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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

Sprint 1

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

Showcase: Initial RO Spec Draft

Sprint 2

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.

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

Showcase 6. A Taxonomy of Workflow Evolution (Pinar)

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

  1. Outline the drivers for evolution of workflows.
  2. Outline how evolution is handled in Scientific Workflow systems and repositories.
  3. Outline how evolution information could be exploited for preservation of workflows.
  4. 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, WFE-236

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

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

Goal: To come up with a characterization of:

  1. Potential causes of workflow/RO decay,
  2. Where they come from, where are the problems producing the decay originated,
  3. How they can be identified, and
  4. 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

ResultsTaxonomy of RO-Workflow Decay

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

  1. 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
  2. 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
  3. 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)
  4. 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.

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

JiraWFE-302

This showcase includes the following stories:

  • WFE-303 which represents the work to be done to create a wiki page
  • 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:  RO Examples

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

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:

<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  Stian Soiland-Reyes,  Duncan Hull,  Mustafa,  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>

-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.

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  the querying and end-users testing. The showcase description and main outcomes can be found at 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. 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.  It's write once read not possible. Biovel, wf4ever and scape need this and need to work together .

Epichttps://jira.man.poznan.pl/jira/browse/WFE-260, WFE-204

Storieshttps://jira.man.poznan.pl/jira/browse/WFE-261https://jira.man.poznan.pl/jira/browse/WFE-262

Marco: for some reason I could not see the Jira items. I would like to check if the items from the 'user view on provenance' table can be addressed by the proposed showcases.

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. 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 https://www.pivotaltracker.com/projects/495929. Stories tagged with "checkro" are in play for this showcase.

The main stories are:

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.

Sprint 3

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, 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 it), along with the annotations that have been placed both on the 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. We don't have sub-ROs yet.

Outcome: Results can be found at Showcase 12 RO visualization

Jira: Epic WFE-264, Story WFE-239

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.

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

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 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/

Showcase 21. RO testbed (Dani)

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

Outcome: RO testbed

Showcase 45 Collaboration Spheres Mockup (Esteban)

Jira issue: 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: The complete notes regaring the showcase can be found at: Collaboration+Spheres

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

Showcase 43. Best Practices for developing workflows (Kristina)

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

Background: 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. 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 presentationWorkflow Best Practices, Workflow Design Best Practices, and the sprint folder in Dropbox for the powerpoint and sources (Sprints -> Showcase43_BestPracticesWorkflowDesign)

Jira: Story WFE-413

Next steps: work this towards a publication and mapping to wf4ever results (in particular the Taxonomy of RO-Workflow Decay).

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

The Research Object Evolution model enables the representation of the different stages of the Research Objects life-cycle, 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 roevo Ontology and it is built on top of the core ro ontologies.

JIRAWFE-236

This showcase is related to three issues:

  • Conceptualization of RO evolution (WFE-256), including tasks for definition of terminology, evolution scenarios, and analysis of background material.
  • Implementation of RO evolution model (WFE-257), including the creation of the corresponding OWL ontology
  • Taxonomy of workflow changes (WFE-258)

Sprint 4

Showcase 8. Service substitution (Khalid)

Member: Dani and Jun

Jira: Story 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. The results of this showcase are reported in three wiki pages.

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

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

Daily chat: 16h CEST Link to chat

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

(2)VOTables management:

  1. 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.
  2. 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.
  3. 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
  4. 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
  5. 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: SAMP

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  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 
  • 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

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

Members: Graham,  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  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. Type: Decay 3 Type: Decay 5)

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 , and the work done is here.

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

Daily standup: 15:30 BST / 16:30 CESThttp://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

Showcase 49. Website content updates (Oscar)

Lead: Oscar

Member: Jose, Dave, and Jun

Wiki page: Showcase 49 - Website content updates

JIRA: WFE-477

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

Member: Raul, Piotrek, Oscar, Graham, Pique, Marco

Wiki Page: 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. As a first step for this showcase, the visualization was implemented in the RODL portal.

