiment.org/announcements/28

A short video about Taverna and myExperiment has been released on YouTube on

                http://www.youtube.com/user/eiusproject

This was made by the e-Infrastructure Use Cases and Service Usage Models (eIUS) project funded by JISC. It focuses on a bioinformatics case study, with Paul Fisher and Andy Brass talking about their use of Taverna and myexperiment in their research on Trypanosomiasis.

See the myExperiment wiki videos page for more information

                http://wiki.myexperiment.org/index.php/Videos

-- Dave

http://www.myexperiment.org/announcements/14

We're pleased to announce that we've remodelled the myexperiment wiki to support the myExperiment developer community.

There is now a Developers' section where those of you developing over the API can share information about your projects.  It currently includes Google gadgets, the Taverna plugin, workflows for Facebook and the Java API.  This section also carries information about people running their own myExperiments, and myExperiment developer documentation.

The other information is now organised into Users, News and About. Previously you needed a wiki account to get at anything other than the main page, but now everything is publicly available, so you won't need to use your old accounts.

 

We’re really keen that everyone working over the API uses the wiki, if only to list who you are and what you’re doing – then all the developers will be able to help out as the community grows.

To get an account so that you can contribute content to the Developer pages please email Don Cruickshank on dgc@ecs.soton.ac.uk

http://www.myexperiment.org/announcements/6

myExperiment is discussed by Jim Hendler in his article Reinventing Academic Publishing, Part 3 in IEEE Intelligent Systems January/February 2008, page 2-3.

http://www.myexperiment.org/announcements/32
myExperiment now has additional support for uploading BioExtract Server workflows http://www.bioextract.org/help/brief_overview.html
 
Users can now do a "one click" upload of a BioExtract Server workflow and we will automatically detect it and extract the metadata and a preview image. There will also be a custom run option to allow users to directly execute these workflows on the BioExtract Server.
http://www.myexperiment.org/announcements/23

We've had a great week at the eScience events in Indianapolis, with three myExperiment presentations and one on Biocatalogue.  The slides for the main myExperiment talk are now up on Slideshare on http://www.slideshare.net/dder/myexperiment-defining-the-social-virtual-research-environment-presentation/

But the main news is that Carole Goble received the inaugural Microsoft Research Jim Gray eScience Award, in recognition of her achievements in the application of computing technology to scientific insight and innovation.  See the pics on http://wiki.myexperiment.org/index.php/News !

-- Dave

 

http://www.myexperiment.org/announcements/80

We have updated the main layout of myExperiment to tidy up and reduce the amount of space taken up by the main navigation bar and menus.

 

If you have any comments on the new look, or notice any issues, please email us at bugs@myexperiment.org

http://www.myexperiment.org/announcements/18

A paper on the designof myExperiment has just been published online by the Future Generation Computer Systems journal. 

It's called The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows and the URL is http://dx.doi.org/10.1016/j.future.2008.06.010

For those without access to the journal content, a preprint is available on http://eprints.ecs.soton.ac.uk/15709/

If you're using myExperiment in your research we would be very pleased if you could mention myExperiment and cite our papers if appropriate.  We'd also like to hear from you and keep a list on the Wiki of projects and papers that have used myExperiment.

This and other publications are listed on the wiki on http://wiki.myexperiment.org/index.php/Papers

DDeR

http://www.myexperiment.org/announcements/27

We're pleased to announce that JISC has awarded myExperiment a second phase of funding, in which myExperiment will be integrated with EPrints in Southampton and the new Fedora-based Institutional Repository in Manchester. Our many other planned enhancements include extending the packs mechanism to support search and versioning of pack contents, supporting a broader range of contribution types, enabling user-provided controlled vocabularies for smarter discovery, implementing analytics for effective recommendations, and developing richer expression of relationships between items to support provenance, discourse and rights flow. We're very excited to be starting this new phase and we look forward to working with you all to develop myExperiment's new capabilities.

http://www.myexperiment.org/announcements/69

 A Fellowship at the Software Sustainability Institute provides researchers from all disciplines with £3000 to spend on travel and more. The deadline for applications is 20 September 2012 at 16.00 UTC. If you want to benefit from a Fellowship, please apply now.

