Showcase catalogue

This page is going to be used by show case leaders to record the progress of their show cases.

They should a child page for their individual show case, and in it record the JIRA issues that are associated with their show case.

See also: [http://www.wf4ever-project.org/wiki/display/docs/Show+case+backlogs]\\
{toc}


h2. Sprint 1

h3. Showcase: Wiki documentation (Oscar)

*Goal:* As a project manager I want everybody in the project to have a clear idea of the current status of all our work and everybody outside the project to have a clear idea of our main results and their status, so that the project members have always an up-to-date status, and 3rd parties can know how to use our results.
* Wiki Hackathon (done) \--> From now on a list of pending tasks will be available at [Wiki and Website]
* Primers (done)
* How-to

*Participants*: Oscar, Sean, Khalid, Pique, Marco, Daniel


h3. Showcase: Initial RO Spec Draft



h2. Sprint 2


h3. Showcase 14. Initial RO Primer (Jun)

*Goal*: Deliver an initial draft of RO primer ([http://titanpad.com/RO-primer-v2])


*Members*: Oscar, Khalid, Sean, Stian, Daniel, Esteban, Marco, Pique, and Raul

*JIRA*: [https://jira.man.poznan.pl/jira/browse/WFE-279]

















































*Outcome*: We created an initial RO primer [http://wf4ever.github.com/ro-primer/] that is under internal review. The showcase has served its purpose and we propose to close it.






h3. Showcase 17. RO Spec Final (Sean)

*Goal*: Add more examples to the initial RO spec ([http://wf4ever.github.com/ro/])

*Members*: Khalid, Stian, Daniel, Esteban, and Jun

*JIRA:* [https://jira.man.poznan.pl/jira/browse/WFE-266]





























































h3. Showcase 6. A taxonomy of Workflow Evolution (Pinar)

*Outcome*: Create an initial taxonomy related to workflow evolution. Specifically we analyzed:

# Outline the drivers for evolution of workflows.
# Outline how evolution is handled in Scientific Workflow systems and repositories.
# Outline how evolution information could be exploited for preservation of workflows.
# Extend the relevant sub-section of RO Evolution model to cater for workflow evolution



The tasks performed were:
* Literature survey
* myExperiment/Taverna analysis [^WFsWithRevComments.v0.1.txt]
* RO evolution model/ontology
* Storyboards of different lifecycles

*JIRA*: WFE-255, WFE-300, [WFE-258|https://jira.man.poznan.pl/jira/browse/WFE-258], WFE-236

*Members*: *Pinar*, Oscar, Raul, Pique, and Marco

h3. Showcase 7. A Taxonomy of repair and diagnosis (Jose Manuel)

*Goal*: To come up with a characterization of:

# Potential causes of workflow/RO decay,
# Where they come from, where are the problems producing the decay originated,
# How they can be identified, and
# How we can measure/estimate their impact on the RO.

We will obtain input from previous work and from the case studies. Each item will be illustrated with an example from a particular domain. The final outcome of the sprint will be a taxonomy providing such set with a structure (if any such structure can be identified).

*Members*: José Manuel, Marco/Kristina, Pique, Alan Williams, Daniel, Khalid, and Aleix

*Results*: [Taxonomy of RO-Workflow Decay|docs:Taxonomy of RO-Workflow Decay]





































h3. Showcase 9. Astro-Taverna wishlist Sprint 2 (Susana)

*Goal*: a version of Taverna software with a first list of functionalities/wishes implemented

*Members*: Stian, Pique, Juande and Lourdes (possibly)

Specific targets (to finish in this sprint, two weeks):

*(1) Connection with the Virtual Observatory Services: Search and use VO services*
# [WFE-192|https://jira.man.poznan.pl/jira/browse/WFE-192]: As an astronomer user of Taverna I want to query the Virtual Observatory registry, so that I can know which services are suitable for my workflow
# [WFE-193|https://jira.man.poznan.pl/jira/browse/WFE-193]: As an astronomer user of Taverna I want to visualize the list of Virtual Observatory(VO) services fulfilling a query to the VO registry, so that I can choose the most suitable for my workflow
# [WFE-195|https://jira.man.poznan.pl/jira/browse/WFE-195]: As an astronomer user of Taverna I want to inspect information related each one of the VO services fulfilling a query to the VO registry, so that I can know how to use this service (e.g, the inputs needed)
# [WFE-196|https://jira.man.poznan.pl/jira/browse/WFE-196]: As an astronomer user of Taverna I want to add a chosen VO service to my workflow, so that I can use the data extracted from the VO service in my workflow.

*Conclusion*: Due to time constraints and over booking, none of the targets were addressed. They have however been well specified and estimated, and are the target of the following sprint 3.




h3. Showcase 15. Creation of concrete RO examples (Raul)

*Goal*: A wiki page describing concrete RO examples generated for different workflow systems, and different users (one bio and one astro), and implement them in the RODL (next step)

*Member*: Pique, Stian, Daniel and Marco

*Jira*: [WFE-302|https://jira.man.poznan.pl/jira/browse/WFE-302]


























































This showcase includes the following stories:

* [WFE-303|https://jira.man.poznan.pl/jira/browse/WFE-303] which represents the work to be done to create a wiki page
* [WFE-304|https://jira.man.poznan.pl/jira/browse/WFE-304] which represents the work to be done to implement the RO examples in the RODL (this story may not be finished in the second sprint)

*Outcome*:  [docs:RO Examples]




































h3. Showcase 26. Recommender: Explainability Showcase (Rafael)

*Goal*: Provide an explanation on why a recommendation is given to a user so that she can: (1) provide better feedback, (2) be able to better measure the relevance of such recommendation. This showcase includes heavy updates in the Recommender System, but also some minor updates in the RO Portal since it must include a new link for the explanation.