Sprint 5

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, Story WFE-239, WFE-513

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T Key Summary Assignee P Status Created Remaining Estimate
Technical task WFE-619 Implement easy-wins of taverna-prov Stian Soiland-Reyes Minor Open Sep 03, 2012 3 days
Technical task WFE-599 Installation instructions Stian Soiland-Reyes Major Resolved Jul 18, 2012
Technical task WFE-596 Taverna/wf-specific PROV-O extension Stian Soiland-Reyes Major In Progress Jul 17, 2012 2 days
Technical task WFE-595 Taverna Server support for PROV-O Stian Soiland-Reyes Major Resolved Jul 17, 2012 1 day
Technical task WFE-594 Command line support for PROV-O Stian Soiland-Reyes Major Resolved Jul 17, 2012 3 hours
Technical task WFE-585 Expose wfprov Stian Soiland-Reyes Major Open Jul 10, 2012 5 hours
Technical task WFE-584 Expose wfdesc Stian Soiland-Reyes Major Open Jul 10, 2012 5 hours
Technical task WFE-583 Expose provenance (untranslated) Stian Soiland-Reyes Major Open Jul 10, 2012 5 hours
Technical task WFE-582 Expose working directory Stian Soiland-Reyes Major Open Jul 10, 2012 5 hours
Technical task WFE-581 Expose output folder Stian Soiland-Reyes Major Open Jul 10, 2012 2 days
Technical task WFE-580 Expose input folder Stian Soiland-Reyes Major Open Jul 10, 2012 3 days
Technical task WFE-578 API specification for Workflow Runner Stian Soiland-Reyes Major Resolved Jun 27, 2012 0 minutes
Technical task WFE-524 Set up Taverna Server Stian Soiland-Reyes Blocker Resolved Jun 12, 2012 2 hours
Technical task WFE-522 Upload provenance/intermediate values to RODL Stian Soiland-Reyes Major Closed Jun 11, 2012 4 hours
Technical task WFE-521 Embed smaller values in RDF Stian Soiland-Reyes Minor Open Jun 11, 2012 1 day
Technical task WFE-520 Deploy PROV-O Taverna plugin (similar to Astro Taverna) Stian Soiland-Reyes Blocker Resolved Jun 11, 2012 0 minutes
Technical task WFE-519 Save intermediate values in structured folders(but avoid duplicates) Stian Soiland-Reyes Critical Resolved Jun 11, 2012 0 minutes
Technical task WFE-518 Add Data Bundle manifest (and scufl2 wf) Stian Soiland-Reyes Major Open Jun 11, 2012 1 day
Technical task WFE-517 Embed checksums/metadata of blobs Stian Soiland-Reyes Major Open Jun 11, 2012 4 hours
Technical task WFE-516 Relative links to saved data Stian Soiland-Reyes Major Resolved Jun 11, 2012 4 hours
Showing 20 out of 31 issues Refresh

Showcase 67. Integration Prerequisites Showcase (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 
    • Check Collaboration Spheres needs
    • Implement myExperiment interfacing requests
    • Implement Collaboration Spheres interfacing requests

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

jira:

Showcase 54. Align RO Provenance Models with W3C PROV Ontology (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.

Showcase 56. Generate a corpus of provenance (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:

  1. Identify a set of workflows to be rerun from myExperiment (Khalid, Pinar, Jun).
  2. 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).
  3. Identify a set of workflows from Wings to be rerun (Dani).
  4. Create an index wiki page for the addition of the workflow entries.
  5. Rerun the workflows and store the results

Showcase 58. RO-Enabled myExperiment mock-up (Piotr/Pique)

Members: 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.  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: ?Showcase 58 RO-Enabled myExperiment mock-up

Jira: Epic WFE-528, Story WFE-529WFE-563

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

Members: Pique, Julian

Goal: This is a first approach to begin a collaboration for the integration of activities with several groups (VAMDC, 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 PDL-described web services, and astro group in Wf4Ever is particularly fond of  using PDL to elaborate a semantic ontology for characterization of web services. Some of us in Wf4Ever have been thinking in adding some Aladin 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.

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 de facto 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 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.

Showcase 61 Astronomy Golden Examplars (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 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

Showcase 65. Linking taxonomy of decay with minim models (Esteban)

Related to 70. Workflow decay actions

The  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

Showcase 68. Improving the Wf4Ever APIs (Graham)

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

See:

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)

Showcase 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

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.

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

Wiki: Showcase 62a

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), and a pack containing the nested workflow and the workflows used for the components (282).

Sprint 6

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 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

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

Summary: 

  • 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.

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: Stian, Khalid, Jun, Pinar, Dani?

Jira: https://jira.man.poznan.pl/jira/browse/WFE-513

Wiki: Showcase 74

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T Key Summary Assignee P Status Created Remaining Estimate
Technical task WFE-619 Implement easy-wins of taverna-prov Stian Soiland-Reyes Minor Open Sep 03, 2012 3 days
Technical task WFE-599 Installation instructions Stian Soiland-Reyes Major Resolved Jul 18, 2012
Technical task WFE-596 Taverna/wf-specific PROV-O extension Stian Soiland-Reyes Major In Progress Jul 17, 2012 2 days
Technical task WFE-595 Taverna Server support for PROV-O Stian Soiland-Reyes Major Resolved Jul 17, 2012 1 day
Technical task WFE-594 Command line support for PROV-O Stian Soiland-Reyes Major Resolved Jul 17, 2012 3 hours
Technical task WFE-521 Embed smaller values in RDF Stian Soiland-Reyes Minor Open Jun 11, 2012 1 day
Technical task WFE-520 Deploy PROV-O Taverna plugin (similar to Astro Taverna) Stian Soiland-Reyes Blocker Resolved Jun 11, 2012 0 minutes
Technical task WFE-519 Save intermediate values in structured folders(but avoid duplicates) Stian Soiland-Reyes Critical Resolved Jun 11, 2012 0 minutes
Technical task WFE-518 Add Data Bundle manifest (and scufl2 wf) Stian Soiland-Reyes Major Open Jun 11, 2012 1 day
Technical task WFE-517 Embed checksums/metadata of blobs Stian Soiland-Reyes Major Open Jun 11, 2012 4 hours
Technical task WFE-516 Relative links to saved data Stian Soiland-Reyes Major Resolved Jun 11, 2012 4 hours
Technical task WFE-515 Update PROV-O export to use latest ontologyhttp://www.w3.org/TR/prov-o/ Stian Soiland-Reyes Blocker Resolved Jun 11, 2012 0 minutes
Technical task WFE-514 Check current PROV-O plugin from within Raven (Taverna's plugin system) Stian Soiland-Reyes Critical Resolved Jun 11, 2012 0 minutes
Story WFE-513 Taverna PROV-O export Stian Soiland-Reyes Critical In Progress Jun 11, 2012

Summary: There are three points that we will aim to achieve in this showcase:

1- Finish the implementation of PROVO export in Taverna to handle intermediate data

2- Checking and implementing the mappings between PROVO and wfprov.

