April!24,!2015

Synthetic)Biology)Standards)

Consortium*Kick!off#

Workshop(Report

Matthew'Munson,'Sarah'Munro,'and'Marc'Salit

National'Institute'of'Standards'and'Technology

Executive)Summary

The!kickoff!meeting!for!the!Synthetic!Biology!Standards!

Consortium!(SBSC)!was!held at!the!Stanford!University!Li!Ka!

Shing!Conference!Center!on!March!31,!2015. The!meeting!was!

hosted!by!NIST!and!sponsored!by!the!ABMS!program!at!

Stanford!University.

This!workshop!was!an!open, public!meeting,!with!an!invitation!

published!in the!United!States!government!Federal!Register!

(https://federalregister.gov/a/2015Q06839) and!distributed!

by!email to!the!synthetic!biology!community.!A!total!of!123!

people!attended!the!workshop,!including!11!remote!

participants. For!a!list!of!all!workshop!participants!see!

Appendix!A.

The!objective!of!the!SBSC!is!to!collectively!build!the!metrology!

infrastructure!to!support!a!fully!integrated, global!synthetic!

biology!enterprise.!The!consortium!will!provide!safe!harbor!for!

collaborative!standards!development,!and will!maintain!a!

broad!portfolio through multiple technical!working!groups.

Successful!working!groups!will!be!organized!around!a!clear!

vision!of!specific!metrology!products—standards,!including!

reference materials,!reference!data,!reference!methods,!and!

documentary!standards—that!will!enable!interoperability!and!

reproducibility.!

The!charge!to!the!workshop!was!to!identify!several!initial!

working!groups!with!critical!mass,!leadership!teams,!and!a!

clear!path!forward!to!deliver!standards!to support!the!growth!

of!the!bioeconomy.

During!the!workshop!meeting!participants!developed terms'of'

reference for!SBSC!working!groups.!Terms!of!reference!for!each!

candidate!working!group!addressed!problem!definition,!

relevance,!and!identified!specific!actions!for!success.

Volunteers!proposed!initial!ideas!for!candidate!working!group!

activities!during!a!series!of!panels!in!the!morning!session.!Then!

in!the!afternoon,!attendees!selfQorganized!for!parallel!working!

group discussions.

At!the!conclusion!of!the!workshop, six!working!groups!

presented!draft!terms!of!reference.!Immediate!next!steps!for!

the!consortium!will!be!to!establish!NISTQhosted!discussions!

(via!email!and!conference!call)!for!each!working!group!to!

refine!their!terms!of!reference!and!begin!developing!metrology!

products.

For!more!information!on!SBSC!activities!visit!

http://jimb.stanford.edu/sbsc!or!contact!the!NIST!SBSC!team!

Matthew!Munson,!Sarah!Munro,!and!Marc!Salit!by!email!at!

sbsc@nist.gov
April!24,!2015 1

SBSC)Context)and)Operating)Principles

The!Synthetic!Biology!Standards!Consortium!(SBSC)!will!be!

based!on!a!NISTQhosted!consortium!model,!which!has!been!

successfully!used!to!develop!standards in!the!past.!In!this!

model,!NIST!will!provide!safe!harbor!for!collaborative!work!

amongst!all!interested!parties,!so!that!collectively!we!can

develop!technical!standards!solutions!that!will!address!specific!

problems!identified!by!the!consortium.

It!was!stated!by!NIST!at!the!outset!of!the!workshop!that!

participation!in!SBSC!is open,!free,!and!voluntary. NIST!will!not!

fund!work!of!SBSC!participants. As previously stated by!NIST in!

the!Federal!Register!Notice,!NIST!reminded!participants!of!the!

expectation!that!“no!proprietary!information!will!be!shared!at!

the!workshop.” Standards!developed!by!the!SBSC!will!be!

technology!agnostic!and!free!to!practice.

The!broad!technical!portfolio!of!the!SBSC!will!be!established!

and!maintained!through multiple!ad'hoc technical!working!

groups.!This!will!allow!a!variety!of standards!development!

efforts!to!proceed!in!parallel.!It!is!expected!that!working!

groups!will!form!as!needs!arise!and!dissolve!when!needs!are!

met. Decision!making!in!the!consortium!will!be!consensusQ

based!and!dataQdriven.!A!steering!body!will!be!established!to!

develop!operating!principles for!the!consortium.

