Towards Lensfield

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Lensfield is a desktop and filesystem-based tool designed as a “personal data management assistant” for the scientist. It combines distributed version control (DVCS), software transaction memory (STM) and linked open data (LOD) publishing to create a novel data management, processing and publication tool. The application “just looks after” these technologies for the scientist, providing simple interfaces for typical uses. It is built with Clojure and includes macros which define steps in a common workflow. Functions and Java libraries provide facilities for automatic processing of data which is ultimately published as RDF in a web application. The progress of data processing is tracked by a fine-grained data structure that can be serialized to disk, with the potential to include manual steps and programmatic interrupts in largely automated processes through seamless resumption. Flexibility in operation and minimizing barriers to adoption are major design features.

Technology

Towards Lensﬁeld: data
management, processing and
semantic publication
for vernacular e-science

Nick Day, Jim Downing, Lezan Hawizy, Nico Adams and
Peter Murray-Rust
Unilever Centre for Molecular Science Informatics,
University of Cambridge

This presentation: CC-By-SA Jim Downing

Linked Data

CC-By-SA-NC jmelchio

CC Images from Flickr

Selling Linked
Data
Make it transparent
Make it easy

CC-By mrslogic

Selling Linked Data

• Visualizations
• Data management
• Automation

Lensﬁeld Principles

• Make it easier to do the right thing
• Vernacular
• KISS and Embrace constraints

Constraints

• Work on the desktop without
infrastructure installation
• Processing tasks could be anything and
aren’t predictable

Jumbo-Converters
• Library of chemistry ﬁle format
converters, semantiﬁers and enhancers
• Part of the CML Java libraries
• http://sourceforge.net/projects/cml/

Version Control
• Mercurial • Track script changes
with data
• Excellent support for
experimentation • Automatically ignore
deterministic
• Backup to remote intermediates
machine

• P2P sharing

Build metaphor

• Describing state transitions rather than
process better for provenance tracking
• Alternative to graphical programming
languages / workﬂow packages
• hard problems are re-use and
comprehension

Clojure
• Strong on concurrency
• Functional
• Software Transactional Memory
• Lisp
• Snapshots, pause and resume,
continuations

Future Development

• Templated Parameter Sweeps & sensitivity
analysis
• Design of Experiments
• Multicore performance testing
• Grid processing

Users
• CLARION project
• Embargo management and publication of
Electronic Lab Notebook data.
• OREChem
• Distributed chemistry eScience using
Linked Data.
• Computational Chemical engineering

http://code.google.com/p/lensﬁeld/

CC-By-NC ilonameagher

Users
You?

... to use Lensﬁeld!

Thanks
Colleagues Funds
Nick Day
John Aspden
Lezan Hawizy
Peter Murray-Rust
Collaboration and Inspiration
Nico Adams (Dept of Genetics, Cambridge)
Jerry Winter (Unilever)
Noel Ruddock (Unilever)
Markus Kraft, Weerapong Phadungsukanan (Chemical
Engineering, Cambridge)

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Towards Lensfield

1. Towards Lensﬁeld: data management, processing and semantic publication for vernacular e-science Nick Day, Jim Downing, Lezan Hawizy, Nico Adams and Peter Murray-Rust Unilever Centre for Molecular Science Informatics, University of Cambridge This presentation: CC-By-SA Jim Downing

2. Linked Data CC-By-SA-NC jmelchio CC Images from Flickr

3. Selling Linked Data Make it transparent Make it easy CC-By mrslogic

4. Selling Linked Data Citations

5. Selling Linked Data • Visualizations • Data management • Automation

7. Demo http://code.google.com/p/lensﬁeld/

8. Lensﬁeld Principles • Make it easier to do the right thing • Vernacular • KISS and Embrace constraints

9. Constraints • Work on the desktop without infrastructure installation • Processing tasks could be anything and aren’t predictable

10. Re-use

11. Jumbo-Converters • Library of chemistry ﬁle format converters, semantiﬁers and enhancers • Part of the CML Java libraries • http://sourceforge.net/projects/cml/

12. Version Control • Mercurial • Track script changes with data • Excellent support for experimentation • Automatically ignore deterministic • Backup to remote intermediates machine • P2P sharing

13. Build metaphor • Describing state transitions rather than process better for provenance tracking • Alternative to graphical programming languages / workﬂow packages • hard problems are re-use and comprehension

14. Clojure • Strong on concurrency • Functional • Software Transactional Memory • Lisp • Snapshots, pause and resume, continuations

15. Future Development • Templated Parameter Sweeps & sensitivity analysis • Design of Experiments • Multicore performance testing • Grid processing

16. http://fascinator.usq.edu.au/

17. Users • CLARION project • Embargo management and publication of Electronic Lab Notebook data. • OREChem • Distributed chemistry eScience using Linked Data. • Computational Chemical engineering

18. http://code.google.com/p/lensﬁeld/ CC-By-NC ilonameagher Users You? ... to use Lensﬁeld!

19. Thanks Colleagues Funds Nick Day John Aspden Lezan Hawizy Peter Murray-Rust Collaboration and Inspiration Nico Adams (Dept of Genetics, Cambridge) Jerry Winter (Unilever) Noel Ruddock (Unilever) Markus Kraft, Weerapong Phadungsukanan (Chemical Engineering, Cambridge)

Towards Lensfield

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