3- Planing and generating workflow provenance corpos.

Given the above, I would suggest the following (optimistic) scheduling for the showcase.
(Phase 1 and Phase 2 will be done in parallel. Then Phase 3 and Phase 4 are run in parallel. The last stage is Phase 5. )

Phase 1- Stian will be implementing the rest of the Taverna provo export.
Time: 4 days
People: Stian

Phase 2- Others to examine the workflows that were identified in showcase 56 as executable 1. And define a strategy that we want to adopt for selecting the input values that will be used for the generation of the provenance of workflow results. Decide how the corpus that will be generated will be stored. A simple zip file, or what? A set of research objects, each of which with a workflow and its provenance traces? In this phase, we will focus on Taverna workflows. If Dani can make it, then we can include Wings workflows.
Time: 4 days
People: Jun, Pinar, Khalid, Dani?

Phase 3- Stian to check the mappings between PROVO and wfprov, to see if the mappings that Jun, Dani and Khalid agreed on.
Time: 1 day

Phase 4- Others, to start executing the workflows and generating the provenance corpus. (6 days)
Phase 5 - Implement the mappings provo <-> wfprov (5 days) ((Stian can start this phase when he finishes Phase 3))

The above planning is optimistic as most of us will be partly involved in the showcase.
I would suggest to go a head with this schedule, and if needs be, then we may need another showcase to complete the work.

1 http://www.wf4ever-project.org/wiki/display/docs/Provenance+corpus

Outcome: PROVO-compliant Taverna plus sample provenance traces in PROVO + wfprov <-> PROVO mappings + a workflow provenance corpos

Sprint Summer

Showcase 75. Hackaton preparations (Piotr)

Goal 1: discussions of the scope of work

Goal: To create user scenarios that will be implemented during the hackaton. User scenario must clearly define user expectations and be accompanied by a technical analysis that identifies actions for the hackaton and missing pieces, if any.

Results: In the hackaton, scenarios 1 and 3 from ?RO-enabled myExperiment user scenarios will be implemented. The technical analysis can be found at the Integration hackathon page.

Members: Piotr, Graham, Stian, Raul, Reinout, Don (scenario 1), Rafa, Aleix, Don (scenario 3).

Goal 2: pre-hackaton software development

Goal: To implement the software components that are necessary to do the integration during the hackaton. These include: installing an RODL instance for myExperiment, implementing and testing ROSR 6 in RODL and its clients, integrating recommendation service and collaboration spheres.

Members: Piotr, Don, Graham, Rafa, Aleix.

Jira issues

Things to do before the hackaton:

Loading
T Key Summary Assignee P Status Created Remaining Estimate
Story WFE-641 Add support for ROSR 6 API to RO manager Piotr Holubowicz Major Resolved Sep 05, 2012
Story WFE-640 Verify correct implementation of ROSR 6 API in RODL Piotr Holubowicz Major Resolved Sep 05, 2012
Technical task WFE-625 Investigate the options to upgrade the authorization framework in myExperiment from OAuth 1 to OAuth 2 (or other) Don Cruickshank Major Resolved Sep 05, 2012
Technical task WFE-624 Prepare an English dLibra installation instruction and a downloadable installer Piotr Holubowicz Blocker Resolved Sep 05, 2012
Story WFE-618 Prepare minim models that can rate resources Graham Klyne Major Resolved Aug 31, 2012
Story WFE-614 Make myExperiment display ROs from RODL Don Cruickshank Major Resolved Aug 29, 2012 1 day
Story WFE-613 Deploy an RODL instance for myExperiment Piotr Holubowicz Major Resolved Aug 29, 2012 1 day

Things planned for the hackaton:

Loading
T Key Summary Assignee P Status Created Remaining Estimate
Technical task WFE-682 Extract scufl2 bundle contents as RO resources Piotr Holubowicz Major Resolved Sep 25, 2012
Technical task WFE-681 Create a method for listing annotation bodies Stian Soiland-Reyes Major Open Sep 25, 2012
Technical task WFE-680 Create a stub implementation of getting t2flow annotations Stian Soiland-Reyes Major Resolved Sep 25, 2012
Technical task WFE-679 Show the annotation authors in Taverna Stian Soiland-Reyes Minor Open Sep 24, 2012
Story WFE-678 Create a Ruby client library for ROSR service. Graham Klyne Major Resolved Sep 24, 2012
Technical task WFE-677 Query RODL SPARQL endpoint for workflow annotations Stian Soiland-Reyes Major Open Sep 24, 2012
Story WFE-676 Add web services from wfdesc as aggregated resources Piotr Holubowicz Major Resolved Sep 24, 2012
Story WFE-659 Add RO annotation interface and mechanisms to myExperiment Don Cruickshank Major Resolved Sep 13, 2012
Technical task WFE-639 Creation of the first version the item-group/aggregation based algorithm Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Technical task WFE-638 Update Recommender Service REST API interface to the new storage mechanisms Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Technical task WFE-637 The Recommender Service should provide mechanisms to store the context of the recommendations Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Story WFE-636 Improve the integration between the Collaboration Spheres and Recommender Service Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Technical task WFE-635 The Collaboration Spheres use the SPARQL endpoint + myExperiment API for accessing to the different entities that (workflows, files, packs, users, etc.) Aleix Garrido Major Closed Sep 05, 2012
Technical task WFE-634 Deploy the new Collaboration Spheres webpage in the wf4ever sandbox Aleix Garrido Major Resolved Sep 05, 2012
Technical task WFE-633 Improve the tooltips and help of the Collaboration Spheres Aleix Garrido Major Closed Sep 05, 2012
Technical task WFE-632 Create a separate webpage for the Collaboration Spheres Aleix Garrido Major Closed Sep 05, 2012
Story WFE-631 Separate the "simple" list based interface from the advanced visualization mechanisms Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Technical task WFE-630 Add a button that allows the user accessing to the advanced recommendations webpage (i.e. the Collaboration Spheres webpage) Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Technical task WFE-629 Create simple web page that shows the results of the recommender Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Story WFE-628 Show a simple webpage with recommendations based on users profile and previous activities Rafael Gonzalez Cabero Major Resolved Sep 05, 2012
Showing 20 out of 25 issues Refresh

