Re: [Myexperiment-discuss] Upload any type of Workflow you want...

[Coles S.J.]

Ola,

My response is primarily my own opinion. I am a Chemistry rep on myExperiment, 
but am not concerned with core development. I will put these points forward in 
our upcoming meeting, but it is up to the core team to answer your specifics. I 
am confident that the project will consider and address these matters.

Best,
Simon.

Simon Coles
Manager, EPSRC National Crystallography Service
School of Chemistry
University of Southampton
Southampton, UK. SO17 1BJ.
t: +44(0)2380 596722
f: +44(0)2380 596723
e: address@hidden
w: http://www.ncs.chem.soton.ac.uk
--



On 27/10/2008 16:39, "Ola Spjuth" <address@hidden> wrote:

Dear Simon,

Thanks for your answer. Let me know how I should proceed with this
matter. And I still would like to know if I should set up my own
myExperiment server or use the central one, and where docs are for
developing plugins to it.

Cheers,

/Ola

On 23 okt 2008, at 15.02, Coles S.J. wrote:

> QSAR would be an excellent test case for myExperiment, as would
> Will's OpenMicroscopy data.
>
> I like to think of myExperiement as a place to share PROCESS
> information and data. It just so happens that Bioinformaticians
> workflows are the low hanging fruit in that there is already a
> community built up and they have something in a useable/
> understandable format that they want to share!! That is why they
> were chosen as the first step to enlightenment! There is more to
> come from different disciplines, but they are harder to master. At
> this point in time you are correct - myExpt is workflow centric, but
> I hope that it is in a transition phase! All research is performed
> as some kind of 'workflow' or other but it can be exceptionally
> difficult to capture digitally.
>
> We are looking at its suitability for a variety of chemistry data /
> experiments (synthesis, analytical instruments, computational
> simulations) and QSAR would be a good intermediate step. This is in
> the planning stages right now and therefore it could be factored in
> as another use case. Containing files and describing them through
> tags etc is possible but the tricky part is describing the process
> and linking to inputs/outputs for each step in a machine readable/
> reproducible way.  We are looking at stringing together (and
> describing in a digitally exchangable way) processes that arise from
> humans doing things with physical stuff (i.e. Cookery recipies with
> chemicals) and analytical instruments producing data and simulations
> that occur in a computer...once you step outside the boundary of the
> digital world and start interfacing with the real world describing
> processes in a workflow/myExpt way becomes really hard and will
> require quite a lot of bespoke plugin development...UsefluChem's
> EXPLANS  will be
>
> Simon.
>
> Simon Coles
> Manager, EPSRC National Crystallography Service
> School of Chemistry
> University of Southampton
> Southampton, UK. SO17 1BJ.
> t: +44(0)2380 596722
> f: +44(0)2380 596723
> e: address@hidden
> w: http://www.ncs.chem.soton.ac.uk
> --
>
>
>
> On 23/10/2008 13:23, "Ola Spjuth" <address@hidden> wrote:
>
> Hi,
>
> I find Gernot's question very interesting and would like to enquire
> about something similar. We are developing a new standard for
> exchanging QSAR experiments in a new XML format. We were thinking of
> setting up our own repository, but I'd much rather use myExperiment
> for this. In a way you could call the setup of a QSAR experiment for a
> workflow (is this the terminology you'd like us to use?).
>
> Anyway, having QSAR experiments in myExperiment would require some
> specific modules/plugins in myExperiment to render/present/summarize
> the QSAR xml files for users, as well as means to validate them
> against a schema etc. What is the procedure for plugging specific
> components into myExperiment? Are there any docs for this? How would
> you make them available for other users to install and use (will it be
> like facebook apps)? I briefly studied the myExperiment wiki but found
> no pointers to develop such plugins. Do we need to set up our own
> myExperiment server in order to customize it to our needs, and in that
> case is it possible to keep this synchronized with the main
> myExperiment repository?
>
> A general question: myExperiments seems currently very workflow-
> centric. Judging from the name (myExperiment, not myWorkflow) I assume
> that the site is aimed for extensions towards other types of
> experiments (I guess this is a question of definitions, as everything
> in principle can be called a workflow). Are there other extensions you
> are working towards to broaden myExperiments, or do you envision
> several myExperiment sites focused towards different domains?
>
> Looking forward to learning more about this :-)
>
> Cheers,
>
>    /Ola Spjuth
>
>
>
> On 23 okt 2008, at 08.44, Gernot Stocker wrote:
>
>> Hi myExperiment -Team,
>> congratulations for this great new feature and it brings me to the
>> question whether it could
>> be also used to exchange xml-based experiment protocols? Within the
>> next days we are
>> going to release a new version of our software iLAP which offers
>> despite other features
>> some kind of ELN functionality. There, experiment protocols can be
>> exported as xml
>> "workflows" which are the basis for a web based data aquisition
>> wizard.
>>
>> First, is it allowed to exchange also iLAP protocols via
>> myExperiment? Which format do you
>> use for your workflows in order to achieve a better integration of
>> our protocols within
>> myExperiment? Or can we use our own? Is there a developer
>> documentation available for
>> such an integration path?
>>
>> Sorry for the newbe questions, but your announcement encouraged me
>> to follow this idea
>> with more energy.
>> Thanks,
>> GS
>>
>> On Thursday 23 October 2008, David De Roure wrote:
>>> 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
>>>
>>> http://www.myexperiment.org/announcements/20
>>>
>> --
>> Gernot Stocker,
>> Institute for Genomics and Bioinformatics(IGB)
>> Petersgasse 14, 8010 Graz, Austria
>> Tel.: ++43 316 873 5345
>> http://genome.tugraz.at
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