*Members*: Piotr, Rafael

*Story*:  As a researcher I want the recommender system to provide an explanation on why a recommendation is given to me so that I can judge its relevance/I can be able to provide bettter feedback

*JIRA: *[WFE-288|https://jira.man.poznan.pl/jira/browse/WFE-288]




































*Outcomes* (up to 28/3/2012)

The first main outcome is the parameterization of the recommender system, both of its general structure and its different recommenders. Therefore:

\-The recommender system structure and configuration is no longer hardcoded in Java, but it is a set of modules that can be set up in a declarative fashion. For that we use an XML deployment document that will be documented by the end of this week in the recommender system section in the wiki

\-Each of the recommendation algorithms that the recommender system uses can be configured separately and in a declarative fashion also.

The second outcome is that we have included an explanation for each of the recommendation algorithms.

\-For the collaborative filtering algorithms (both the one that recommend files and workflows) is already finished (and uploaded to the project github) For example, for the user Jun Zhao we obtain a recommendation like this:

{panel}<recommendation>

<explanation>The workflow entitled BLAST using DDBJ service(URI:[http://www.myexperiment.org/workflow.xml?id=23]) is recommended to you since users with similar tastes and interests as yours (such as&nbsp; Stian Soiland-Reyes,&nbsp; Duncan Hull,&nbsp; Mustafa,&nbsp; Alan Williams, Paul Fisher) found it useful

</explanation>

<resource>[http://www.myexperiment.org/workflows/23]</resource>

<strength>4.3333335</strength>

<title>BLAST using DDBJ service</title>

</recommendation>{panel}

\-The keyword content based recommender explanations are still in development, but will be finished for tomorrow.

The rest of the week (thursday + friday) will be devoted to documenting all these new features of the recommender system and will be available in its section. As soon as everything is available, we also send some recommendation results to the users, to check whether they like the explanations or not, to update them according to their needs.


h3. Showcase 22. A Provenance showcase, Querying provenance of the workflow results (Esteban)

The main goal is to provide a transfer from Taverna and Wings environments towards the wfprov definition in order to allow the incorporation of I&A functionalities. This will be achieved by a proof of concept importing a few examples (1 or 2) from Taverna and Wings and allowing&nbsp; the querying and end-users testing. The showcase description and main outcomes can be found at&nbsp;[http://www.wf4ever-project.org/wiki/display/docs/Showcase+22+Querying+workflow+execution+provenance]




































*Stories*: The RO model refers to provenance traces of workflow runs. Much of the preservation activity refers to provenance.&nbsp;Taverna currently stores provenance and intermediate results (essential for replay) in a database on the desktop. Which is then deleted by the user when they run out of space.
* the provenance is not actually exposed through an api or query
* the intermediate data is not actually exposed through an api and query
* the provenance is stored in a local database not on a server
* the ref manager needs reworking

So we have the capture of provenance but we do not enable access to it or storage of it or publication of it. &nbsp;It's write once read not possible.&nbsp;Biovel, wf4ever and scape need this and need to work together .

*Epic*:&nbsp;[https://jira.man.poznan.pl/jira/browse/WFE-260], WFE-204

*Stories*:&nbsp;[https://jira.man.poznan.pl/jira/browse/WFE-261],&nbsp;[https://jira.man.poznan.pl/jira/browse/WFE-262]




































{color:#ff6600}Marco: for some reason I could not see the Jira items. I would like to check if the items from the '{color}{color:#ff6600}[user view on provenance|docs:User view on Provenance]{color}{color:#ff6600}' table can be addressed by the proposed showcases.{color}












h3. Showcase 37. RO checklist evaluation (Graham)

This showcase was related to 10 (reviewing with ROs), 22 (RO provenance querying), 32 (User view of provenance), and maybe others.&nbsp;Its goal was to create a framework for evaluating ROs against a checklist, using some minimum information model ideas to guide the evaluation.

The outcome will be a utility which can accept an RO and a checklist, and produce a report of how well the RO complies with the checklist requirements. Initial requirements will focus on simple issues like (a) is there an execution-ready workflow instance, (b) is required workflow input data present, (c) are the workflow execution results present, etc. This framework can be expanded later to cover a wider range of checklist requirements.

The active planning for this showcase is in Pivotal Tracker, at&nbsp;[https://www.pivotaltracker.com/projects/495929]. Stories tagged with "checkro" are in play for this showcase.

The main stories are:
* evaluate completeness of RO ([https://www.pivotaltracker.com/story/show/26123933])
* review completeness of RO ([https://www.pivotaltracker.com/story/show/26123943])
* Use multiple checklists ([https://www.pivotaltracker.com/story/show/26124107])
* RO to assist automating elements of review process

The main target for completion in the first sprint is the first of these, with any additional stories tackled as time permits.

