Capturing Process

Richard Grant Mat Todd Hide Plausible Accuracy Pedro Beltrao John Branwen Rich Apodaca Dupuis Neil Saunders Steve Wilson Simon Coles Noel Tony Hey Pawel SzcsesnyRichard Akerman Gorelick Dave de Roure Jon Tim O’Reilly Victoria Stodden Jeremy Frey ISIS LSS Group Udell Jean-Claude Bradley Jeremiah Faith Martyn Bull Michael Barton John Cumbers Clay Shirky Bora David Crotty Helen Egon Willighagen Brian Kelly Tony Williams Tim O’Reilly Berman Zivkovic Maxine Clarke Andrew Michael Nielsen Frank Mitch Martin Fenner Milsted Jenny Rohn NormanWaldrop Wilson Greg Yaroslav Nikolaev Iain Emsley Rafael Sidi Lee Smolin Lorie LeJeune JonathanHooker Bill Timo Hannay Gray Ken Shankland Paulo Nuin Deepak Singh Shirley Wu Liz Lyons PLoS STFC Friendfeed Peter Binfield Benjamin Good Dorothea Salo Peter Murray-Rust Richard Akerman Jen Dodd Chad Orzel Lakshmi Shastry ISIS Computing Group Jon Eisen Jenny Hale ciFoo 2008 Flanagan Bill Matt Wood Michael Eisen Jon Tansley Victor HenningGoogle Björn Brembs campers Rufus Pollock John TIM HUBBARD Gavin Bell Andy Powell Harry Collins Wilbanks Mike Ellis Garret Lisi DUNCAN HULL Euan Adie Peter Suber Gavin Baker The BioGang Sabine Hossenfelder Paul Walk Flickr Kevin Kelly Kaitlin Thaney Richard Curry Atilla Csordas Ian Mulvaney

Capturing Process In silico, in the lab, and all the messy in betweens

Laboratory Computational procedures procedures Procedure Experiment Analysis Data Data Material(s) Sample(s) Physical objects Digital objects

http://www.ﬂickr.com/photos/halfchinese/113968722 CC-BY

Data is dynamic... http://www.ﬂickr.com/photos/idletype/282855293/ CC-BY

Inspiration from coding best practice Repositories for storage/backup Strong record of who and when Roll-back, diffs, and reversion Testing as part of the process Scripting for solid replication

Working independently... http://www.ﬂickr.com/photos/tswicegood/3233621766/ CC-BY-SA

...data integration http://www.ﬂickr.com/photos/tbisaacs/3087193160/ CC-BY

...but commits are freetext

DVCS systems can provide who, when, what and differences between versions But it doesn’t provide the relationships between objects...

Have a good provenance trail... http://www.ﬂickr.com/photos/a4gpa/195354385 CC-BY-SA

...but not a good map of how that relates to everything else http://www.ﬂickr.com/photos/normanbleventhalmapcenter/2674855383 CC-BY

If we have the map... ...if we capture the connections

http://is.gd/thVr

...and on to a semantic web of data

...but what about in here? http://www.ﬂickr.com/photos/mararie/2151361243 CC-BY-SA

Lab book as a journal... http://www.ﬂickr.com/photos/nbachiyski/2186228572 CC-BY

Blog as journal...

Description, date categorisation, objects, identity, accessibility... ...not of much interest to most people

http://biolab.isis.rl.ac.uk/projects/blog/

http://is.gd/thMB

Laboratory Computational procedures procedures Procedure Experiment Analysis Data Data Material(s) Sample(s) Physical objects Digital objects

A web of objects...

A web of objects... ...and the process that connects them

...but still not semantic

Tagging goes some way... ...but how to enforce tagging?

Templates create a virtuous circle [table] [row] Lane[col]Sample[col]ul [/row] … [row] 4[col][[Dna:%]][col][[box]] [/row] … [/table] [[Section>Procedure]] [[Procedure_Type>electrophoresis_agarose]] [[Sandpit_group>DrexelDemo]]

Self assembling ontology? Sequence ontology: SO:0000696 “oligo” SO:0000155 “plasmid” ...but... SO:0000006 “PCR product” or SO:0000412 “rest. fragment”? Mixing up of process of production and material type?

We need a robust ontology or controlled vocabulary for experiments... ...but with that in hand http://www.ﬂickr.com/photos/peterkaminski/5444915 CC-BY

We can build a semantic web of objects ...and the processes that connect them

Linked open data and linked open objects http://is.gd/thVr

Building for the future? http://www.ﬂickr.com/photos/blahﬂowers/1382374610 CC-BY-SA

Capture it at source... ...in context http://ﬂickr.com/photos/jason_burmeister/2053139930 CC-BY

Capture as much as possible automatically Slide adapted from original by Simon Coles

In silico capture the process step by step... http://www.ﬂickr.com/photos/stevoarnold/2787234769 CC-BY

In silico capture the process step by step... ...one way or another the semantics can be baked in http://www.ﬂickr.com/photos/stevoarnold/2787234769 CC-BY

In the lab capture each object as it is created...

In the lab capture each object as it is created... ...and capture the plan and track execution step by step

Plan = Template = Minimal Information Foo = Semantics

Data repositories... ...as easy to use as Flickr

More natural interfaces... http://www.ﬂickr.com/photos/bekathwia/2910518374 CC-BY-SA

More natural interfaces... ...to capture and communicate http://www.ﬂickr.com/photos/bekathwia/2910518374 CC-BY-SA

...Pages from a project need to be linked in a 3D web of relevance...I want to be able to annotate a...collaborator's work by drawing on it...as I would write on [their] whiteboard... Mat Todd http://is.gd/yVQK http://www.ﬂickr.com/photos/andypowe11/2938538086 CC-BY

But who (and what) can you trust? http://www.ﬂickr.com/photos/joi/2941559903 CC-BY

We trust people... ...not objects

A semantic social web of objects (and data, and process and...)

(Some of) the people I trust... ...in dierent ways and for dierent things

http://friendfeed.com

Code Data Sample Process http://friendfeed.com/lists/isisbiolab

Data ﬁnds the data, then people ﬁnd people. Jeff Jonas/Jon Udell via Deepak Singh

It’s the objects that are the centre of the social interaction and not the people

But that can only work if these objects are...

http://ﬂickr.com/photos/virtualsugar/316200555/ CC-BY

Connected research changes the playing ﬁeld

Connected research changes the playing ﬁeld ...availability of resources key

We need to capture objects as they are created...

We need to capture objects as they are created... ...and to capture their relationships

The rest we can build bit by bit as we go

Communicate ﬁrst, standardize second. Jean-Claude Bradley

Capturing Process

0 comments

Notes on slide 1

4 Favorites