Comments on: A simple Taverna tutorial – Part 2: Multiple sequence alignment http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/ Casual ramblings of a bioinformatician Mon, 10 Dec 2007 04:20:34 +0000 http://wordpress.com/ hourly 1 By: alper http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/#comment-100 alper Mon, 10 Dec 2007 04:20:34 +0000 http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/#comment-100 Hi Kearan, My question is not related to workflow per se. I saw in your "uniprottutorial.png" picture that you're using ubuntu linux (I guess) and the window list shows that you have Eclipse IDE and Taverna are open at the same time. In my case, even openning one of those applications clogs the memory. Does your machine handle two big Java-based applications well? ?If yes, what is your hardware specifications? thanks.. Hi Kearan,
My question is not related to workflow per se. I saw in your “uniprottutorial.png” picture that you’re using ubuntu linux (I guess) and the window list shows that you have Eclipse IDE and Taverna are open at the same time. In my case, even openning one of those applications clogs the memory. Does your machine handle two big Java-based applications well? ?If yes, what is your hardware specifications?
thanks..

]]> By: Gareth http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/#comment-57 Gareth Tue, 21 Aug 2007 11:11:12 +0000 http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/#comment-57 Hi Kieran, seeing some of the workflows you're producing has restored my faith in Taverna. However, I am still struggling to get to grips with some of the various technologies involved. Specifically, what do I do with the java code posted above? For code you used in the previous tutorial, you wrote: "This can be used as a web service by saving the file as .jws and saving it to your jakarta/webapps/axis directory". Presumably, I should attempt to do the same with this. I don't have jakarta, but if I did, is it as simple as just dropping the jws file into the directory and then searching for it using the scavenger? What is special about jakarta that allows this to work? I have access to an apache server, would this do what is required? Many Thanks, Gareth. Hi Kieran, seeing some of the workflows you’re producing has restored my faith in Taverna.
However, I am still struggling to get to grips with some of the various technologies involved. Specifically, what do I do with the java code posted above? For code you used in the previous tutorial, you wrote: “This can be used as a web service by saving the file as .jws and saving it to your jakarta/webapps/axis directory”. Presumably, I should attempt to do the same with this.

I don’t have jakarta, but if I did, is it as simple as just dropping the jws file into the directory and then searching for it using the scavenger? What is special about jakarta that allows this to work? I have access to an apache server, would this do what is required?

Many Thanks, Gareth.

]]> By: Duncan Hull http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/#comment-53 Duncan Hull Fri, 03 Aug 2007 18:48:08 +0000 http://kierenlythgow.wordpress.com/2007/07/23/a-simple-taverna-tutorial-part-2-multiple-sequence-alignment/#comment-53 Hi Kieran, these workflows look useful, can you upload them to http://www.myexperiment.org ? Its exactly the kind of thing we'd like people to share. Cheers. Duncan Hi Kieran, these workflows look useful, can you upload them to http://www.myexperiment.org ? Its exactly the kind of thing we’d like people to share. Cheers. Duncan

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