 

The funding is flexible, and can be used to pay for travel to conferences, setting up and running workshops, and starting new collaborations. In return for funding, Fellows keep the Software Sustainability Institute up to date with the latest news from their discipline. More information about the Fellowship is available on the Fellowship page.

The Software Sustainability Institute is a national facility for cultivating world-class research through software. It comprises experts from the universities of Edinburgh, Manchester, Oxford and Southampton.

http://www.myexperiment.org/announcements/5

myExperiment.org has been mentioned in Nature magazine, Volume 451 Number 7181 pp1024-1025 (February 2008).

See here or here.

http://www.myexperiment.org/announcements/78

The myExperiment team are planning a refresh of the myExperiment site and service. In order to help us with this, we'd like to know the features and services that are most important for our users. Please take a few minutes to fill in the following short survey: 

https://docs.google.com/forms/d/1kKBe3zaS5xc21f8n34hCUIwdgBNhJdANas0MBzs7vUA/viewform

Thanks in advance for your input!

Sean


 

http://www.myexperiment.org/announcements/13

Have you ever wanted to group together your research work, create collections of workflows or build a list of resources for a specific purpose?

We are pleased to announce a new and exciting feature on myExperiment... Packs. These allow you to collect together various different things (which may be inside myExperiment or elsewhere) to form collections that can then be shared, tagged and commented on.

Packs use the existing sharing mechanisms and social features that you already enjoy in myExperiment. Just go to the new Packs tab to find out more.

We've designed packs in response to your input. Don't forget to give us feedback :-)

Thanks,
The myExperiment Team

http://www.myexperiment.org/announcements/64

myExperiment suffered downtime from 3am this morning when we had a problem with the main web server. Service was restored at around 11am UK time. We don't believe there's been any loss of data.

http://www.myexperiment.org/announcements/61

NB This announcement has been superseded by the July 2012 launch of myExperiment in Galaxy (DDeR 2012-07-14).

Are you a user of the Galaxy open, web-based platform for data intensive biomedical research?

We've been working with the Galaxy team to develop support for myExperiment in the Galaxy interface. We're pleased to announce that this is now approaching release on the Galaxy public server during May 2012 (and will be available in the Galaxy release later in June-July).

We're looking for testers and people to help create Galaxy content on myExperiment - watch out for announcements, and please contact us if you're interested in being one of our testers. The contact for our Galaxy integration work is Finn Bacall at the University of Manchester, UK.

There is further integration work in the Netherlands Bioinformatics Centre (NBIC) between Galaxy and the Taverna workflow system, using myExperiment - this is called eGalaxy and it enacts Taverna workflows through Galaxy.

http://www.myexperiment.org/announcements/70The myExperiment service has moved to new hardware. If there are any issues about the move then please don't hesitate to contact me at dgc@ecs.soton.ac.uk Thanks, Don.
http://www.myexperiment.org/announcements/82

myExperiment will be down briefly on Monday 25th July while maintenance work is carried out at our data-centre.

This work should take no more than 15 minutes.

 

http://www.myexperiment.org/announcements/73

Content was unavailable for a short period in the morning of 8 August when a problem arose in the pipeline generating Linked Data from the live myExperiment content. We are grateful to the server support team for prompt resolution of the problem and apologise for any inconvenience caused to those accessing website pages and RDF output in the earlier part of the morning.

-- Dave

 

http://www.myexperiment.org/announcements/2

You can now write reviews for Workflows on myExperiment.

This links in with the existing ratings feature - when writing (or updating) a review, you have the option of setting a rating as well (or updating an existing rating).

Note that you can only ever have one rating and one review for each Workflow, and neither is compulsory (so you can have a review without a rating).

Don't forget to give us feedback!

