Group: Taverna 2 beta tester programme

Members of this groups are the participants of the Taverna 2 beta tester programme.

If you want to be a beta tester and are not already a member of the group, use the request membership of the group link above.

 

Created at: Tuesday 05 August 2008 @ 10:51:32 (BST)

Unique name: t2beta


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Workflow

Taverna 1

Original Uploader

Workflow Retrieve Single Molecule from ZINC - structure and figure (v1)

Created: 24/08/08 @ 22:52:26 | Last updated: 25/08/08 @ 21:57:16

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieve_single_molecule_from_zinc_-_structure_and_figure_19577_1
The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds. With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data inst...

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Workflow

Taverna 1

Original Uploader

Workflow echo (v1)

Created: 18/09/08 @ 14:44:53 | Last updated: 18/09/08 @ 14:44:54

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 License

Echo_27636_1
The workflow tests the standard-compliance of web service descriptions of ARC-1, a development of the EU project "KnowARC" to modernise the grid infrastructure ARC of the NorduGrid. Learn more about it on http://www.knowarc.eu and http://www.nordugrid.org. If you have computers in spare - join us - and help you very own and many other sciences. And you make many interesting contacts just en passent. No authorisation is required for this very experimental service.

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Workflow

Taverna 1

Original Uploader

Workflow dbfetch tutorial (v1)

Created: 22/09/08 @ 01:05:37

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 License

Dbfetch_tutorial_7935_1
This workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is alw...

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Comments Comments (17)

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  • Wednesday 20 August 2008 @ 16:41:57 (BST)

    one quick comment (hope this is the right place):

    While dragging the activity into diagram/workflow area mouse icon turns like a 'not allowed' black circle with a line. This seems counterintuitive. Probably an icon with some kind of arrow or affirmation depending upon the target area would be better.

  • Wednesday 20 August 2008 @ 16:46:34 (BST)

    another:

    one of the tab in the local workers configuration shows dependencies in the form of "group--artifact--version". isnt it a technical thing only concerned for by the developers?

    Also the script for the internal worker is now exposed, which is really good i think but probably a "restore default" button should be provided so that if some user messes it up while playing it could be quickly restored back.

  • Thursday 21 August 2008 @ 10:22:04 (BST)

    We've created a short introduction to the Taverna 2 workbench red beta that highlights the changes since Taverna 1, new features, and any known issues in this beta with suggested workarounds.

    We're currently registering in Jira the known issues with the red beta, we'll also Jiraize any issues reported through comments here.

  • Monday 25 August 2008 @ 13:47:41 (BST)

    my first t2 comments (25/8/2008)

    * Preferences:
      ** Can I set which disk is used for 'on-disk storage'?
      ** When I add a WSDL activity as http://ws.adaptivedisclosure.org/axis/services/SearcherWS?wsdl, I do not see it in the activities palette. It does work when I add it via Activities->New
      ** In some cases you need to click 'Apply', in other cases you don't.

    * Activities palette:
      ** Would it be possible to add mouse-over information in the activities pane? (In 'type' mode you can't distinguish between services with the same name.)
      ** Is it possible to use 'url' as indicator for 'provider' and use that for organising services. It seems not many service providers provide the information that could organise services; 'url' is then a good indicator for 'provider'.
      ** Would it be good to choose default settings that most closely resemble the list as we know it from Taverna 1?
      ** I would like to see extra information (metadata) in the information pane (bottom left) when I click on something in the activities palette.

    * Designing and running my workflow
      ** Load from url not yet supported in red beta?
      ** After 'Run workflow' it takes quite a while without any apparent activity before an error message is shown.
      ** My workflow 'http://www.myexperiment.org/workflows/154' does not run. Can general suggestions for workflow designers be derived from my errors, i.e. what one needs to change in workflows created in Taverna 1?
      ** I would like to see my descriptions in the information pane (bottom left) when I click an item in the design pane (in addition to wsdl info).
      ** I would like to see an automatic 'good citizens' mark somewhere (e.g. for amount of descriptions).
      ** Has the 'create iteration strategy' been made obsolete by something?

    * also noticed the 'block' icon when dragging a service to the design pane as others did.
     

  • Tuesday 26 August 2008 @ 10:59:33 (BST)

    I've added some packs for Workflows that don't run properly, Workflows that won't load and Workflows that run as expected.