A key outcome from the early work will be a demonstrable checklist evaluator, which is aligned with RO and WF description designs produced by other project work packages, and which can be built upon to support user quality reviews.

h2. Sprint 3


h3. Showcase 12. Visualisation of ROs (Piotr)

Members: Piotr, Raul, Pique and Kristina

*Stories*
* As a user of ROs (in potentially different roles, e.g. creator,&nbsp;reviewer, reader) I want to be able to visualise ROs in a repository.
* I want to be able to see the basic structure of the RO (what's inside&nbsp;it), along with the annotations that have been placed both on the&nbsp;aggregated contents and on the RO itself.
* I want to first see the information most important to me and be able to inspect the other details later.
* I want this visualization to be provided without the need for the installation of additional tooling (e.g. via a web interface)
* -I want to be able to navigate into sub-ROs that are aggegrated in an RO and visualise those.-&nbsp;_We don't have sub-ROs yet._

*Outcome*: Results can be found at&nbsp;[docs:Showcase 12 RO visualization]





















*Jira*: Epic&nbsp;[WFE-264|https://jira.man.poznan.pl/jira/browse/WFE-264], Story&nbsp;[WFE-239|https://jira.man.poznan.pl/jira/browse/WFE-384]






















*Results (copied from the results page)*: The showcase contributed to RO visualization in 2 aspects: user requirements and technical analysis. The user requirements show a detailed vision of what data should comprise the RO visualization in long term as well as potential related functionalities. This has been illustrated by sample mockups aggregated from previous work. This vision has been confronted with current status of the project. Some basic conclusions are: There is a lot of user emphasis on RO provenance (authorship, credits, reusability) or RO stats (number of views, downloads) which have not been addressed much in RO models so far. This puts additional motivation for showcases #29, #30, #31 and #32. Some nice visualization options can be provided by utilizing RO services that are in development. This may be implemented in showcase #5 but for this to happen, RO evaluation services must become connected to the RO model (i.e. should be used by RODL/RO Portal, or should save their results as annotations, etc). User scenarios has always put emphasis on user roles. However, there is no user model in Wf4Ever, which includes no access rights or collaboration policies. This puts additional motivation for showcases #34, #45 and for additional work on user model. RO visualization should include workflow visualization, which may be done as a separate showcase one day.

*Future work (copied from the results page)*: The user requirements should become input for related showcases, as listed above. Some visualization elements that can be implemented today, will probably be implemented before sprint 4. If it's not possible, we will decide if we need another sprint to finish the implementation, or we move the remaining work to other showcases such as #5. At some point in time, mockups may be created that show how all data listed by users are gathered in a reference web application (RO Portal?) creating the desired RO visualization. This may well be done in another showcase.

h3. Showcase 9. Astro-Taverna wishlist Sprint 3 (Susana)

Members: *Susana*, Stian, Aleix, Julian, Juande and Pique

Daily stand-up Skype chat: 08:45 BST / 09:45 CEST - [http://s11.no/s/skype:?chat&blob=bo8C2fpzMthI2qJpgb9uJAKuhnI70McUOTOq-l-62q5EXER9ID7tSOYOXANncVEwz7sNPBaF2RLll1iqEIm0dvxHhP6y0Ehm_VSnxyD8mIFdUJ9BbbsG8GQ]















































*Related JIRA Issues*


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*Conclusions*

The objectives of this showcase for this sprint have been achieved. In the development version of Taverna a user can query to the Virtual Observatory, see information about the VO services and insert the VO service selected to a workflow. The Vizier Catalogue perspective of Taverna was simplified, but it found that this simplified form does not add any new functionality and vizier services can be searched in the VO service perspective as well, so we decided not implement it for now.

For more information see&nbsp;[docs:Showcase 9 Astrotaverna]






































At the same time, Julian, Aleix and Susana have used this sprint to follow a tutorial to learn how implement Taverna plugins in order to be able to implement the simplest plugins related to the rest of the showcase.

*AstroTaverna plugin for Taverna*: [http://wf4ever.github.com/astrotaverna/]








































h3. Showcase 21. RO testbed (Dani)

Members: Khalid, Aleix, Esteban, Jose, Graham, Jun and possibly Marco and Pique

Outcome:&nbsp;[docs:RO testbed]




































h3. Showcase 45 Collaboration Spheres Mockup (Esteban)

[Jira issue: https://jira.man.poznan.pl/jira/browse/WFE-390|https://jira.man.poznan.pl/jira/browse/WFE-390]




































*Goal*: The main purpose of this showcase is to create a mockup to represent the visual metaphor related with the relations/similarities between the diferrent users, different ROs, and in between them. This similarities will be mostly measured by recommendation criteria. The main outcomes of this showcase will be a definition of the type of relations that has to be represented, identification of the best appealing metaphor, identification of the similarity criteria to be used as meap psuring criteria, and the validation of this terms according to users.