 

http://www.myexperiment.org/announcements/38

We've updated the myExperiment wiki page that lists papers that mention or feature myExperiment (but were not written by the core myExperiment team). It's on http://wiki.myexperiment.org/index.php/Mentions

If you've written papers that aren't on this list - or know of other papers - please let us know by emailing dder@ecs.soton.ac.uk

We're planning to promote these papers more strongly, and this will help others find out about your papers.

Thanks for your contributions!

http://www.myexperiment.org/announcements/29

A new project to link the myExperiment system with two existing electronic laboratory notebook (ELN) systems developed in Southampton, currently in use in several departments, has been announced today (June 11, 2009). By integrating these ELNs with myExperiment we will pave the way for longer term takeup in the experimental laboratory science communities, including Chemistry, Physics, Biology and Engineering.

The project will commence in July 2009 and will be led by Prof Jeremy Frey, who is based in the School of Chemistry at Southampton and is one of the partners in the myGrid Platform.

For more info please see http://wiki.myexperiment.org/index.php/MyExperimentalScience

-- Dave

http://www.myexperiment.org/announcements/15

For all Taverna users out there, we have developed a (beta) plugin that allows you to browse myExperiment, search for workflows, view tag clouds, view workflows and open them, all directly within the Taverna Workflow Workbench.

With this plugin (and the WHIP Launcher installed), you also have the option to "Launch in Taverna" all the workflows in myExperiment (that you have download access to). This creates a 'one click' launch experience for users of Taverna looking to try out and reuse workflows from myExperiment.

For full details and installation instructions, please go here.

As always, we value your feedback.

The myExperiment Team

http://www.myexperiment.org/announcements/24

Hello everyone,

Taverna 2.0 the first release of Taverna 2 - the new improved version
of Taverna - is available for download.

Taverna 2 workflows have new capabilities but you can still run existing Taverna 1 workflows in Taverna 2.

Issue Reporting
===============

If you notice any problems with Taverna 2.0 that are not included
in the issues then please report them on the taverna-users mailing
list.

Increased Functionality
=======================

Taverna 2.0 has greatly improved functionality over Taverna 1. It includes:

    * An improved user interface
    * A configurable flexible activity (service) palette
    * A new graphical workflow editor including
          o Drag and drop of activities into the workflow
          o Graphical creation/deletion of input and output ports
          o Graphical creation/deletion of links
          o Activity selection by clicking
          o Expansion of ports on individual activities
          o Expansion of individual nested workflows
          o Zooming
          o Unlimited undo and redo of edits
    * A greatly improved enactor offering
          o Pipelining of data from iterative calls of an activity so
            that subsequent activities are started as soon as possible
          o Streaming of data from individual calls of activities so
            subsequent activities can start
          o Production of output results as soon as possible
          o Support for WSRF services
          o Error reporting to allow traceback and debugging of problems
          o Error resilience so that one faulty piece of data does not
            stop a workflow run
    * A contextual view to show and edit information about an activity
    * A graphical interface for user preferences
    * Improved monitoring of workflow enactment
          o Monitoring of iterations of activities
          o Progress viewing within nested workflows
    * Support for URLs in local workers
    * Customization of local workers as workflow-specific beanshells
    * Saving/closing of all workflows
    * Opening of multiple workflows in one go
    * Cyclic dependency detection within workflows
    * Expansion into nested workflows using the Workflow Explorer
    * Online help
    * Explicit support for while loops and conditional processing

Installation
============

For details on how to install and run Taverna 2.0 please see the
download documentation

License
=======

Taverna 2.0 is licensed under the the Lesser General Public License
(LGPL) Version 2.1.

Issues and Future Roadmap
=========================

There are some known issues with Taverna 2.0. A roadmap
describes our plans to solve them and, also, to increase Taverna 2's functionality.

Alan
 

http://www.myexperiment.org/announcements/10

 

You can now access myExperiment through the REST API, so you can bring myExperiment functionalities through in your favourite apps/interfaces/mashups.

See http://www.myexperiment.org/mashup  for documentation (and a google gadget)  - it's also linked from our page footer.