The!charge!to!the!workshop!was to identify the!initial!slate!of!

working!groups with!clearly!defined problems that!could!be!

addressed!by!technical!standards.!Working!groups!were!asked!

to!develop!terms!of!reference!and!identify!technical!leaders!for!

each!of!the!working!groups.

Appendix!B contains!slides!presented!by!NIST!for!workshop!

framing.

Workshop)Structure

The!workshop!started!with panel!discussions!in!the!morning!

and!parallel!working!group!meetings in!the!afternoon.

Technical!working!group!panels!were!developed!from

volunteers!who indicated!leadership!interest in!advance

(Box 1).!Each!panelist!was!asked!to!prepare remarks!in!

response!to!these three%guiding%questions:

• What!problem!will!this!working!group!solve?!

• Who!needs!this!problem!solved?

• What!products!will!you!develop!together!to!solve!the!

problem?!What!will!success!look!like?

A!moderated!discussion!followed!each!panel!presentation,!

with!time!allotted!at!the!end!of!the!morning session!for open!

technical!working!group pitches.
April!24,!2015 2

Parallel!working!group!meetings!were!held!in!the!afternoon to!

develop!terms!of!reference,!driven!by!the!three!guiding!

questions.!Participants!attended!the!group!of!their!choosing.!

The!groups!prepared!summaries to!present!to!the!consortium!

as!a!whole (Boxes!2!– 7).

Panel)Discussions

Brief!summaries!of!each!panel!discussion!are!provided!in!the!

following!subsections!and!Box!1 shows!the!names!and!

affiliations!of!the!volunteer!panelists for!the!candidate!working!

groups.

Automation)and)Protocol)Interoperability

All!panelists!expressed!the!common!goal!of!achieving!

interoperability!to!allow researchers!to!build!upon!each!other’s!

results.!The!discussion!raised!a!number!of!questions!around!

achieving!this!goal.!With!respect to!minimal!information!

standards!for protocol!definition,!there!was!debate!regarding!

the!right!set!of!information!to!specify!and!the!right!level!of!

abstraction!to!focus!on.!There!was!discussion!of!establishing!

communications!standards!for!instrumentation!to!allow!

automated!workflows,!but!it!was!unclear!how!to!incentivize!

manufacturers’ participation!in!the!standard.!It!was!suggested!

that!a!set!of!benchmark!protocols!could!be!specified!with!a!

focus!on!the!ability!to!achieve!the!desired!output.!Each!

protocol step!could!be!specified!in!conjunction!with!a!method!

for!validating!proper!execution.!The!cost!efficiency!of!

implementing!this!approach!for!every step!was!questioned.

Box!1:!Panel!Participants

Candidate!

Working!Group

Panelist Affiliation

Automation!and!

Protocol!

Interoperability

Will!Canine Opentrons

Tim!Gardner Riffyn,!Inc.

Max!Hodak Transcriptic

Eric!Klavins University!of!Washington

DJ!Kleinbaum Emerald!Therapeutics,!Inc.

Morgan!Paull Stanford!Bioengineering

Sean!Ward Synthace,!Ltd.

Flow!Cytometry Jake!Beal Raytheon!BBN!Technologies

Traci!Haddock iGEM

Digital!Biological!

Information

Nathan!Hillson Joint!BioEnergy!Institute

Richard!Kitney Imperial!College!London

Nicholas!Roehner Boston!University

Herbert!Sauro University!of!Washington

Performance!

Metrics!for!

Engineered!Strains

Patrick!Boyle Ginkgo!Bioworks

Amor!Menezes University!of!California,!

Berkeley

Measurement!for!

Regulated!

Applications

Paul!Freemont Imperial!College!London

Todd!Kuiken Woodrow!Wilson!Center

Megan!Palmer Stanford

DNA!Construction

Connor!Dickie Synbiota,!Inc.

Michael!Fero TeselaGen!Biotechnology

Enoch!Yueng Caltech

Security William!So FBI
April!24,!2015 3

Flow)Cytometry

This!panel!focused!on!the!extension!and!dissemination!of!

existing!flow!cytometry!standards!for!single!channel!

calibration!to!multiple!channels.!This!updated!standard!will!

allow for!quantitative!crossQcorrelations!on!a!cellQbyQcell!basis.!