Showcase 80. ROification process in the development of M22 User Deliverables

In the process of packing digital methods and materials into a Multi-Wf Centric Research Object, there is a need for the users to understand the functionalities of RO Manager CLT as well as the different mappings of potential annotations to Wf4Ever models (wfdesc, wfprov, roevo, etc.)

Goals

  • Techs to assist users in the process of ROification of digital methods and materials for a given experiment.
  • Users to provide feedback on the use of RO Manager CLT and Wf4Ever models
  • To achieve a fully annotated and consistent RO for both M22 User Deliverables
  • Techs to record annotation patterns generated by users in a pattern catalog

Leading: Pique, Kristina

Members: Pique, Kristina, Julian, Graham, Raul, Jun, Daniel, Marco?, Stian?,  Piotr? 

Daily stand-up Skype chats: Mon 10am, Tue 10am, Wed 10am, Fri 12am

WikiROification process in the development of M22 User Deliverables

Sprint 7

Showcase 75. Hackaton preparations (Piotr)

Goal 1: discussions of the scope of work

Goal: To create user scenarios that will be implemented during the hackaton. User scenario must clearly define user expectations and be accompanied by a technical analysis that identifies actions for the hackaton and missing pieces, if any.

Results: In the hackaton, scenarios 1 and 3 from ?RO-enabled myExperiment user scenarios will be implemented. The technical analysis can be found at the Integration hackathon page.

Members: Piotr, Graham, Stian, Raul, Reinout, Don (scenario 1), Rafa, Aleix, Don (scenario 3).

Goal 2: pre-hackaton software development

Goal: To implement the software components that are necessary to do the integration during the hackaton. These include: installing an RODL instance for myExperiment, implementing and testing ROSR 6 in RODL and its clients, integrating recommendation service and collaboration spheres.

Members: Piotr, Don, Graham, Rafa, Aleix.

Showcase 80. ROification process in the development of M22 User Deliverables

In the process of packing digital methods and materials into a Multi-Wf Centric Research Object, there is a need for the users to understand the functionalities of RO Manager CLT as well as the different mappings of potential annotations to Wf4Ever models (wfdesc, wfprov, roevo, etc.)

Goals

  • Techs to assist users in the process of ROification of digital methods and materials for a given experiment.
  • Users to provide feedback on the use of RO Manager CLT and Wf4Ever models
  • To achieve a fully annotated and consistent RO for both M22 User Deliverables
  • Techs to record annotation patterns generated by users in a pattern catalog

Leading: Pique, Kristina

Members: Pique, Kristina, Julian, Graham, Raul, Jun, Daniel, Marco?, Stian?,  Piotr? 

Daily stand-up Skype chats: Mon 10am, Tue 10am, Wed 10am, Fri 12am

WikiROification process in the development of M22 User Deliverables

66. Integration of the stability service

Led by Aleix

Participant: Jun, Esteban, Raul and Graham

showcase 66

44. Workflow abstraction  (Esteban)

Participants: Pinar, Dani and Khalid

The general goals are indexing, classifying, and comparing workflows to make them more usable by scientist. This showcase is divided into serveral sprints and the objectives of the first sprint (44a) can be summarized as:

  • Definition of the wf4ever use case to be accomplished (p.e. assistive workflow design accesing to large workflow databases, see Daves mail thread 23/02/2012 [1])
  • Definition of semantic information which provides means to describe concrete workflows
  • Identification of similarity criteria at different levels of a workflow (process, sub-workflow, and workflow levels) and of the areas involved (SoA) (syntactic and semantic approaches)
  • Definition of an indexing structure

[1] https://lists.isoco.net/pipermail/wf4ever/2012-February/003191.html

74. PROVO export in Taverna 

Led by Khalid

Participants: Jun, Pinar, Stian, Dani?

The objectives of this showcase are:

  • To finish the implementation of PROVO export in Taverna to handle intermediate data
  • Check and implement the mappings between PROVO and wfprov.
  • To plan and generate a workflow provenance corpos.

showcase 74

81. Update checklist evaluation tool at RO Manger (Graham)

TODO: A showcase for recommender

Sprint 8

83. Creating a folder structure in an empty RO

The Wf-RO transformation should create an initial folder structure in a RO created from a workflow. This structure must be preserved in RODL and displayed in myExperiment.

