Download - Blogs Logs Pods: Smart Labs
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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
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TalkTalk Laboratory Notebooks Laboratory Notebooks Laboratory BlogBooksLaboratory BlogBooks Instruments and BlogjectsInstruments and Blogjects Semantic BlogsSemantic Blogs
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“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/
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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
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PDB deposited
structures
CCDC deposited structures
The Data Explosion
Exponential growth
The future overwhelms the past, but the past must not be lost
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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
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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
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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?
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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’
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Permanent, documented and primary record of laboratory
observations
Electronic Laboratory Notebooks
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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
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Cross reference
Ontology and Folksonomy
Folksonomy (also known as collaborative tagging, social classification, social indexing, and social tagging)
Provenance, Probity and Priority
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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.
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Electronic Laboratory Notebooks
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He is charged with expressing contempt for meta-data
meta
Key is to make recording of the metadata easy and as automated as possible
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COSHHCOSHHLeverage off things we already Leverage off things we already have to dohave to do
“We have a cunning plan”
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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
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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.
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The Two InterfacesThe Two Interfaces
Planning and Review Implementation
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ProcedureProcedure
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Into the Lab!Into the Lab!
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Into the Lab!Into the Lab!
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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?
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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
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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
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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
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TemplatesTemplates
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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>
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Link to objectsLink to objects
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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
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19 June 200810:32
/
Journal publication
Test Data
RESULTS!Conference reports
Grant Applications
Analysis
Management
Time Line View
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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
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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
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“I just realized, Howard, that everything in this apartment is more sophisticated than we are”
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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
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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
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Lab environment data and experimental output linked
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Comments and Comments and AnnotationAnnotation
A picture worth a thousand words! Chemists like to sketch!
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Can we have both the web 2.0 Blog style and the Semantics of the ELN?
YES!
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Simple Experiment OntologySimple Experiment Ontology
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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
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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
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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
6363
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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
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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