David De Roure, Sean Bechhofer, Carole Goble, David Newman

sean.bechhofer@manchester.ac.uk @seanbechhofer

http://humblyreport.wordpress.com

1st International Workshop on Social Object Networks (SocialObjects 2011), Boston, October 9th 2011.

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Scientific Social Objects

•  Workflows are the new rock and roll!

•  Machinery for coordinating the execution of services and linking together resources

•  Scientist friendly (for some class of scientists)

•  Repetitive and mundane boring stuff made easier •  Enable automation

•  Make science repeatable (and sometimes reproducible)

•  Encourage best practices

•  Shareable Carole  Goble  

E. Science laboris

•  Paul writes workflows for identifying biological pathways implicated in resistance to Trypanosomiasis in cattle

•  Paul meets Jo. Jo is investigating Whipworm in mouse.

•  Jo reuses one of Paul’s workflow without change.

•  Jo identifies the biological pathways involved in sex dependence in the mouse model, believed to be involved in the ability of mice to expel the parasite.

•  Previously a manual two year study by Jo had failed to do this.

Carole  Goble  

Reuse, Recycle, Repurpose

“There are these great collaboration tools that 12-year-olds are using. It’s all back to front.”���

Robert Stevens

Carole Goble e-Science is me-Science: What do Scientists want? EGEE, 2006

  A sharing platform for scientists

  A repository of research methods

  A community social network of people and things

  A Social Virtual Research Environment

  A probe into researcher behaviour

  Distinctive features supporting credit and attribution

  Open source (BSD) Ruby on Rails app

  REST and SPARQL interfaces, supports Linked Data

  Part of product family including BioCatalogue, MethodBox and SysmoDB

~4700  members,  270  groups,  ~2000  workflows,  ~200packs  

myExperiment

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myExperiment

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myExperiment Content

•  User accounts

–  Groups –  Friendships

•  Various types of Contributables –  Workflows, files, presentations

–  Versions

–  Compositions   Workflows – services, tasks

  Packs – workflows, files, URIs.

•  Annotations –  Attribution, Credit, Ratings, Tags,

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Scenario: Sharing Workflows

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Scenario: Finding Help

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Scenario: Matching Tasks

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Search Engine

reviews ratings

groups

friendships

tags

Enactor

files

workflows

HTML  

RDF Store

SPA

RQ

L en

dpoi

nt

Managed REST API

facebo

ok  

iGoo

gle  

android  

XML  

API  config  

mySQL

profiles

packs

credits

myExperiment For Developers

reviews ratings

groups

friendships

tags

files

workflows RDF Store

SPA

RQ

L en

dpoi

nt

mySQL

profiles

packs

credits

Modularised  myExperiment  Ontology  

myExperiment  data  model  (evolving!)  

rdf.myexperiment.org  

DC,  FOAF,  SIOC  (Seman8cally-­‐Interlinked  Online  Communi8es)  

Tran

sfor

m

SPARQL endpoint

SPARQL endpoint

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It is effectively a generic API whereby the user can specify exactly what information they want to send and what they expect back -- rather than providing query/access mechanism via specific API functions. In some ways it has the versatility of querying the myExperiment database directly, but with the significant benefit of a common data model which is independent of the codebase, and through use of OWL and RDF it is immediately interoperable with available tooling. Exposing data in this way is an example of the cooperate don't control principle of Web 2.0.

Use of existing vocabularies (FOAF, SIOC etc) allows for mashup/integration with other sources. Packs can also link to external resources. Links out and Links in to to the “Linked Data Cloud”.

Users

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Things

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Community Sharing

Personal Preservation

Friendships

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SELECT ?requester ?accepter WHERE { ?membership rdf:type mebase:Friendship. ?membership mebase:has-requester ?requester. ?membership mebase:has-accepter ?accepter. }

Groups

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SELECT ?group ?user WHERE { ?group rdf:type mebase:Group. ?group sioc:has_member ?user. }

Tagging

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SELECT ?wf ?user WHERE { ?wf rdf:type mecontrib:Workflow. ?t mebase:annotates ?wf; rdf:type meannot:Tagging; mebase:has-annotator ?user. }

Packs and Contents

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SELECT?pack ?contrib WHERE { ?pack rdf:type mepack:Pack. ?pack ore:aggregates ?contrib. }

Workflows and services

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SELECT?wf ?uri WHERE { ?wf mebase:has-current-version ?v. ?v mecomp:executes-dataflow ?d. ?d mecomp:has-component ?c. ?c rdf:type mecomp:WSDLProcessor. ?c mecomp:processor-uri ?uri. }

Research Objects: Beyond the Pack •  Argumentation: Convince the reader of the ���

validity of a position [Mesirov]

–  Reproducible Results System: facilitates enactment and publication of reproducible research.