Participants: Piotr, Don, Raul, Stian (consultations only), Finn.

84. Adding RODL Annotation support to myExperiment

The RO-enabled myExperiment must provide support for round-tripping the annotations to and from RODL. It must be possible for workflows to be associated with an RO and, once linked, annotations entered from myExperiment must be transferred to RODL and pulled back again when showing a workflows.

Participants: Don, Finn, Piotr, Kristina.

85. Improve RODL performance

The performance of RODL instance in the sandbox has been poor recently. This must be improved since RODL is a crucial component of the RO-enabled myExperiment. This issue related to both RODL implementation and sandbox server performance, and it also includes providing an option to create an RO by uploading a zip archive.

Participants: Filip, Piotr, (optionally Graham).

86. Investigate the possibility of using RightField for RO-ification

The RightField tool seems fit for creating mass annotations but it has one crucial limitation, which is the lack of possibility to select the subject of the annotations. The showcase objective is to investigate the source code of the tool and the possibility of implementing the missing feature, may be in cooperation with Stuart, the author of RightField.

Participants: Reinout, Kristina/Pique for user validation.

Updates for this showcase are added here: Showcase+86+example+spreadsheet

27.B Scientific Content Recommender

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

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.

Work description:

The objective of this showcase is to include external scientific content in the set of possible recommended items. We will start including content from OAI-PHM e-print services and repositories, since is an standard-driven way to access many OAI-PHM compliant repositories. The tasks to be done are:

Participants:Rafa

Sprint 9

83. Creating a folder structure in an empty RO (Finn)

The Wf-RO transformation should create an initial folder structure in a RO created from a workflow. This structure must be preserved in RODL and displayed in myExperiment.

Participants: Piotr, Finn and Don (0.5)

See Showcase 83. Creating a folder structure in an empty RO

Finn adding another level of abstraction to ROSRS Ruby client library to simplify RO manipulation (including creation of folders, adding resources to folders etc.).

84. Adding RODL Annotation support to myExperiment (Don)

The RO-enabled myExperiment must provide support for round-tripping the annotations to and from RODL. It must be possible for workflows to be associated with an RO and, once linked, annotations entered from myExperiment must be transferred to RODL and pulled back again when showing a workflows.

Participants: Don, Finn, Piotr, Kristina.

See Showcase 84. Adding RODL Annotation support to myExperiment.

86. Investigate the possibility of using RightField for RO-ification (Reinout)

Had discussions with Katy and Kristina. Will take a first step at enhancing the current Rightfield functionality for Kritina's annotation requirements.See this RightField and WF4Ever child page for more details.

Participants:Reinout, Kristina/Pique for user validation.

91. RO Evolution API implementation (Filip)

Showcase 91. RO Evolution API implementation

88. Provenance collection for myExperiment workflows using KEGG services (Jun)

Proposed members: Jun, Khalid (0.5), Aleix (possibly), Sean (part of it)

See show 88. provenance collection for Kegg workflows in myexperiment

44. Workflow abstraction (Esteban)

Integrate the API with the RO Portal

Goals:

  • To provide two services:
    • for recommending next process of a workflow based on previous defined processes (helping for designing)
    • for getting the workflows URIs given a sequence of defined processes that they match with.
  • Integrate these services into the portal by using also the provenance of workflow results as dataset.

Current status: developing the two processes is alsmost finished. From now an on we will work on the integration of the services into the portal.

Proposed members: Esteban, Raul and Aleix

25. User Feedback Handling (Rafa)

Requirement: As a researcher I want that the recommender system to take into account my feedback so that it can provide better tailored recommendations for me.

Goals:

  • To be able to handle users information related with the Recommender Service
    • Lots of users
    • We cannot assume that all of them are myExperiment users
  • To represent and store user feedback representation (both implicit and explicit)
  • To design recommendation algorithms that use effectively user's feedback

Actions:

  • Learn to use the Cassandra NOSQL database
  • Users
    • User representation creation (from the perspective of the Recommender Service)
    • Users information handling (Cassandra DAO creation)
  • User feedback handling
    • Feedback representation creation
    • Feedback handling (Cassandra DAO creation)
    • Recommender Service REST API interface update 
  • Recommendation algorithms
    • Algorithms results update research
    • Implementation of the possible updates

Member: Rafa

66b. (continue) Analytics based on the stability service. (Aleix)

Create and consume new roevo traces and final integration with the new checklist evaluation service available at the sanbox.

Member: Aleix

72. First steps for a collaboration with related astro initiatives for an Astrotaverna enhancement (Pique)

Work together with PDL visitors to verify our implementation.

Members: Pique and Julian

90. Preparing the M22 deliverable for scientific publication (Kristina)

Transform the M22 deliverable to a scientific publication. This relates to the extended abstract presented at SWAT4LS 2011. We have an invitation to submit it as a full-length manuscript to the Journal of Biomedical Semantics. Working title is: Applying a workflow-centric research object model to genomics workflow preservation.

Goal: Submit a manuscript to the Journal of Biomedical Semantics.

