Logs, Blogs and PodsLogs, Blogs and Pods

Smart Electronic Laboratory Smart Electronic Laboratory NotebooksNotebooks

e-Research Open Meeting 2009e-Research Open Meeting 2009ReadingReading

Jeremy G. FreyJeremy G. Frey

School of Chemistry School of Chemistry University of SouthamptonUniversity of Southampton

TalkTalk Laboratory Notebooks Laboratory Notebooks Laboratory BlogBooksLaboratory BlogBooks Instruments and BlogjectsInstruments and Blogjects Semantic BlogsSemantic Blogs

“The internet wasn't created for mockery! It was created so scientists from different universities could share

datasets....”

Simpson, H. The Simpsons (2005), Eds. Groening, M., Brooks, J.L. & Simon, S., Series 16, Episode 8, Original air date (US) 06-Feb-2005.

http://www.tvtome.com/tvtome/servlet/GuidePageServlet/showid-146/epid-346864/

The CombThe CombeeChem ProjectChem Project ‘‘End to End’ linkingEnd to End’ linking

Data (life-)cycleData (life-)cycle Do things ‘right’ at the startDo things ‘right’ at the start

Make sure the metadata is of Make sure the metadata is of high qualityhigh quality

Record properly at source in Record properly at source in Digital FormDigital Form

Extensive provenanceExtensive provenance Publication@SourcePublication@Source

The Chemistry LabThe Chemistry Lab People & Machines working People & Machines working

togethertogether

PDB deposited

structures

CCDC deposited structures

The Data Explosion

Exponential growth

The future overwhelms the past, but the past must not be lost

Chemists and Chemists and programmingprogramming

Many Chemists think that Many Chemists think that they can program!they can program!

You still use FORTRAN!!

What about that! His brain uses old vacuum tubes

If only I knew exactly how she did this experiments

I know all this supplementary information could be useful but will people really remember the format? Is it worth all the hassle?

I wish I could get the numbers from this graph - the pdf is not much use.

I wish I had recorded things at the start the way I do now…..

Typical laboratory conversations

Some problems are due to the lack of information recorded at the time, others are due to loss of information over time.

Supervisors and Managers

I am sure we collected that information a few years ago…I am sure we collected that

information a few years ago…

The details should be in her lab book…..

The details should be in her lab book…..

Can you read what it says here….?

Can you read what it says here….?

Can you find the files of data that were used

to make the plot?

Can you find the files of data that were used

to make the plot?

Faraday’s laboratory notebooks are also remarkable in the amount of detail that they give about the design and setting up of experiments, interspersed with comments about their outcome and thoughts of a more philosophical kind. All are couched in plain language, with many vivid phrases of delightful spontaneity….

Peter Day, ‘The Philosopher’s Tree: A Selection of Michael Faraday’s Writings’

Permanent, documented and primary record of laboratory

observations

Electronic Laboratory Notebooks

Observations are nevercollected on note pads,

filter paper or other temporary paper for later transfer into a

notebook

If you are caught using the “scrap of paper” technique,

your improperly recorded data may be confiscated by your TA

Cross reference

Ontology and Folksonomy

Folksonomy (also known as collaborative tagging, social classification, social indexing, and social tagging)

Provenance, Probity and Priority

BUT – the data needs to be recorded somewhere! The data only lives if connected to the laboratory notebook to provide the context. This link while essential is often fragile.

Electronic Laboratory Notebooks

He is charged with expressing contempt for meta-data

meta

Key is to make recording of the metadata easy and as automated as possible

COSHHCOSHHLeverage off things we already Leverage off things we already have to dohave to do

“We have a cunning plan”

1 1 2 2 1 3 1 4

Sample of 4-flourinatedbiphenyl

Add CoolReflux

Butanone Sample ofK2CO3Powder

Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text

3 5

Add

g

Sample ofBr11OCB

2 6

Reflux

2 7

Cool

Water

Measure

30 ml

9

Liquid-liquid

extraction

DCM

Measure

3 of 40 ml

10

Dry

MgSO4

11

Filter(Buchner)

12

RemoveSolvent

by RotaryEvaporation

13

Fuse

Silica

14

ColumnChromatography

Ether/PetrolRatio

Butanone dried via silica column andmeasured into 100ml RB flask.

