Alan R Williams | 7 May 13:57 2013

Changes to REST API for components

Hello everybody,

At the moment, components (and component profiles, families and 
versions) are implemented in myExperiment as packs, files, workflows and 
versions of them. When the REST API is used to talk to myExperiment, the 
components can only be dealt with as their myExperiment implementation.

This makes it hard for clients to talk to myExperiment about components. 
At the moment, the Java code in Taverna for talking to myExperiment is 
"hairy" and complicated. There is a need for Ruby applications to also 
be able to talk to myExperiment about components.

It would greatly help the BioVeL and SCAPE projects if the REST API 
dealt in components. There would then by one place for the mapping to 
the underlying implementation i.e. myExperiment side. This would allow 
later changes to the myExperiment implementation without the rewriting 
of the Ruby and Java Gems/packages.

What further information do the myExperiment development team need about 
the requirements?

Gmail | 10 Dec 21:56 2012

Request for the provenance data from scientific workflow executions


My name is Chalalai Chaihirunkarn, a Ph.D. student in the School of Computer Science at Carnegie Mellon University. I'm currently working on research that aims to enhance the usability of scientific software under the advisement of Professor James D. Herbsleb. 

We are interested in software co-occurrence inside scientific environments leveraged by scientific communities. We expect to identify the softwares that are used in collaboration and plan to suggest improvements of software tools present in such environments.

MyExperiment would be an effective environment for our studies. We have found that data source information, process definitions, dependencies among processes, and process execution periods, from the provenance of scientific workflows generated by Taverna, could massively benefit our research. 

We would like to request assistance from anyone who could send us provenance data from workflow executions, or could suggest how to access those data. The data could be in any format such as XML files, spreadsheets, or database scripts. The data would remain private and used only for research purposes. 

If you have any questions regarding our research and the use of the provenance data, please feel free to contact me at chalalai-AD0acThlWL4@public.gmane.orgu.

We would really appreciate your interest and participation. 

Thank you,

Chalalai Chaihirunkarn
PhD. student in Computation, Organizations, and Society
School of Computer Science, Carnegie Mellon University
500 Forbes Ave. Pittsburgh, PA, 15213. USA

Myexperiment-discuss mailing list
Alan R Williams | 7 Nov 09:52 2012

Profiles for how to share

Hello everybody,

I have requested before that there is the ability for a group 
administrator to set up profiles for how objects should be shared 
(including which layout to use). Having to do everything by hand has 
just caused problems for the BioVeL project. Can this be increased in 

Alan R Williams | 2 Nov 17:43 2012

Doodle poll for meeting to discuss contextualization of menus

Hello everybody,

The top-level menus on myExperiment do not do what many users expect. 
For example, when visiting a Group page, users think that the Workflows 
tab will then show the Workflows _for that group_. However, it currently 
shows all the workflows on myExperiment and the group's workflows are 
under the Shared Items tab of the groups' page mixed up with the group's 
other items.

It is proposed to

(1) hold a one hour skype call to discuss what functionality users want (*)

(2) allow a gap of several days for myExperiment coders to eliminate 
some suggestions as impossible

(3) a second one hour skype call to agree on a solution to be implemented

I have created a Doodle poll for the first one hour call. We hope to 
have it sometime in the next two weeks.

The poll is at

If you cannot make the skype call but have suggestions then please 
e-mail me or myexperiment-discuss@...  Also, if you are
with the current functionality and do not want it changed, please e-mail 
or join the call.

Thanks in advance,


(*) Because it is only a one hour call, discussion should be focused on 
this topic and should be limited to what users want, not how coders 
can/cannot achieve it.
Mark Thompson | 20 Sep 12:48 2012

change or bug in the read-workflow rest API?


I'm maintaining an application (t2-web) that depends on the
MyExperiment REST-API. It was working fine until recently. In the XML
output of "read workflow" it looks for an element <components> should
contain information about the inputs and outputs of a workflow as
<source> and <sink> elements.

However, if I look at the output of:
then the <components> element is empty. Actually, I tried a few
different Taverna workflows, and <components> is always empty.

Is this a bug in the rest-api XML output, or has the API changed recently?

Mark Thompson
Alan R Williams | 12 Sep 16:06 2012

Social side of myExperiment

Hello everybody,

In BioVeL we are developing workflows in several related biovdiversity 
domains. The BioVeL workflows are being kept on myExperiment.