Members first sprint: Kristina, Harish, Marco, Reinout

Suggested members for next sprint: Kristina, Jun, Khalid, Oscar, Marco (Stian and Sean for support)

Sprint 10

Showcase 84. Improving the myExperiment RO interface (Don)

Showcase 97: Add folder support to ROSRS clients (Piotr)

Showcase 95. Displaying ROs in MyExperiment (Stian + Khalid)

Members: Stian, Khalid, Don

Stian and Khalid will take a look how to do presentation of RO in the UI. and Don will do the backend stuff

Showcase 96: Traffic light display from checklist results (Graham)

Showcase 87. Towards hundreds of myExperiment ROs (Dani)

Members: Dani, Rafa, Sean and Raul

Showcase 98. Add support for ROEVO to RO manager (Fillip)

Members: Fillip and Raul, and Graham, Susana and Kristina as the helpers

Showcase 66b. Analytics/Predictions based on the stability service (Aleix)

Showcase 44b. Macro annotation and categorization (Esteban)

Review sprint

Showcase 99. Prepare a live demo for the Y2 review

Members: Piotr (coordination), Marco, Kristina, Graham, Stian, Aleix, Rafa, Khalid, Filip, Don.

Progress: see ?Showcase 99. Prepare a live demo for the Y2 review

Sprint 12

114. Deliverable reissue (Jose) (Completed)

WP2-4 leaders launch reissue of deliverables D2.2v1, D3.2v1 and D4.2v1. Main changes will include new sections with content about design (description, UML diagrams, etc), implementation of the components, and place in the architecture. Updates must be consistent with each other, both content-wise and format-wise. We expect the reviewers' report in a couple weeks. The new version of the deliverables should be ready for QA by then.

Jose will coordinate the team consisting of Sean, Khalid, Oscar/Rafa, and Esteban.

115. Knowledge Hub kickstart  (Jun) (Completed)

Defining the strategy towards the creation of the Knowledge Hub, selection of domains, planning, and definition of milestones.

Main target domains:

  • Astronomy, IVOA (Lourdes, Pique)
  • Bio (Marco)
  • Business, through the alliance with TIMBUS (Sean, Kev, Raúl, others)
  • Publishers, through GigaScience (Marco)
  • Others: Scholarly (through Beyond the PDF) and research data (RDA)

Communication strategy, web site updates...

The goal of this sprint: OXF will lead on creating a preliminary structure of the knowledge hub front page and ask for content from Pique and Kristina, and others, including Sara.

Outcome: Wiki page documenting the structure of the knowledge hub

116. Golden ROs in the Web site (Kristina) (Completed)

Kistina to finalize the Bio RO and Miguel Angel to update the web site with both ROs from Astro (done) and Bio.

117. Wf4Ever community inbox (Jun) (Ongoing)

Enable a mechanism to receive input from the community, available from the Web site. There is a Wf4Ever Google group already created by Stian: wf4ever inbox

We are gathering also possible mailing lists to circulate the google group. This is recorded in a shared TitanPad page.
Jun: will circulate the inbox in various channels

All: sign up to the google group

Outcome: the showcase is complete because the knowledge hub is still not launched.

118. Complete the Y2 demo (Don) (Incomplete & Postponed)

Finalizing the implementation of cardboard parts in the demo. Outcomes:

  • Contribute to tooling development
  • Generation of materials for theKnolwedge Hub

Team: Piotr, Kristina, and Don
The goal of the sprint: produce a demo for the beyond pdf 2 workshop in <3 weeks time. Includes polishing up, a first cut at the provenance trace presentation in myExperiment, and possibly evolution UI.

119. Design of a new demo scenario in the publisher domain, with Gigascience (Marco and Pique) (Postponed)

Next scenario in our code-to-demo development approach. Marco et al.

Goal: Marco, and Kristina (?), Pique, and possibly Lourdes and Pitor will work on this together, to create a user scenario that will drive the next sprint

100. Analysis of KEGG workflows decay (Graham) (Completed)

123. RO bundle spec and API (Stian) (To be completed)

Piotr and Graham to be consulted for reviewing.

62d.Concept Profile creation workflow (Kristina) (Ongoing)

What: Concept profile matching is a knowledge discovery method that proved successful in generating hypotheses about molecular mechanisms explaining the results from genotype-phenotype studies. This technology has been implemented in the Anni standalone application (http://biosemantics.org/anni) and Web services (http://www.biocatalogue.org/services/3330). At the core of this technology are the concept profiles, which are currently generated using a number of custom scripts and manual operations.

Aim: To move towards a more customizable and service oriented architecture of the concept profile generation pipeline by developing a set of workflows and services that represent individual steps of the pipeline. To aid interoperability, Semantic Web standards will be adopted to interface with these components.

See Concept Profile creation child page

Whom: Kristina Hettne, BioSemantics Development team (lead: Eelke van de Horst), wf4ever liaison for ROification

44c. Discover workflow pattern similarities and linking (Esteban) (Completed)

This showcase aims to discover how similar are two workflows based on the shared parts that they have and link them.

The results of this showcase can be found at http://www.wf4ever-project.org/wiki/display/docs/44c.+Discover+workflow+pattern+similarities+and+linking

120. Annotate RO-enabled workflows with motifs (Khalid) (completed)

After discussion with Dani and Pinar, the objectve of this showcase was modified.

We are realising that we need to first agree on what should go in the motif otology. In this last week of the spint we can do that.