•  Results are reinforced by reproducability [De Roure]

–  Explicit representation of method.

•  Verifiability as a key factor in scientific discovery.

J. Mesirov Accessible Reproducible Research Science 327(5964), p.415-416, 2010 http://dx.doi.org/10.1126/science.1179653

D. De Roure and C. Goble Anchors in Shifting Sand: the Primacy of Method in the Web of Data Web Science Conference 2010, Raleigh NC, 2010 http://eprints.ecs.soton.ac.uk/20817/

Stodden et. al. Reproducible Research: Addressing the Need for Data and Code Sharing in Computational Science Computing in Science and Engineering 12(5), p.8-13, 2010 http://dx.doi.org/10.1109/MCSE.2010.113

Research Objects as Social Objects

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Research Objects as Social Objects

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Research Objects

•  Aggregations intended to foster Reuse, Repurposing and Repeatability of investigations

•  A generalisation of the pack •  Rich social interactions

–  Sharable –  Citeable

–  Credit and Attribution –  Provenance

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Wf4Ever

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…technological infrastructure for the preservation and efficient retrieval and reuse of scientific workflows in a range of disciplines.

FP7 Digital Libraries and Digital Preservation iSOCO, University of Manchester, Universidad Politécnica de Madrid, University of Oxford, Poznan Supercomputing and Networking Centre, Instituto de Astrofísica de Andalucía, Leiden University Medical Centre

•  Architecture/implementation for workflow preservation, sharing and reuse

•  Research Object models •  Workflow Decay, Integrity and Authenticity

•  Workflow Evolution and Recommendation •  Provenance

•  Driven by Use Cases

Astronomers Questions When accessing a workflow •  Can I use it for my purposes (in my

words)? •  If I can expect it to run, when was

it was last run, by whom? •  What it does quickly, by one of

–  example input / output (and trying it) –  a description –  ‘reading’ its key parts

–  what it was used for –  related workflows its creator –  contacting the creator or last user

•  How I need to cite the author and workflow?

When sharing a workflow •  What rights others have?

•  What a good workflow is to get a good score?

–  Make my workflow findable, reusable, and ready for review

–  Instructions to authors –  Two types of contributions: serious

science, preliminary/playing around

•  If my workflow may have issues –  What the system or other users think

it does

•  How it relates to other things

•  Share freely or anonymously upon request?

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Other Work

•  Volume of data is not enough, but additional consideration of content could help us.

•  Approach also being considered for recommendation in Wf4Ever.

•  Organising workflows into categories. Now available as “Topics” tab.

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Wei Tan, Jia Zhang, Ian Foster Network Analysis of Scientific Workflows: A Gateway to Reuse IEEE Computer 43(9) pp54-61 http://dx.doi.org/10.1109/MC.2010.262

Jia Zhang Wei Tan, John Alexander, Ian Foster, Ravi Madduri, Recommend-As-You-Go: A Novel Approach Supporting Services-Oriented Scientific Workflow Reuse, Proceedings of the 2011 IEEE International Conference on Services Computing, 2011 http://dx.doi.org/10.1109/SCC.2011.120

Julia Stoyanovich, Ben Taskar, and Susan Davidson Exploring Repositories of Scientific Workflows WANDS 2010 http://wands2010.doc.ic.ac.uk/

Wrap up

•  myExperiment as a platform for sharing

–  Contributables, Annotations, Users –  APIs RDF/SPARQL endpoints

–  Come and play! •  Workflows (and their constituent parts) as social objects

•  Various networks layered on those objects

•  Compositional nature of the objects –  Workflows combining services

–  Packs combining objects •  Research Object as a future vision for composite Scientific

Social Objects

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Thanks!

•  myExperimentTeam

–  http://www.myexperiment.org/ •  Wf4Ever Team

–  http://www.wf4ever-project.org/ •  Manchester Information Management Group

–  http://img.cs.manchester.ac.uk

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