*Members*: Esteban, Rafa, and Pique/Marco

*Outputs*:&nbsp;The complete notes regaring the showcase can be found at:&nbsp;[Collaboration+Spheres|http://www.wf4ever-project.org/wiki/display/docs/Collaboration+Spheres]




































* &nbsp; &nbsp;Establishment of relations to consider between ROs and Users
* &nbsp; &nbsp;Definition of the visual metahor to be used for visualizing the relations and recommendation services
* &nbsp; &nbsp;User interpretation of the relations and metaphor
* &nbsp; &nbsp;Simple initial mockup visualization
* &nbsp; &nbsp;Real output data for recommendation to be used by the collaboration spheres module&nbsp;







h3. Showcase 43. Best Practices for developing workflows (Kristina)

*Participants:*&nbsp;Kristina (presenter), Carole, Marco, Katy Wolstencroft. Khalid provided valuable input. We involved local LUMC users for feedback.

*Background:*&nbsp;Researchers developing Workflows, especially those who are new to workflows, could be greatly helped by 'best practices' from experienced workflow developers. At the same time, to stimulate creation of 'good' workflows, our work in wf4ever should help workflow developers with advice, recommended procedures, and tools.&nbsp;This sprint was aimed at the upcoming BioVEL meeting in Sweden, which is a community fits the above. The main outcome of this sprint is a presentation, entirely aimed at (new) users of workflows. A second aim is to use the insights into best practices to validate our taxonomies, checklists, etc. and in some cases inspire the content of the presentation.

*Results*: [Preparations for BioVEL presentation|http://www.wf4ever-project.org/wiki/display/docs/Workflow+Best+Practices+-+preparations+for+BioVEL+presentation],&nbsp;[Workflow Best Practices|http://www.wf4ever-project.org/wiki/display/docs/Workflow+Best+Practices], +[+Workflow Design Best Practices+|http://www.wf4ever-project.org/wiki/display/docs/Workflow+Design+Best+Practices]+,&nbsp;and the sprint folder in Dropbox for the powerpoint and sources (Sprints \-> Showcase43_BestPracticesWorkflowDesign)

*Jira:*&nbsp;Story&nbsp;[WFE-413|https://jira.man.poznan.pl/jira/browse/WFE-413]





















*Next steps:*&nbsp;work this towards a publication and mapping to wf4ever results (in particular the&nbsp;[Taxonomy of RO-Workflow Decay|http://www.wf4ever-project.org/wiki/display/docs/Taxonomy+of+RO-Workflow+Decay]).

h3. Showcase 36. Definition of the RO evolution model (Raúl)

The&nbsp;*Research Object Evolution model*&nbsp;enables the representation of the different stages of the Research Objects life-cycle,&nbsp;their dependencies, as well as the corresponding versions of Research Objects and their aggregated resources, with the associated changes in these resources. The concrete realization of this model is the&nbsp;*roevo*&nbsp;Ontology and it is built on top of the core ro ontologies.

*JIRA*:&nbsp;[WFE-236|https://jira.man.poznan.pl/jira/browse/WFE-236]



This showcase is related to three issues:
* Conceptualization of RO evolution ([WFE-256|https://jira.man.poznan.pl/jira/browse/WFE-256]), including tasks for definition of terminology, evolution scenarios, and analysis of background material.
* Implementation of RO evolution model ([WFE-257|https://jira.man.poznan.pl/jira/browse/WFE-257]), including the creation of the corresponding OWL ontology
* Taxonomy of workflow changes ([WFE-258|https://jira.man.poznan.pl/jira/browse/WFE-258])

h2. Sprint 4


h3. Showcase 8. Service substitution (Khalid)

Member: Dani and Jun

Jira: Story [WFE-454|https://jira.man.poznan.pl/jira/browse/WFE-454]
























The algorithm for repairing workflows assumes that the provenance of a large number of workflows is captured, and in addition, similarity between services can be detected based on the analysis of their provenance. To be of practical use, therefore, we will need to have a large amount of workflows for which the provenance is captured and stored. Because of this, I am tacking the liberty to re-purpose the objective of this sprint to have a useful outcome in a short term. Specifically, I would like this sprint to focus on developing a set of canned queries for exploring the services based on their use within workflows. This kind of canned queries can be useful for curator who wishes to repair workflows, but also for users who simply wish to have an idea about how a given service is used in workflows. In particular, we will focus on the canned queries specified by the following stories:

* Story 1: As a curator or a user, I want to locate the service operations that are mostly used in workflows within the myExperiment repository so that I can gain knowledge about popular service operations.
* Story 2: As a curator or a user, I want to locate the service operations that are used in recently uploaded workflows in the myExperiment repository so that I can gain knowledge about the trend is service usage.
* Story 3: As a curator or a user, I want to locate the service operations (processors) in the myExperiment repository that are connected to a given operation to gain understanding on how such an operation is used within workflows.
* Story 4: As a curator or a user, I want to locate the service operations (processors) in the myExperiment repository that are connected to operations (processors) that are connected to a given, eventually missing, operation op in one or more workflows so that I can identify the operations that are compatible with op in terms of parameters.