Progress: This sprint is completed. 

Purl of the ontology: http://purl.org/net/wf-motifs 

124. Improve the RO index and search in RODL (Filip and Raul) (Completed)

What: The RODL offers an OpenSearch interface based on dLibra. However, it provides only a basic search interface and cannot be used if the objects are not stored in dLibra. The goals of this showcase are to, in order of priority:

  • Configure a search & index service (Solr) for RO metadata. The service should index ROs using dynamic fields taken from semantic annotations. It may optionally index text documents in the ROs.
  • Connect the simple search interface to the Portal.
  • Design a simple faceted search interface for ROs. Either demonstrate how the Solr search interface can be used for that, or implement an intermediate RODL service that supports faceted search based on Solr.
  • Connect the faceted search interface to the Portal (and RO manager, optionally).

Who. Piotr, Filip, Raul

Showcase 124. Improve the RO index and search in RODL

125 AstroTaverna Paper (Pique) (Ongoing?)

What: Write down a paper to be published in Astronomy and Computing Journal, describing how AstroTaverna plugin and devels address identified needs in the domain of VO-based workflows. 

Whom: Pique, Julian, Juande, Stian, Susana, Lourdes

105.a Development of Taverna client/plugin for VO asynchronous web services (Julian) (Completed)

What: Development of a AstroTaverna plugin that could be used as a client to access VO-compliant web services. These web services are described via PDL standards (Parameter Description Language), and provide interoperability in the orchestration of web services. Most of these services are asynchronous (in principle), hence the plugin/client should manage asynchronous responses and service states in AstroTaverna. 

Whom: Julian, Pique, Carlo Maria Zwölf (Observatoire de Paris Meudon)

105.b Development of VO compliant asynchronous prototype web services (Pique and Julian) (Completed)

What: Development of prototype asynchronous web services described by PDL. These services will be used to check the validity of the developments related with the AstroTaverna client/plugin for PDL async services (previous SC 105.a) Similar services will be used in the 3rd Golden Exemplar, and as the ones conceived and developed in this prototype they should be compliant with IVOA standards (DALI, UWS, SIAP, PDL)

Whom: Carlo Maria Zwölf (Observatoire de Paris Meudon), Pique, Julian

Sprint 13

118. Completing the Y2 demo (Don)

In this sprint, this showcase will be led by Kristina's need of finishing up her RO application ppaer, whose deadline is May 3.

Showcase+118.+Complete+the+Y2+Demo

119. Design of a new demo scenario in the publisher domain, with Gigascience (Jun)

This showcase uses a GigaScience publication and encode its essential experiment information using the RO model, nanopublication and ISA model. The goal is to investigate how these three models could work together to enhance a scholarly article. The showcase is expected to be run over several sprint.

And in Sprint 13, we aim to achieve the following:

  • Identify the case study article
  • Identify the material to be encoded in an RO

Progress by April 9:

  • Identified a case study article to work with
  • Created a simple RO using alpha myexperiment (pack 398)
  • Raised any related RO creation issues to Don
  • Continuing communication with Peter Li for missing data and related information

Progress by April 17:

  • No further progress on the case study, blocked by the ISA team

127. Development of RO Community Portal Web site (Jun)

This showcase was approved in the PMB meeting (2013-0326) as a high priority task and we will work together with the nanopublication community to build this web site as a sister project.

The goal is to release researchobject.org at the end of the sprint.

Progress by April 9:

  • Drafted some key content and shared in the project dropbox folder: wf4ever/resources and figures/RO publicity web site/
  • Received feedback from Khalid and help from Kristina, Pique and Piotr
  • Drafted project content and function requirements and passed to external web designer
  • Expecting some delay on the launching because the design works part-time
  • Plugged this activity in the nanopublication bi-weekly call, as well as our launch of the ROSC community group

Progress by April 17:

  • Have an initial function agreement with the web designer (ongoing)
  • Received helpful feedback from Susana Garcia, who will continue helping me with the content in the next few weeks
  • Publish initial charter for the ROSC CG (ongoing)
  • Received feedback from Carole and will integrate them

129. Notification service in RODL (Piotr)

What. Our long term goal is to add more advanced and proactive preservation features to RODL, in particular by integrating RODL with dArceo (a preservation system made by PSNC). As the first step towards this goal, we want to add a notification service to RODL, which will allow to notify users in case of events related to their Research Objects. Depending on the progress, the notifications generated by the end of the 2-week showcase may be based on real or mock events.

Who. Piotr, Filip, Users.

123. RO bundle spec and API (Stian)

Wrap up left overs from last sprint.

120. Annotate RO-enabled workflows with motifs (Khalid)

Progress: This showcase can be considered as completed. 

Purl of the ontology: http://purl.org/net/wf-motifs 

131. A minimal model for annotating workflow/components (In collaboration with Biovel and Scape projects) (khalid and Stian)

The objective of this showcase is to create a (sort of) minimal model that can be used to specify the terms (and vocabularies) that can be used to specify annotations for Taverna workflows and component using an XML format that was created by the developers in Scape and adopted by Biovel later.

Progress: Stian and Khalid created a spreadsheet to collect information about the terms that can be used for annotating and creating the Taverna workflow (component) profile. That has been done, and now Stian is working with Alan and Donal to create the profile using an XML representation that Alan and Donal are using.

