Wf4Ever: Preserving workflows as digital Research Objects

EGI Community Forum 2012, Workflow Systems workshop

Leibniz Supercomputing Centre, Münich, 2012-03-28

Stian Soiland-Reyes myGrid, University of Manchester

2

My background

myExperiment - Web 3.0 virtual environment, library and social network for workflows

~5000 registered users

~2200 workflows

~21 different systems

Taverna - Scientific Workflow Management System

~85000 downloads

~EU projects: SCAPE, BioVeL, HELIO,

e-Lico, VPH-SHARE, EGI-INSPiRE….

http://www.myexperiment.org/

http://www.taverna.org.uk/

“A biologist would rather share their toothbrush than their gene name”

Mike Ashburner and others Professor in Dept of Genetics,

University of Cambridge, UK

“Facebook for Scientists” ...but different to Facebook!

A repository of research methods

A social network of people and things

A Social Virtual Research Environment

A probe into researcher behaviour

Open source (BSD) Ruby on Rails app

REST and SPARQL, Linked Data

Influenced BioCatalogue, MethodBox and SysMO-SEEK

myExperiment currently has 5378 members, 292 groups, 2273 workflows, 534 files and 217 packs

http://www.myexperiment.org/

http://www.myexperiment.org/workflows

http://www.wf4ever-project.org/

Workflow Preservation

Research Objects

Provenance

Recommendation

Astronomy and Genomics

7

» Scientific workflows enable automation of scientific methods and encourage best practices to be shared

» Workflows need to be preserved for

› Reuse, fundamental for incremental scientific development

› Method reproducibility, key for credit and publication

» Workflow preservation is complex!

» Heterogeneous types of information need to be aggregated, including workflows and related resources forming research objects

» Research objects need to be trusted and understandable n years from now

» Social aspects need to be addressed in order to support reuse in scientific communities

Challenges Wf4Ever

Preservation of scientific workflows in data-intensive science

Reusable. The key tenet of Research Objects is to support the sharing and reuse of data, methods and processes.

Repurposeable. Reuse may also involve the reuse of constituent parts of the Research Object.

Repeatable. There should be sufficient information in a Research Object to be able to repeat the study, perhaps years later.

Reproducible. A third party can start with the same inputs and methods and see if a prior result can be confirmed.

Replayable. Studies might involve single investigations that happen in milliseconds or protracted processes that take years.

Referenceable. If research objects are to augment or replace traditional publication methods, then they must be referenceable or citeable.

Revealable. Third parties must be able to audit the steps performed in the research in order to be convinced of the validity of results.

Respectful. Explicit representations of the provenance, lineage and flow of intellectual property.

The R.* dimensions

Replacing the Paper: The Twelve Rs of the e-Research Record” on http://blogs.nature.com/eresearch/

9

Forms of decay Wf4Ever

Workflow Decay • Service decay

• Flux/decay/unavailability

• Data decay • Formats/ids/standards

• Infrastructure decay • platform/resources

Experiment Decay • Methodological changes

• New technologies

• New resources/components

• New data

10

Preservation, Conservation, Recreating

Preserving Archived Record Fixed Snapshots Review Rerun & Replay

Conserving Active Instrument Live Rerun & Reuse Repair & Restore

Recreating Archived Record Active Instrument Live Rebuild Recycle Repurpose

11 http://www.gridworkflow.org/kwfgrid/gwes/docs/

Flux

Flux

Flux

Redo

Decay at different abstraction levels Workflow Decay

12

Research objects

13 13 13

Research Objects as Social Objects

14

Research Object model core (simplified) http://purl.org/wf4ever/ro#

ro:Resource ro:ResearchObject

ro:Manifest

ro:AggregatedAnnotation

ore:aggregates

ro:annotatesAggregatedResource

wfdesc:Workflow

ore:isDescribedBy

Note: This figure shows a simplified view of the RO core.

RO specification: http://wf4ever.github.com/ro/

15

Research Object model core http://purl.org/wf4ever/ro#

16

RO model: Workflow Description http://purl.org/wf4ever/wfdesc#

17

Workflow Provenance (wfprov) http://purl.org/wf4ever/wfprov#

18

Technical infrastructure

• Models Semantic Web Encoding

• Research Object

• Annotation

• Provenance

• Evolution and Versioning

• Services Web APIs, REST services

• Foundational, Extension, User

• APIs, Architecture

• Principles • Map into standards

• Adopt standards

• Lightweight components

• Ecosystem • Command line

• Portal

• Third party systems

19

Foundation Services

Extension Services

User Clients

Services The Wf4Ever Proposal

20

Lifecycle Services

Storage Services

Wf4Ever Reference Implementation

Access & Usage Clients

Data Management & Analysis Services

Stability

Evaluation

Completeness

Evaluation Recommender

RO Portal RO Manager Tool

RO Digital Library

ROBox

Dropbox Client

Prototype, Dec 2011

Taverna Workflow

Mgmt System

21

Year 1 (Dec 2010 Dec 2011) Roadmap

» Exploration (2011)

Problem specification and requirements identification

Better understanding of workflow preservation needs from the domains (what does it mean to preserve a scientific workflow?)

Proofs of concepts

Preliminary models, components, and integrated reference implementation

Result identification

22

Year 2 (Dec 2011 Dec 2012) Roadmap

Realization/validation (2012) › Validate the models, architectures and software in practice

› Distributed components with different access/security arrangements – forming REST APIs and specifications

› RO Content Campaign: Generate 1000s of ROs

› First productization phase: Stable releases of models and reference implementation

› Decay monitoring and notification (why my wf is no longer stable), reacting to decay, attribution and credit support beyond recommendation. Detailed use of provenance

› Execution and interoperability support (SHIWA integration)

23

Year 3 (Dec 2012 Dec 2013) Roadmap

» Exploitation (2013)

› Final productization phase

› Deployment in user environments and systems, enhanced with workflow preservation capabilities

› RO-enabled myExperiment

› RO-enabled Galaxy

› RO-enabled dataVerse

› … and more!

› Deployment in publishers e.g. Elsevier, Digital Science, GigaScience

24

Collaborations and impact

» SHIWA – Sharing Interoperable Workflows

» Publishers/journals: Elsevier, GigaScience (by BGI)

» OpenPHACTS (nanopublications)

» SCAPE (dataset preservation)

» BioVel (biodiversity - species preservation!)

» Dataverse (data repository)

» Galaxy (workflow system for genomics)

» GenomeSpace (data integration platform)

25

Thank you!

Any Questions?

http://www.wf4ever-project.org/

This work is licensed under the Creative Commons Attribution 3.0

Unported License. To view a copy of this license, visit

http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative

Commons, 444 Castro Street, Suite 900, Mountain View, California,

94041, USA.