The outcome of this sprint is a set of caned queries in the form of SPARQL queries and description of the parameters that need to be bound, as well as a textual description of the form of the results that can be expected from the queries execution.&nbsp;The results of this showcase are reported in three wiki pages.
* [myExperiment canned queries|http://www.wf4ever-project.org/wiki/display/docs/myExperiment+Canned+SPARQL+Queries]
* myExperiment component ontology \-> RO wfdesc ontology&nbsp;[http://www.wf4ever-project.org/wiki/display/docs/Mapping+myExperiment+Component+Ontology+to+RO+wfdesc]
* [RO myExperiment pack vs. ROs|http://www.wf4ever-project.org/wiki/display/docs/RO+vs.+myExperiment+pack]



h3. Showcase 9. Astro-Taverna wishlist Sprint 4 (Susana)

Members: *Susana*, Stian, Aleix, Julian, Juande and Pique

Daily chat: 16h CEST [Link to chat|http://s11.no/s/skype:?chat&blob=4Z7OgN2hJv3DztRqSTDjqLcaT4m9akCIsFLxHC24Ev2fX6fb3XNvhRTreLia9mLFVczvB5XfgjOahvwy67qDevujLptw1dhH_r0y7BcDsk0tJU2pcN0jso5Klj1flhLx]































Objectives: VOTable visualization (as a spreadsheet). Taverna and SAMP connection. Extraction of information from the VOTable. Check the astrotaverna plugin

*(2)VOTables management:*
# [WFE-203|https://jira.man.poznan.pl/jira/browse/WFE-203]: As an astronomer user of Taverna I want to send the VOTable obtained as a result of my workflow to Topcat, Aladin or other SAMP-VO software, so that I can perform advanced scientific analysis provided by specific VO software.
# [WFE-197|https://jira.man.poznan.pl/jira/browse/WFE-197]: As an astronomer user of Taverna I want to use local services for extracting columns, rows and/or one or several cells from VOTables, so that I can use pieces of a VOTable as inputs for components of my workflow.
# [WFE-198|https://jira.man.poznan.pl/jira/browse/WFE-198]: As an astronomer user of Taverna I want to extract the semantics (utypes) of VOTables columns, so that I can select and extract columns by their utypes
# [WFE-199|https://jira.man.poznan.pl/jira/browse/WFE-199]: As an astronomer user of Taverna I want to extract the description/metadata of VOTables, so that I can know some specific information about the data and so manage them properly
# [WFE-200|https://jira.man.poznan.pl/jira/browse/WFE-200]: As an astronomer user of Taverna I want to see the VOTable obtained by a Virtual Observatory service component of my workflow as a spreadsheet in the Results perspective of Taverna , so that I can visualize better the VOTable data.

Documentation: [docs:SAMP]
































h3. Showcase 27.(A+B) Scientific Content Social Recommender Showcase (Rafa)

As a researcher I want the recommender system to provide scientific resources so that I can be able to use&nbsp; in my research and as .

As a researcher I want the recommender system to provide content-based recommendations based on the way that search and retrieving of scientific content is already performed by researchers, allowing search in fields such as authors, abstract, keywords, publication dates, etc.

As a researcher I want that the recommender system provides recommendations based on my social network so that I can better collaborate with my peers/have a better understanding of the SoA

Work description:
* Inclusion of new scientific content sources: More precisel OAI-PHM sources
** Read and analyze “The Open Archives Initiative Protocol for Metadata Harvesting”
** Include the two first candidate sources:
*** CiteSeerX
*** Arxiv.org
* Update of the current index:That includes:
** Update of the index structure
** Update of the indexing tools&nbsp;
* Creation of the new recommender as an extension of the already existing WorkflowKeywordConteBased recommender
* Basics for the social recommender
** Learn how to use and deploy neo4j (and the cypher query language)
** Definition of the similarity function
** Implementation of the similarity function (java+neo4j)
* Building of the social networks
\**Social network
\**Design and code myExperiment social network harvester
\**Authorship network

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h3. Showcase 47. I&A evaluation and integration (Esteban)

Members: Graham,&nbsp; Aleix, Jun and Jose

This showcase main goal is to integrate the work done related with I&A to provided some initial I&A funcionality to be consumed by an end-user.Thisgoal contains the following sub-goals:
* Define and create&nbsp; MINIM web service funcionalities (p.e. completeness)
* Define and create I&A service funcionalities (p.e. replayability)
* Define a simple interface for showing the funcionalities developed

Outcomes: I&A integrated services (replayability and repeatibility) + simple visualization and checklist services (completenes and taxononomy decays p.e.&nbsp;[Type: Decay 3|http://www.wf4ever-project.org/wiki/display/docs/Taxonomy+of+RO-Workflow+Decay#TaxonomyofRO-WorkflowDecay-3.Serviceitselfnotcontactable.]&nbsp;[Type: Decay 5|http://www.wf4ever-project.org/wiki/display/docs/Taxonomy+of+RO-Workflow+Decay#TaxonomyofRO-WorkflowDecay-5.Dataunavailability])

This showcase will be integrated later on into the wf4ever portal.


