Hi Changjiang, We are currently working on a command line tool for Taverna 2 that will enable you to execute workflows without starting the GUI. It will be very similar to the existing Taverna 1 command line tool (http://www.taverna.org.uk/download/associated-tools/command-line-tool/). According to our Roadmap (http://www.taverna.org.uk/introduction/road-map/), the tool will be available by the end of May 2010. This tool could be used as a simple Taverna Server in the first instance - note that this will create one JVM instance per wf invocation so will not scale well.
A "proper" Taverna 2 Server (beta) is scheduled for July 2010 according to the Roadmap. It will enable you to submit workflows for execution, monitor their progress and collect results as they become available. It could be used from your portal for example. You can see the proposed architecture at : http://www.mygrid.org.uk/dev/wiki/display/developer/Taverna+Server There is also the Taverna 1 Server (http://www.taverna.org.uk/download/taverna-server/) that can be used if your are in a hurry - you'd have to re-write your workflows using Taverna 1. Taverna 1 Workbench even has a plugin to let you remotely execute workflows from the Workbench itself. Note that we are also working on wrapping workflows in portals - please check our wiki pages at: http://www.mygrid.org.uk/dev/wiki/display/portals/Home Note that this is still work in progress and is using a prototype (unsupported) Taverna 2 Server that will be replaced by the proper Taverna 2 Server in July 2010. There are also other projects that are doing similar things (wrapping worklfows in portals) that you can have a look at: - NeISS (http://www.taverna.org.uk/introduction/related-projects/neiss/) - IMPACT (http://www.impact-project.eu/) Regards, Alex Katy Wolstencroft wrote: > -------- Original Message -------- > Subject: RE: [Taverna-users] Help: The published WorkFlow not working > (can not even be loaded). > Date: Fri, 7 May 2010 10:28:53 -0400 > From: CJ Mei <[email protected]> > To: <[email protected]> > References: > <[email protected]>,<[email protected]> > <[email protected]>,<[email protected]> > <[email protected]>,<[email protected]> > > > > > Hi, Katy, > > Thank you for all your help. I have another question. We are building a > facility for average bio-scientists to do bio-informatics study. They > may not have any idea even how to use Taverna. Is there a way to "wrap" > Taverna so that a WorkFlow can be started remotely? Say, I build a web > page for researchers to access. The user need only to input a search > term and an email address and submit. The page will then start on > Taverna, remotely, the corresponding WorkFlow and to obtain a set of > sequences, and then to align them, and then to "BEAST" them and then to > return the user (email) the result(s): tree file or some thing > associated. Is there a interface or API to do that? > > Thank you. > > *梅長江* > *Mei, Changjiang > * > >> Date: Fri, 16 Apr 2010 10:12:03 +0100 >> From: [email protected] >> To: [email protected] >> Subject: Re: [Taverna-users] Help: The published WorkFlow not working >> > (can not even be loaded). > >> Hi, >> >> I'm pleased that the sequence length problem is solved. >> Unfortunately, we don't host services, Taverna simply provides the >> technology that allows you to use distributed services together. There >> are over 3500 web services available in the public domain in biology and >> this number is continually growing. Taverna can connect to these web >> services and many other types of service, such as BioMart processors, >> R-Scripts and local java services. >> If you contact the BEAST and PAUP service providers, you may find that >> they are already planning to provide a web service interface, in which >> case, we can just use it in Taverna. If they are not, the other >> alternative if for you to host it locally. We can give you advice about >> doing that if needed. >> >> Sorry it is not a more positive answer, >> >> Best wishes, >> >> Katy >> >> CJ Mei wrote: >> >>> Oh, the long sequence problem is resolved so far. Thank you, Katy, for >>> your help. The version you sent me yesterday works fine with our >>> sequences of 2000+ bps. I can now get sequences aligned, and obtain >>> guide tree, phylogenic tree and NJ tree. The next task for me would be >>> further analysis with packages like BEAST, or PAUP*. If you guy can >>> incorporate those tools into Taverna, it would be greatly increase >>> Taverna's power. PAUP* is a commercial software (not expensive, >>> though). While BEAST is a free ware so that the incorporation should >>> not be too complicated. >>> >>> One more question I have to you that although I've got NJ tree, what >>> software package do I use to display it, or further analyze it? What's >>> "NJ" stand for? >>> >>> Thank you for your constant help. >>> >>> **梅長江** >>> *Mei, Changjiang >>> * >>> >>> >>> >>> >>> >>> >>>> Date: Thu, 15 Apr 2010 