27.B Scientific Content Recommender (Rafa)

Update current paper ingestion tool (OAI-PMH) so that it can use Solr as an indexer. 

126. Generate RO Monitoring traces for existing ROs (Aleix)

The main goal of this showcase is to extend the work that was done for the Y2 review related with the "stability service" which has changed to "RO monitoring". Insetad of capture the data for a unique RO we aim to do it for a set of existing ROs over time. The algorithm will run against the RO with a defined time frequency and the results will be available in xml and json.

Participants: Aleix

44b. Macro annotation and categorization (Esteban)

This showcase will annotate the different macros which are dicovered by showcase 44a. This annotation may should be done manually providing the user expertise into the system. The main outcome of this showcase will be the annotated set of sub-workflows identified at 44a and the updated trie structure including this annotations into it.

Related links: http://www.wf4ever-project.org/wiki/display/docs/Short-term+workplan

128. Evaluate checklist toolkit (Graham)

We completed an evaluation for the current tool by running the Kegg case study in showcase 108. In this showcase, we will evaluate the capability of the toolkit against Matt's MIM service and other quality service for open Linked Data. This will be input to D4.3 and D4.2v2.

See: http://www.wf4ever-project.org/wiki/display/docs/Showcase+128+-+Evaluate+checklist+toolkit

130. School on Workflows for Spanish Virtual Observatory (Pique)

What: Hands-on school on workflows to be held in European Space Agency Center (ESAC) in Madrid, on April 5th 2013. Design and prepare the program for the school, develop a set of workflows to work with in the hands-on session. Discuss and design roadmap to introduce workflows in the spanish astronomical community with the help of Spanish Virtual Observatory (SVO)

Benefits: Community engagement

Whom: IAA

106. AstroTaverna "hello world" examples / starter pack (Pique)

What: Develop small workflows that show how AstroTaverna can be used, these workflows should be representative enought in astronomy research and astronomy digital experiments. They will be added to AstroTaverna as a StarterPack Perspective in order to allow astronomers learn by example.

Benefits: Community engagement

Whom: IAA

62d. Concept Profile creation workflow (Kristina)

This showcase needs to go over several sprints. See child page

133. Knowledge Hub Actual Setup (Sara)

This showcase needs to go over several sprints.

(Sara) The first document identified as a priority to start the Knowledge Hub has been a document as: "Best practices for Archival Processing for Research Objects" (similar to this one for geospatial datasets:http://www.geomapp.net/docs/GIS_Archival_Processing_Process_v1.0_final_20111102.pdf)

I'm setting possible parallels between the document that we have taken as example and the work on the architecture that Wf4Ever has done (although the geospatial document only refers to the archival ingest functionality). As a result, I am designing a template. The methodology thought to develop the document consists of the following steps:

  1. [Design a scheme of the mapping to OAIS functions] Draw the parallel between the functionalities required by a scientific workflow preservation infrastructure --described in D1.3v2- and those functions established by OAIS.
  2. Think about process steps and key questions for the repository with regard to each function of the OAIS mapping.
  3. Finally, establish recommended best practices for each process step/question.

Other documents deemed relevant for the KH would be the following best practices (proposal):

  • Archival metadata elements for the preservation of research objects
  • Guide to design a workflow preservation plan
  • High-level architecture model for RO repositories

(17th of April/Sara)  Coordinating the work to develop the "Best Practices for Archival Processing of ROs" and "Archival Metadata Elements for the preservation of RO" documents. We hope to progress with these two documents for the next week.

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Page: 44c. Discover workflow pattern similarities and linking Page: KnowledgeHub Brainstorming Page: ROification process in the development of M22 User Deliverables Page: Shocase 87 - Towards hundreds of myExperiment ROs Page: show 88. provenance collection for Kegg workflows in myexperiment Page: Showcase 9 Astrotaverna Page: Showcase 12 RO visualization Page: Showcase 43 Best Practices for developing workflows Page: Showcase 44a Workflow Abstraction Page: Showcase 50. Visualization of RO evolution Page: Showcase 53 Nanopublications meet Research Objects Page: Showcase 58 RO-Enabled myExperiment mock-up Page: Showcase 61 Astronomy Golden Examplars Page: Showcase 62a The Anni Exemplar Workflow Page: Showcase 62d.Concept Profile creation workflow Page: Showcase 65 Linking taxonomy of decay with minim models Page: Showcase 74 Taverna PROVO export, Mapings between PROVO and wfprov, and Workflow Provenance Corpus Page: Showcase 83. Creating a folder structure in an empty RO Page: Showcase 84. Adding RODL Annotation support to myExperiment Page: Showcase 86 example spreadsheet Page: Showcase 90. Preparing the M22 deliverable for scientific publication Page: Showcase 91. RO Evolution API implementation Page: Showcase 95 - Displaying ROs in MyExperiment Page: Showcase 96 - traffic light display for checklist evaluation Page: Showcase 97. Add support for folders to the ROSRS client Page: Showcase 99. Prepare a live demo for the Y2 review Page: Showcase 100. Analysis of KEGG workflows decay Page: Showcase 116. Golden ROs in the Web site Page: Showcase 118. Complete the Y2 Demo Page: Showcase 123 RO bundle spec and API Page: Showcase 124. Improve the RO index and search in RODL Page: Showcase 128 - Evaluate checklist toolkit Page: Showcase 129. The notification service