The complete description can be found at [Showcase 47 Description|http://www.wf4ever-project.org/wiki/display/docs/Show+case+backlogs#Showcasebacklogs-INPROGRESS\SPRINT4\%26nbsp%3B47.I%26Aevaluationandintegration], the tasks to be done at JIRA number: [WF3-437|https://jira.man.poznan.pl/jira/browse/WFE-437] , and the work done is [here.|http://www.wf4ever-project.org/wiki/pages/viewpage.action?pageId=3506198]




























h3. Showcase 48. A first "round-trip" myExperiment integration (myExp \-> Taverna \-> RODL \-> myExperiment) (Kevin)

*Members*: *Kevin*, Don, Piotr (some), Raul(some), Stian (some)

*Results*: [Showcase 48 - A first round-trip myExperiment integration|docs:Showcase 48 - A first round-trip myExperiment integration]

























*Daily standup*: 15:30 BST / 16:30 CEST[http://s11.no/s/skype:?chat&blob=CqMOjhfwRakyz5YNDxxmmdJHtqTnHiCRX-EK-mu_CyH6Rf10hWjWU6G379MbGq4QD9dhNE6_9FnzHXZGFqtmwG-wwhE_qZIfd_nJTglTtn-dV40Ndlc9ZyN9gAw8pygVpPE]





















A showcase to do a first pass integration between myExperiment and Wf4Ever tools and services.

Technical goals:
* When a workflow from myExperiment is added to an RO in RODL, myExperiment will display metadata from that RO (via the ROSR API)
* Persistent identifiers for the workflow through the round-trip
* myExperiment using the ROSR API
* myExperiment presenting/visualising an RO

Secondary goals:
* Encourage team-working between Wf4Ever and myExperiment
* Build familiarity with myExperiment internals within Wf4Ever















h3. Showcase 49. Website content updates (Oscar)

Lead: Oscar

Member: Jose, Dave, and Jun

Wiki page: [Showcase 49 - Website content updates|docs:Wiki and Website]
























JIRA: [WFE-477|https://jira.man.poznan.pl/jira/browse/WFE-477]
























h3. Showcase 50. Visualization of RO evolution RO Social aspects (Raul)

Member:&nbsp;*Raul*, Piotrek, Oscar, Graham, Pique, Marco

Wiki Page:&nbsp;[Showcase 50. Visualization of RO Evolution|http://www.wf4ever-project.org/wiki/display/docs/Showcase+50.+Visualization+of+RO+evolution]





















The goal of this showcase was to implement the visualization of RO evolution based on the roevo ontology. The evolution includes both the direct version dependencies, and the contribution relationships (e.g., derivedFrom). Additionally, the set of changes associated with each version should be displayed.&nbsp;As a first step for this showcase, the visualization was implemented in the RODL portal.

h2. Sprint 5


h3. Showcase 0. Automated Workflow execution (Stian)

Related to showcase 56

* Create an agent to automatically execute Taverna workflows (say all public myExperiment workflows) so that we can analyze their decay over time

*Goals*: An agent that can automatically run Taverna workflows found in RODL - all workflows imported from myXP. Uploads results as new ROs with outputs, PROV-O workflow run provenance and intermediate values.

This forms data and infrastructure to be used by other showcases.

Participants: *Stian*, (Piotr?)

Jira: Epic [WFE-238|https://jira.man.poznan.pl/jira/browse/WFE-238], Story [WFE-239|https://jira.man.poznan.pl/jira/browse/WFE-239], [WFE-513|https://jira.man.poznan.pl/jira/browse/WFE-513]













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h3. Showcase&nbsp;67. Integration Prerequisites Showcase&nbsp;(Rafa)

*Goal:* The objective of this showcase is to enable a better logging, debugging and interfacing infrastructures for the Recommender Service in order to enable its integration with myExperiment and the Collaboartion Spheres.

More precisely:
* Logging: Provide a significant logging mechanism (specially for the exchange of messages in the REST interface)
** Learn to use state of the art logging framework
** Implement the necessary logging code for the Recommender Service
* Debugging: Achieve graphical debugging using the Gephi environment
** Learn Gephi internal format
** Generate the Gephi representation
** Add operations to the interface to allow remote debugging
* Interfacing:
** Check myExperiment needs
** Check get the lastest updates in the myExperiment API&nbsp;
** Check Collaboration Spheres needs
** Implement myExperiment interfacing requests
** Implement Collaboration Spheres interfacing requests

Participants: Rafa (UPM), Don (myExperiment), Esteban, Alex (iSOCO)

jira:

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h3. Showcase&nbsp;54. Align RO Provenance Models with W3C PROV Ontology&nbsp;(Jun)

Refactoring of RO Evolution ontology also takes place here.

We do not execute this showcase in a formal sprint mode. Jun will write the alignment based on Raul's updates on the roevo model, and we will send out for comments from the project members.

Members: Raul and Dani and other project members

The mapping is currently documented in a google doc: [https://docs.google.com/spreadsheet/ccc?key=0Ahxrga9AQHb_dGJOcW9TOVdGbTdXRWcwUVJQbW1CbUE]. Anyone can view the document, but if you want to edit it you need to email Jun.

We will move the mapping to the project wiki once it is finalized or by the end of this sprint.


h3. Showcase&nbsp;56.&nbsp;Generate a corpus of provenance&nbsp;(Dani)

Member: Stian (help with generate Taverna logs), Jun, Pinar, Esteban, Pique, Khalid, and possibly others (help finding the right workflows).

*Goal: Generate a Corpus of provenance traces from Taverna and WINGS platforms.*

+Requirement+: The provenance traces should be modeled with the RO model. The Taverna export is necessary.