Some of the domains have related resources such as facebook groups and 
youtube videos. So, the workflow is part of a dynamic social world. I 
was wondering if there is a presentation or roadmap about how it is 
intended for myExperiment to deal with this (assuming it is).

Danius Michaelides | 12 Sep 12:25 2012

myExperiment down


Regrettably myExperiment went down earlier today and we are working on
resolving the problem and bringing the service back online. Please except
our apologies.

myExperiment team
Julien Wollbrett | 10 Sep 11:46 2012

problem to update a workflow


I have a problem to update a workflow named : Oryza Sativa QTLs and genes retrieval from TropGene, Gramene and Ensembl
I try to "upload new version" but  I have a problem with main metadata.
When I try to infer metadata I have this message :
we are sorry but something went wrong

And when I enter custom metadata I have this message :
There were problems with the following fields:
  • Title can't be blank

even if my title is not blank.

Julien Wollbrett

Myexperiment-discuss mailing list
Katy Wolstencroft | 28 Aug 11:41 2012

problems with myExperiment

Hi all,

I'm having trouble logging into myExperiment today and performing 
searches. I just get the "We're sorry, but something went wrong" message.




Dr. Katy Wolstencroft
Research Fellow
School of Computer Science
1.17 Kilburn Building
University of Manchester
M13 9PL
Frey J.G. | 19 Aug 03:19 2012

It as a Utility Information/launch meeting 4th Sept Royal Society

Subject: Re: It as a Utility Information/launch meeting 4th Sept Royal Society

Sorry for the imposition but I need some help in publicising our new network on IT as a Utility so please could
I ask you to forward the details of the IT as a Utility Meeting on the 4th September to those who might be interested
Thanks for your help

Subject: It as a Utility Information/launch meeting 4th Sept Royal Society

ITaaU Information Event

ITaaU Information Event
Tuesday 4th September 2012
At the Kohn Centre,
Royal Society, 6-9 Carlton House Terrace, SW1Y 5AG
14:00 – 17:00

Meeting programme will be updated at

The Background: The Digital Economy RCUK Theme
Introduction to the ITaaU Network
ITaaU Events and Opportunities
Design for Usable IT (USTWO)
The ITaaU Network and EU FP7 and Beyond (Dr. Mike Surridge, IT Innovation)
The ITaaU Network and Asia (Prof. Gerard Parr, University of Ulster)
Cloud & Pervasive Computing (Rob Fraser, Microsoft UK)
Summary of ITaaU events, opportunities and deadlines

More details will be published on the Network web site shortly. There will be no
registration formalities or charge for this meeting but please email
to let us know that if you are planning to come so we can ensure adequate refreshments. The event is being
held at the Royal Society, Carlton House Terrace, London. Directions can be found online at

IT as a Utility Network+

IT as a Utility (ITaaU) is one of the 4 sub-themes of the RCUK Digital Economy programme
<> . The ITaaU Network
purpose is to promote and enhance the community interested in this aspect of the DE programme and help
co-ordinate activities in this area.

IT as a Utility is about the provision of information and technology in a transparent and highly usable
manner. It is closely related to Grid and Cloud Computing with its emphasis on making IT resources
effortlessly and almost invisibly available the end user. Cloud paradigms for access to applications
and infrastructure are now well established, and are changing the way users interact with applications,
especially where the application is accessible from multiple devices and users.

See (this is being updated and a new version will appear soon)

Also blog post

Jeremy Frey
Danius Michaelides | 7 Jun 12:13 2012

Re: Lots of strange hotmail users

On Thu, 7 Jun 2012, David R Newman wrote:

As David mentioned this is normal behaviour. In the last week, however,
we've been under a more sustained attack from spammers, so the spamming is
probably alot more visible. We're currently trying to deal with it.


> This doesn't sound like anything new.  The spammers on MyExperiment are 
> certainly more resourceful than any other project I have ever been involved 
> with.
> David Newman
> On 07/06/2012 01:14, Alan R Williams wrote:
>>  The sneaky b*****ds. They must have noticed that accounts that are created
>>  with links tend to be deleted. So, at the same time as they are creating
>>  these new accounts, they are also going and putting links into previously
>>  created accounts. I guess that tomorrow they will be filling in these new
>>  accounts.
>>  Grrrr!
>>  Alan
>>  _______________________________________________
>>  Myexperiment-discuss mailing list
>>  Myexperiment-discuss@...
> _______________________________________________
> Myexperiment-discuss mailing list
> Myexperiment-discuss@...