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Re: [Myexperiment-discuss] Re: New types of workflow.

From: Jiten Bhagat
Subject: Re: [Myexperiment-discuss] Re: New types of workflow.
Date: Mon, 27 Oct 2008 23:41:40 +0000
User-agent: Thunderbird (Windows/20080914)

Hi Will,

In terms of using myExperiment to store your XML files as workflows/protocols, please see my last email on 27/10/08 22:56 to Gernot.

Danius can provide more information about what an EXPLAN file is. In terms of how myExperiment handles them - they are uploaded as workflows using the new custom metadata / workflow type mechanism. At the moment they don't have any extended support features (like parsing of metadata and so on), but we will be building these in as we identify the features that are most useful. I.e: we don't do anything custom just yet for EXPLANS.


Will Moore wrote:


 I am interested in sharing a new type of workflow on myExperiment.

I am working on a (Java) tool to describe a protocol as a template that contains experimental variables. This is designed to make it easy for scientists to define a "protocol model" and capture their experimental metadata. See (and watch the demo movie for a good overview).

This project is in an early stage, and I am currently changing the XML file format for the software, but I would like to work towards sharing of protocol files in as many ways as possible, including publishing on myexperiment.

I am interested to hear that you "have" Usefulchem EXPLANS, as I am thinking of defining protocols in a similar layout (although the variables will be in context, rather than at the end). Can you give any more details of how myExperiment handles EXPLANS, what an EXPLAN file is etc?

 Many thanks,


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 (Usefulchem EXPLANS). 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
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