Plan:

# Identify a set of workflows to be rerun from myExperiment (Khalid, Pinar, Jun).
# Identify a set of workflows from the golden exemplars as well. (Since users are developing these workflows, we should have them in the corpus as well) (Esteban, Pique).
# Identify a set of workflows from Wings to be rerun (Dani).
# Create an index wiki page for the addition of the workflow entries.
# Rerun the workflows and store the results

h3. Showcase&nbsp;58. RO-Enabled myExperiment mock-up&nbsp;(Piotr/Pique)

Members:&nbsp;Piotr, Pique, Kristina, Marco, Oscar, Sean, Julian, Lourdes, any other user or Wf4Ever friend (James, Steve Petifer, Robert Stevens).


This is a showcase specifically designed to capture the desires of our users.&nbsp; The Wf4Ever user group are expected to take the leading role in this showcase. The resulting designs will be circulated to a wider user group for further input. This can be informed by the experience with the existing myExperiment interface but we made it clear it shouldn't be constrained by it.

Showcase outcomes page:&nbsp;?[Showcase 58 RO-Enabled myExperiment mock-up|docs:Showcase 58 RO-Enabled myExperiment mock-up]




Jira: Epic&nbsp;[WFE-528|https://jira.man.poznan.pl/jira/browse/WFE-528], Story&nbsp;[WFE-529|https://jira.man.poznan.pl/jira/browse/WFE-529],&nbsp;[WFE-563|https://jira.man.poznan.pl/jira/browse/WFE-563]




h3. Showcase&nbsp;72. First steps for a collaboration with related astro initiatives for an Astrotaverna enhancement&nbsp;(Pique)

{color:#000000}Members: Pique, Julian{color}

{color:#000000}Goal{color}{color:#000000}:{color}{color:#222222}&nbsp;This is a first approach to begin a collaboration for the integration of activities with several groups ({color}{color:#222222}[*VAMDC*|http://www.vamdc.eu/]{color}{color:#222222}, Observatoire de Paris, Observatorie de Strasbourg, Wf4Ever) that are working with the development of tools for workflow management in the astro domain. The main purpose of joining efforts is to avoid duplication of work done by others, be informed of the related work what we all are doing and if we would like to contribute and how. VAMDC project is interested for a potential integration of some of its plugins in Wf4Ever AstroTaverna pack, we all are also interested in adding access from Taverna to{color} {color:#222222}[*PDL-described web services*|http://pdl.obspm.fr/]{color}{color:#222222}, and astro group in Wf4Ever is particularly fond of &nbsp;using PDL to elaborate a semantic ontology for characterization of web services. Some of us in Wf4Ever have been thinking in adding some{color} {color:#222222}*[Aladin |http://aladin.u-strasbg.fr/]*{color}{color:#222222}tasks as plugins in AstroTaverna, since Aladin and Taverna are both developed in java I guess some kind of code re-use will really help.{color}

{color:#000000}Outcome: Most interest has been shown by Obs. Paris for collaboration around PDL study and Taverna integration of a client. Some PDL-described services have been already implemented in Obs. Paris. Development for a client access will provide the possibility to become a{color} {color:#000000}{_}de facto{_}{color} {color:#000000}standard in IVOA. As a first step the collaboration will be focused on the integration of a client access for generic services described with PDL XML&nbsp;{color}{color:#000000}using PDL Java API, a second step will be the development of a small ontology for generic services and tasks on the astro domain based on the study and improvement of PDL. Time schedule will take into account that some results should be exposed in the next IVOA Interop meeting to be held in late October/November.{color}

h3. Showcase&nbsp;61 Astronomy Golden Examplars&nbsp;(Susana)

Members: Lourdes, Pique, Julian, Juande and other IAA members

Goal:
* Make a design of the workflow
* Search the suitable Virtual Observatory services (includes inspecting what parts of NED database have VO services).
* Start a contact with the widely used NED database&nbsp;[http://ned.ipac.caltech.edu/] to explore to make it completely VO compliant.
* Test the different tools (GALFIT, ELLIPSE, scripts python, SEXTRACTOR) from Taverna.

Showcase web page: [Astronomy Golden Examplar|http://www.wf4ever-project.org/wiki/display/docs/Showcase+61+Astronomy+Golden+Examplars]



h3. Showcase&nbsp;65. Linking taxonomy of decay with minim models&nbsp;(Esteban)

Related to&nbsp;70.&nbsp;Workflow decay actions

The&nbsp; main goal of this showcase is to create a minin model or a set of them which allows the inclusion of the different defined decays at showcase 7.


Outcome: a definition of a minim model or a set of them which incorporates the different types of decays


Members: Jun and possibly Jose and Aleix

[Wiki page of the showcase |http://www.wf4ever-project.org/wiki/display/docs/Showcase+65+Linking+taxonomy+of+decay+with+minim+models]











h3. Showcase&nbsp;68. Improving the Wf4Ever APIs&nbsp;(Graham)

Aleix, Piotr, Rafa, Stian, Raul, Graham, Kevin (lurking)

See:
* [http://www.wf4ever-project.org/wiki/display/docs/Showcase+68+-+API+definition+and+implementation]
* [http://www.wf4ever-project.org/wiki/display/docs/Wf4Ever+service+APIs]

We have drafts of several APIs in various states. Original priorities have not been followed closely: we are focusing on the RO SRS API with aggregation and annotation capabilities. A sample client implementation is under construction. We are a bit behind on implementation because discussions about the RO API took longer that anticipated, but we have reached a number of very important points of consensus, which are relevant to the overall project architecture. See [http://www.wf4ever-project.org/wiki/display/docs/RO+SRS+interface+6+-+discussion]. Arguably this (RO SRS) is 3 APIs in one, as it also covers aggregation and annotation. We have also started discussion about the role and structure of the RO EVO API.