    You are encouraged to add your workflows to these packs to indicate what works and doesn't in the Taverna 2 red beta. The myGrid team will investigate any failing workflows and provide comments on what we will do to fix the issue.

    If your workflow does not open at all in Taverna 2, it is likely a translation problem. Please post your workflow to the Workflows that won't load pack.

    If your workflow opens, and the diagram looks roughly like what you expect, but when running it doesn't give you the results you expected from Taverna 1, please post your workflow to Workflows that don't run properly. If there was a workflow that you tried to build from scratch in Taverna 2, but some feature from Taverna 1 was not available or didn't perform as expected, then also add it to this pack.

    If your workflow runs fine in Taverna 2, then please do add it to the Workflows that run as expected pack!

  • Wednesday 03 September 2008 @ 12:40:31 (BST)

    to add to existing comments:

    1-impossible to delete an expanded workflow, you have to contract it first

    2-when adding new services to the activity palette (Activities->New activity->WSDL/soaplab...) no warning is displayed if you enter a wrong address. You can type anything you want in the form still no warnings.

    3-The blue line around selected service in the workflow diagram is sometime confusing. That is, if you click on a service diagram it  will have the blue line all around but if you right-click the next service the blue line still stays with the first service. so you're not sure if you're dealing with the service you've right-click or the service with the blue line around.

  • Wednesday 03 September 2008 @ 14:09:00 (BST)

    to clarify my previous comment 1:

    * 1- impossible to delete an expanded nested workflow, you have to contract it first

  • Tuesday 09 September 2008 @ 16:43:28 (BST)

    Splash screen is on "always on top" mode. Might not be very user-friendly for some..

  • Monday 15 September 2008 @ 10:26:04 (BST)

    The Taverna Team are pleased to announce the latest beta release of Taverna 2 (codenamed amber beta) to the Taverna 2 beta tester programme.

    If you are not part of the beta tester programme but would like to try out an early beta release of Taverna 2 then head over to the Taverna 2 beta tester programme and request membership.

  • Monday 15 September 2008 @ 11:00:25 (BST)

    If you are running OSX 10.4 and could not run the Amber beta, try to download again as I just fixed a minor issue with it's application bundle.

  • Thursday 18 September 2008 @ 10:56:54 (BST)

    Can I make a stupid question. I recently registered myself as a beta tester. How can I get access to a copy of taverna 2 beta? Cheers.

     

  • Tuesday 23 September 2008 @ 16:02:46 (BST)

    The Taverna Team are pleased to announce the latest beta release of Taverna 2 (codenamed yellow beta 2008-09-23) to the Taverna 2 beta tester programme. To download the beta, visit the shared pack yellow beta and from there follow the links for either Windows/Linux or Mac OS X.

    Please add any comments about the beta inside the pack (not here).

    If you are not part of the beta tester programme but would like to try out an early beta release of Taverna 2 then head over to the Taverna 2 beta tester programme and request membership.

  • Friday 07 November 2008 @ 12:29:15 (GMT)

    Hi

    When do you plan to release the source code of t2? I am especially interested in using libraries to create workflows and exute them without gui (and compare it to t1)

  • Tuesday 11 November 2008 @ 10:27:26 (GMT)

    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.

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

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

    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.
    <font> </font>

  • Tuesday 11 November 2008 @ 10:33:09 (GMT)

    Jerzyo: The source code will be available in a couple of weeks time because we are restructuring the source code so it will be easier to build and maintain. We're also moving it to SVN.

    Sign up for the taverna-hackers list to be posted about using the source code. Feel free to post a message there about your plans to use the API!

  • Tuesday 11 November 2008 @ 10:35:56 (GMT)

    Thanks to everyone for their help in testing our early beta versions! The successor of yellow beta, Taverna 2 beta 1, is now publicly downloadable, and futher releases will be published on the myGrid website.

    For feedback on the Taverna workbench, feel free to sign up to the taverna-users mailing list and email us your comments!

  • Wednesday 12 November 2008 @ 23:02:55 (GMT)

    Summary of my first experience with T2.0b1:

    I couldn't run my workflows, but more importantly, the error messages did not really help me solve the problems. Apparently, I have a problem with I/O or dependencies that were not checked in T1 and that I am unfamiliar with. It would be nice if for errors due to known differences the error message would include hints or pointers to help.

    I have sent a more detailed report, including console dumps, to the users list.


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