11:17:30 +0100 >>>> From: [email protected] >>>> To: [email protected] >>>> Subject: Re: [Taverna-users] Help: The published WorkFlow not >>>> >>> working (can not even be loaded). >>> >>>> Hi CJ, >>>> >>>> I don't know of an interface to BEAST unfortunately, but muscle (also >>>> from the EBI and with a web service interface >>>> http://www.ebi.ac.uk/Tools/muscle/) will allow you to input longer >>>> sequences as far as I know >>>> >>>> Best wishes, >>>> >>>> Katy >>>> >>>> CJ Mei wrote: >>>> >>>>> Dear Katy, >>>>> >>>>> Thank you very much for your kind help. Maybe I'm asking too >>>>> > much. Do > >>>>> you have a interface to call BEAST, or a sample WorkFlow I may copy? >>>>> >>>>> Thank you in advance. >>>>> >>>>> *梅長江* >>>>> *Mei, Changjiang >>>>> * >>>>> >>>>>> Date: Wed, 14 Apr 2010 16:56:38 +0100 >>>>>> From: [email protected] >>>>>> To: [email protected]; [email protected] >>>>>> Subject: Re: [Taverna-users] Help: The published WorkFlow not >>>>>> >>>>> working (can not even be loaded). >>>>> >>>>>> Dear C.-J >>>>>> >>>>>> First of all, apologies for the delay in getting back to you. >>>>>> The workflow you are interested in is an asynchronous Taverna 1 >>>>>> workflow. In Taverna 2, we have improved the way we deal with >>>>>> > these > >>>>>> services by adding a looping feature. This makes these workflows >>>>>> >>> much >>> >>>>>> easier to build in Taverna 2, but unfortunately means that the >>>>>> >>>>> Taverna 1 >>>>> >>>>>> implementations do not work in Taverna 2. It should still open in >>>>>> Taverna 2, so we will look into why it couldn't even be viewed. >>>>>> >>>>>> I have attached an updated workflow here that should now work >>>>>> >>> for you. >>> >>>>>> Best wishes, >>>>>> >>>>>> Katy >>>>>> >>>>>> [email protected] wrote: >>>>>> >>>>>>> Hi, there, >>>>>>> >>>>>>> I'm a new bee in Taverna. I'm trying to get familiar with >>>>>>> > it. I'm > >>>>> trying to >>>>> >>>>>>> align a set of sequences and generate a tree out of the alligned >>>>>>> >>>>> set. There is >>>>> >>>>>>> a WorkFlow by Hamish McWilliam at >>>>>>> >>>>>>> http://www.myexperiment.org/workflows/207 >>>>>>> >>>>>>> I downloaded but I can't even load it into Taverna. I did try >>>>>>> >>> the two >>> >>>>>>> sub-WorkFlows by him and they are both successful. I can align a >>>>>>> >>>>> set of >>>>> >>>>>>> sequences (not longer than 1800 bps, though), and I can then >>>>>>> >>>>> generate a nj tree >>>>> >>>>>>> out of the alligned set. But I can't combine the two steps >>>>>>> > (that's > >>>>> a workflow >>>>> >>>>>>> for, right?). I can't reach the author. I hope some one here may >>>>>>> >>>>> be able to >>>>> >>>>>>> help. By the way, what package should I use to display/draw a nj >>>>>>> >>>>> tree generated >>>>> >>>>>>> by ClustalW2? >>>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> C.-J. >>>>>>> >>>>>>> >>>>>>> > ------------------------------------------------------------------------------ > >>>>>>> Download Intel® Parallel Studio Eval >>>>>>> Try the new software tools for yourself. Speed compiling, find >>>>>>> >>> bugs >>> >>>>>>> proactively, and fine-tune applications for parallel >>>>>>> > performance. > >>>>>>> See why Intel Parallel Studio got high marks during beta. >>>>>>> http://p.sf.net/sfu/intel-sw-dev >>>>>>> _______________________________________________ >>>>>>> taverna-users mailing list >>>>>>> [email protected] >>>>>>> [email protected] >>>>>>> Web site: http://www.taverna.org.uk >>>>>>> Mailing lists: http://www.taverna.org.uk/about/contact-us/ >>>>>>> >>>>>>> >>>>>> -- >>>>>> Dr Katy Wolstencroft >>>>>> Research Fellow, School of Computer Science,1.17 Kilburn Building >>>>>> University of Manchester, Oxford Road, Manchester, M13 9PL, UK >>>>>> Tel: +44(0)161 2756276 >>>>>> >>>>>> >>>>>> >>>>> >>> ------------------------------------------------------------------------ >>> >>>>> The New Busy is not the too busy. Combine all your e-mail accounts >>>>> with Hotmail. Get busy. >>>>> >>>>> > <http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4> > >>>> -- >>>> Dr Katy Wolstencroft >>>> Research Fellow, School of Computer Science,1.17 Kilburn Building >>>> University of Manchester, Oxford Road, Manchester, M13 9PL, UK >>>> Tel: +44(0)161 2756276 >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> Hotmail has tools for the New Busy. Search, chat and e-mail from your >>> inbox. Learn more. >>> >>> > <http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1> > >> -- >> Dr Katy Wolstencroft >> Research Fellow, School of Computer Science,1.17 Kilburn Building >> University of Manchester, Oxford Road, Manchester, M13 9PL, UK >> Tel: +44(0)161 2756276 >> >> >> > > ------------------------------------------------------------------------ > The New Busy is not the old busy. Search, chat and e-mail from your > inbox. Get started. > <http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3> > >
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