Progress summary:
* several draft APIs (cf. [http://www.wf4ever-project.org/wiki/display/docs/Wf4Ever+service+APIs])
* issues around making the RO SRS fully RESTful have been substantially resolved
* implementation of sample RO SRS is well under way and will hopefully be substantially done by Friday.
* participants have a better understanding of the characteristics and implications of using REST as an architectural style, which should inform future API specifications and implementations

Outstanding issues:

(Assuming that RO SRS implementation and RO EVO specification draft are completed by Friday)

* RO EVO implementation
* Workflow transformation API, based on current taverna->RO service - there is a sketch for this service, but it was not progressed during the sprint ([http://www.wf4ever-project.org/wiki/display/docs/Wf-RO+transformation+service])
* User management API
* Stability API client implementation
* Recommender API


h3. Showcase&nbsp;48. Round-trip myExperiment-Taverna-RODL (Kevin)

Mini-sprint wrapping up work from the previous period.
* Stian: finishing Taverna version history trace \-> roevo conversion (a day or two effort)
* Piotr: Any small supporting fixes with Stian.
* Don (post-sprint): tidying myExp RO UI so suitable for demo.

*Wiki:* [Showcase 48 - A first round-trip myExperiment integration|docs:Showcase 48 - A first round-trip myExperiment integration]



















h3. Showcase 49. Web site content updates (Oscar)

Goal: finish up the content from the website, as discussed during the PMB meeting

Members: Oscar. It will require some interactions with users and software developers, which will be requested by Oscar in due time.

h3. Showcase 62a. The 'Anni' Exemplar Workflow (The BioSemantics Concept Profile Method for prediction novel biological relations)

Goal: The goal of the showcase is to make the workflow from deliverable D6.3v1 run with the Anni web services (these were not implemented at the time of the creation of the original workflow). The workflow will be re-designed according to the 10 best practices for designing workflows and put on MyExperiment, the RO portal and t2web.

Members: Kristina, Marco, Reinout, Jun

Jira: Story [WFE-544|https://jira.man.poznan.pl/jira/browse/WFE-544]





Wiki: [Showcase 62a|http://www.wf4ever-project.org/wiki/display/docs/Showcase+62a+The+Anni+Exemplar+Workflow]



Summary: In sprint one we focussed on creating a high quality workflow, ready for preserving in a RO. Kristina Hettne did most work on the workflow and kept a blog. Reinout supported Kristina by adding operations, fixing services, and registering services on BioCatalogue. Marco supported Kristina in annotating the workflow and for some workflow components, e.g. by uploading subworkflows to myExperiment cf the 10 best practices.

Outcome: Workflow on myExperiment ([2973|http://www.myexperiment.org/workflows/2973.html]), and a pack containing the nested workflow and the workflows used for the components ([282|http://www.myexperiment.org/packs/282.html]).

h2. Sprint 6


h3. Showcase 61.part 2 (Susana)

Goal: Continuation

Members: Lourdes, Pique, Julian, Juande and other IAA members

Goal:
* Make a design of the workflow
* Search the suitable Virtual Observatory services (includes inspecting what parts of NED database have VO services).
* Start a contact with the widely used NED database&nbsp;[http://ned.ipac.caltech.edu/] to explore to make it completely VO compliant.
* Test the different tools (GALFIT, ELLIPSE, scripts python, SEXTRACTOR) from Taverna.

Showcase web page: [Astronomy Golden Examplar|http://www.wf4ever-project.org/wiki/display/docs/Showcase+61+Astronomy+Golden+Examplars]


h3. Showcase 62a. part 2 (Kristina)

Goal: Part II of showcase 62a, the Bio golden exemplar workflow, and work towards the SWAT4LS publication.

Members: Marco, Reinout, Graham (while available before holidays), Piotr (tiny bits), Stian (only if requiered)


Jira:

Wiki: [Showcase 62a part II|http://www.wf4ever-project.org/wiki/display/docs/Part+II]



Summary:&nbsp;
* Final tweaks and workflow validation (content-wise: validate with data from literature that the workflow performs the analysis it is supposed to do).
* ROification and provenance
* Outline of a paper for the Journal for Biomedical Semantics paper, SWAT4LS issue. (The sprint may also be used for two further papers in collaboration with Jun et al.)

Outcome: Final version of Bio golden exemplar for M22.


h3. Showcase 74. PROVO export in Taverna (Stian)

Goal: To enable the generation of PROVO provenance traces from workflow execution in the Taverna workbench. In combination with showcase 0, this will hopefully help unblocking much of the generation of a corpus of provenance traces.


Members: Khalid \(?), Dani, Aleix

Jira:

Wiki: [Showcase 74|http://www.wf4ever-project.org/wiki/display/docs/Show+case+backlogs#Showcasebacklogs-74.PROVOexportinTaverna]



Summary:


Outcome: PROVO-compliant Taverna plus sample provenance traces in PROVO

h2. Sprint 7


h3. Showcase 75. Hackaton preparations (Piotr)