We’re very keen to hear from people developing over the API to see how you get on and give you any help you need.

http://www.myexperiment.org/announcements/33

The myGrid team are proud to announce the release of Taverna Workbench 2.1.2.

 

The release of Taverna Workbench 2.1.2 includes fixes and improvements to the user interface, workflow engine and extra support for secured WSDL services and access to secure resources on the web.

The release notes contain a detailed description of the changes.

As always, for any questions and feedback, use the Taverna mailing lists or our email support – see our contact details. Also check the documentation and FAQ.

The myGrid team are planning further work towards Taverna 2.2 this spring, as detailed on the road map.

http://www.myexperiment.org/announcements/72


A new version of the myExperiment code base was released on 08/05/13. New features include:

  • A removal of the right hand side bar. User comments had suggested that too much screen real estate was being taken by the side bar. Information that was shown in the side bar has been moved to a drop down in the upper right hand corner. 
  • Additional support for atom news feeds. This is both in terms of the feeds published by myExperiment that advertise new content, and an ability for groups to incorporate feed information into group pages. 

Further overview information about release planning is available on the myExperiment wiki: <http://wiki.myexperiment.org/index.php/Developer:ReleaseSchedule>. For those interested in more details of current development status, please see the myExperiment JIRA: <http://dev.mygrid.org.uk/issues/browse/MYEXP>.
 

http://www.myexperiment.org/announcements/81

Hello everybody,

The Apache Software Foundation has been accepted as a mentoring organization for the 2015 Google Summer of Code. The full list of Apache GSOC projects includes four Taverna-related projects : a production-suitable command line tool, a databundle viewer, OGC WPS support and an Android App for Taverna.


A production-suitable command line tool


This proposed GSOC project is to formalize the command line interface for Taverna Language so that it can achieve some of the below:

  • In collaboration with dev@taverna and the mentor, define command line options for workflow conversions and inspection
  • Find and use an appropriate command line parser library
  • --help
  • Basic error handling (e.g. file not found)
  • Batch processing - e.g. recursive conversions
  • Arguments for choosing input and output formats
  • Unit and Integration Tests for the above (ideally through Maven)

The project can be extended by exposing other parts of the API that don't currently have a command line equivalent, e.g.

  • Workflow validation
  • Workflow statistics (number of processors, links, etc)


A databundle viewer


===================

This GSOC project proposes to create a web-based presentation (but not edit) of a workflow run, e.g. the following user story:

  1. User uploads the databundle file for a workflow run (or provides the URI to one existing elsewhere) into the presentation system
  2. The presentation system shows basic information about the workflow run
  3. User navigates to inputs/outputs
  4. The presentation system presents a list of inputs or outputs - embedding images etc. where possible, download links for large files, inline for small text, etc
  5. User downloads a selected data file


Metadata provided can be presented in many different ways, for instance:

  • Which workflow was executed?
  • Which steps were executed?
  • What step produced this value?
  • What values were produced by this step?
  • What steps used this value?


OGC WPS support


This proposed GSOC project is to, in collaboration with dev@taverna and the mentor

  • Improve/complete the existing Taverna 2.5 WPS prototype support
    • Discovery of WPS services from a user-specified WPS server
    • Configuration of WPS services
    • Execution of WPS services
  • Test WPS support using pre-selected WPS servers and services
  • Migrate the WPS support to the Taverna 3 codebase
  • Document the Taverna 3 WPS service support


An Android App for Taverna


The project would be to:

Extend and complete Taverna Mobile: an Android app to run Taverna workflows available on myExperiment using Taverna Server.

  1. fix the ssl/https parts and use the latest version of taverna server
  2. update the code to remove some legacy dependencies and use the latest APIs
  3. improve the UI and responsiveness

Joining in


If you, or any students you know, are interested in these or any other Taverna projects, then please discuss ideas on the Taverna developers' list dev@taverna.incubator.apache.org and then submit proposals to Google by 27th March. More information is in the GSOC 2015 FAQ

Alan