Used 1ml extra solvent to wash outcontainer.

Started reflux at 13.30. (Had tochange heater stirrer) Only reflux

for 45min, next step 14:15.

Inorganics dissolve 2layers. Added brine

~20ml.

Organics are yellowsolution

Washed MgSO4 withDCM ~ 50ml

Measure

excess

Observation Types

weight - grammes

measure - ml, drops

annotate - text

temperature - K, °C

Key

Process

Input

Literal

Observation

Add CoolRefluxAddAdd Reflux Cool Dry Filter Remove

Solventby Rotary

Evaporation

Fuse ColumnChromatography

Dissolve 4-flourinatedbiphenyl inbutanone

Add K2CO3powder

Heat at refluxfor 1.5 hours

Cool and addBr11OCB

Heat atreflux untilcompletion

Cool and addwater (30ml)

Combine organics,dry over MgSO4 &filter

Removesolvent invacuo

Liquid-liquid

extraction

Extract withDCM(3x40ml)

Fuse compound to silica &column in ether/petrol

4 8

Add

Add

text

Annotate

Annotate

text

Weigh

Annotate

g

Annotate Annotate

text text

Future Questions

Whether to have many subclasses of processes or fewer with annotations

How to depict destructive processes

How to depict taking lots of samples

What is the observation/process boundary? e.g. MRI scan

1.5918

Combechem

30 January 2004gvh, hrm, gms

Ingredient List

Fluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml

image

To

Do

Lis

tP

lan

Pro

ce

ss

Re

co

rd

1 1 2 2 1 3

Sample of 4-flourinatedbiphenyl

Add Reflux

Butanone Sample ofK2CO3Powder

Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text

Butanone dried via silica column andmeasured into 100ml RB flask.

Used 1ml extra solvent to wash outcontainer.

Started reflux at 13.30. (Had tochange heater stirrer) Only reflux

for 45min, next step 14:15.

Add RefluxAdd

Dissolve 4-flourinatedbiphenyl inbutanone

Add K2CO3powder

Heat at refluxfor 1.5 hours

text

Annotate

Annotate

Ingredient List

Fluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml

Smart Tea Project - User Centred Design, Design by Analogy to ensure the correct information is captured simply and easily.

The Two InterfacesThe Two Interfaces

Planning and Review Implementation

ProcedureProcedure

Into the Lab!Into the Lab!

Into the Lab!Into the Lab!

PlansPlans Plans in advance are Plans in advance are usefuluseful

This is the way things This is the way things are supposed to be are supposed to be donedone

The Plan provides a The Plan provides a digital context so digital context so increases the value of increases the value of planningplanning

Key to our ‘Smart Lab’ Key to our ‘Smart Lab’ approach….approach….

But is it the best way?

Laboratory “Blogs”Laboratory “Blogs” Laboratory Laboratory

notebook is a Blognotebook is a Blog Encourage and Encourage and

facilitate facilitate collaborationcollaboration

FlexibleFlexible Need a data Need a data

repositories behind repositories behind the the BBloglog R4LR4L E-BankE-Bank

Implementation of e-lab bookImplementation of e-lab book

Blog based formatBlog based format Purpose built enginePurpose built engine Fully flexible system Fully flexible system

with arbitrary metadatawith arbitrary metadata Full record of changes Full record of changes

(not currently easily (not currently easily accessible)accessible)

http://chemtools.chem.soton.ac.uk/projects/blog/ “Bio Blogs”

http://blogs.openwetware.org/scienceintheopen Discussion

Implementation of e-lab bookImplementation of e-lab book

One post, one item One post, one item approachapproach

Procedures can be Procedures can be tracked back to starting tracked back to starting materials (or forwards materials (or forwards to products) by clicking to products) by clicking throughthrough

Aim to ultimately be Aim to ultimately be interpretable by interpretable by machine and humanmachine and human

TemplatesTemplates

LIVECOP LINK

<METADATA> <TITLE>album09 - jrh4880_19_competent_transformation_from_ligation</TITLE> <SIZE_X>1300</SIZE_X> <SIZE_Y>1026</SIZE_Y> <THUMB_SRC>http://imgstore.chem.soton.ac.uk/albums/album09/jrh4880_19_competent_transformation_from_ligation.thumb.jpg</THUMB_SRC> <PREVIEW_SRC>http://imgstore.chem.soton.ac.uk/albums/album09/jrh4880_19_competent_transformation_from_ligation.sized.jpg</PREVIEW_SRC> <PICTURE_URL>http://imgstore.chem.soton.ac.uk/album09/jrh4880_19_competent_transformation_from_ligation</PICTURE_URL></METADATA>

Link to objectsLink to objects

IssuesIssues The Physical WorldThe Physical World Safety documentationSafety documentation Patent/IP – sign-offPatent/IP – sign-off TrustTrust Will computers survive Will computers survive

in the laboratory?in the laboratory?

Remember we do have a physical world to keep in sync

 19 June 200810:32

 

/

Journal publication

Test Data

RESULTS!Conference reports

Grant Applications

Analysis

Management

Time Line View

EnvironmentEnvironment

Automatically record as much of the Automatically record as much of the laboratory environment as possiblelaboratory environment as possible

Blog for the dayBlog for the day

Pub-Sub systems provide the flexible & extensible approach to distribution of real time laboratory monitoring & archiving

Data Source

ArchiveClient

WebClient

Mobilephone

Data Source

PDA

MessageBroker

TranslatorService BLOG

Smart Laboratory Spaces

“I just realized, Howard, that everything in this apartment is more sophisticated than we are”

Blog-jectsBlog-jects

Equipment become first class Equipment become first class members of the webmembers of the web

Interacts well with Pub-Sub as Interacts well with Pub-Sub as items are attached to topics, items are attached to topics, topics relate the Bog itemstopics relate the Bog items

With automation this evolves to a With automation this evolves to a two-way communicationtwo-way communication

Everything has a network Everything has a network connection – research equipment connection – research equipment will catch up with the fridge & will catch up with the fridge & other commodity goodsother commodity goods

Blog-jectsBlog-jects

Equipment become first class members of Equipment become first class members of the webthe web

Interacts well with Pub-Sub as items are Interacts well with Pub-Sub as items are attached to topics, topics relate the Bog attached to topics, topics relate the Bog itemsitems

With automation this evolves to a two-way With automation this evolves to a two-way communicationcommunication

Live Copy essential Live Copy essential

Lab environment data and experimental output linked

Comments and Comments and AnnotationAnnotation

A picture worth a thousand words! Chemists like to sketch!

Can we have both the web 2.0 Blog style and the Semantics of the ELN?

YES!

Simple Experiment OntologySimple Experiment Ontology

Impact on researchersImpact on researchers Higher Quality RecordHigher Quality Record Easier CollaborationEasier Collaboration Improved planningImproved planning Improved discussionsImproved discussions Efficiency gain in Efficiency gain in

production of production of presentations/reportspresentations/reports

Change the nature of Change the nature of Professor/Student Professor/Student interactions interactions 54

Information Providers Information

Consumers

These are the same people – if we can ‘talk’ to ourselves efficiently over time then that is a good start to be able to ‘talk’ to others

ThanksThanks

RC UK, EPSRC, JISC for fundingRC UK, EPSRC, JISC for funding Colleagues and Students from Colleagues and Students from

the Schools of Chemistry, the Schools of Chemistry, Electronics & Computer Science, Electronics & Computer Science, MathematicsMathematics

IBM, MicrosoftIBM, Microsoft www.combechem.org www.ecrystals.soton.ac.uk chemtools.chem.soton.ac.ukchemtools.chem.soton.ac.uk

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Excerpted from the Onion:

The Recording Industry Association of America announced Tuesday that it will be taking legal action against anyone discovered telling friends, acquaintances, or associates about new songs, artists, or albums.

Data Sharing

"We are merely exercising our right to defend our intellectual properties from unauthorized peer-to-peer notification of the existence of copyrighted material."

A daring daylight raid of copyright material

ACS

ValidationValidation Increasing the value of data Increasing the value of data How to bring all the necessary How to bring all the necessary

information together to enable information together to enable appropriate validationappropriate validation

Increasingly difficult & Increasingly difficult & expensive to achieveexpensive to achieve

Need provenance and context otherwise just a collection of items