Four!key!areas!for!improvement!were!identified: improving!

documentation!for!existing!standards,!accelerating!adoption!

through!community!outreach,!development!of!software!tools!

to!simplify!analysis,!and!investigation!of!open!questions!about!

precision!of!calibration!across!multiple!channels.!Minimal!

information!standards!for!the!reporting!of!cytometry!protocols!

were!proposed.!The!role!of!developing!machine!agnostic!

calibration!procedures!was!explored!as!a!mechanism!to!allow!

comparison!of!results!across!space,!time,!and!technology!

platforms.

DNA)Construction

The!panel!discussion!focused!on!implementation!of!best!

practices!for!assembling!of!DNA!into!larger!constructs,!rather!

than!the!chemical!synthesis!of!oligos.!The'primary'goal'is'the'

transformation'of'cloning'and'sub<cloning'from'an'“art'form'to'

science”. Several!areas!that!would!benefit from!standardized!

methods!were!discussed!including standard!ends!for!subQ

assemblies,!methods!of!reporting!synthesis!or!assembly!errors,!
April!24,!2015 4

and!characterization!of!buildability!with!respect!to!function.

The!burden!of!reQsequencing!parts!ordered!from!various!

repositories!was!noted.!It!was!suggested that!a!third!party!

could!verify!the!sequence!of!deposited!parts,!and!that!this!

entity!could!also!be!responsible!for!annotation.

Digital)Biological)Information

These panelists!agreed!that!biological!design specifications

must!include not!only!the!intended!function, but!also!

information!about context to!enable!reproducibility.

Discussants!proposed that data!sharing!through!the!expansion!

and!curation!of!experimental!data!repositories is!critical!to!

develop!context specifications. Setting!a single!information!

standard!format was!far!less!important!than!enabling!

interoperability!and!seamless!integration!between!existing!

standards and!data!repositories.

A!question!was!raised!during!this!panel!discussion!about!the!

appropriate!timing!for!developing!standards.!Is!there!a!

concern!about!creating!international!conflicts!on!standards?!It!

was!pointed!out!that!due!to!the!long!time!scales!involved!in!

producing!standards!it!is!important!to!bring!people!to!the!table!

early!and!use faceQtoQface!interactions!to!build!trust.!The!point!

was!also!made!that!standards!can!be!flexible!and!scaled!over!

time.!Panelists!proposed!that!the!time!has!come!for!adding!

context!specifications!to!digital!biological!information!

standards.
April!24,!2015 5

Performance Metrics)for)Engineered)Strains

The!panelists!addressed!different!needs;!one!calling!for!

reference!objects,!genetics!parts, and!libraries!of!strains,!the!

other!focusing!on!the!standardization!of!reporting!on!part!

characteristics!in!support!of!predictive!design.!Both!discussed!

the!role!of!context!on!the!performance!of!these!reference!

objects.!These!two!approaches!are!not!in!conflict!with!each!

other, but!are at!different!levels!of!abstraction.!The'need'to'

establish'methods'for'characterizing'performance'for'

contractual/commercial'purposes'was'also'discussed.

Measurements)for)Regulated)Applications

This!panel!discussion!focused!on!the!need!to!develop!public!

acceptance!for!synthetic!biology,!and!achieving!this!by!

cultivating!a!public!perception!that!the!technology!is!safe.!

From!the!perspective!of!detection!of!an!engineered!organism!

after!a!release!the!discussion!was!framed!in!terms!of!three!

questions:!What!is!it?!Where!is!it?!Does!it!matter?!The!final!

question!was!set!aside!as!primarily!a!question!of!regulation

rather!than!measurement.!The!need!for!field!methods!to!be!

robust!to!variations!in!protocol!and!sampling!was!noted.!

Watermarking!of!DNA!was!suggested!as!a!measurement!

strategy!that!would!allow!environmental!tracking.!Concern!

was!expressed!about allowing!regulations!to!get!ahead!of!

measurement!science.

Open)Pitch on)Security

It!was!suggested!that!all!the!working!groups!consider!issues!

related!to!security!in!their!work. It!was!proposed!that!an

evolving!framework!allowing for!supply!chain!resilience!would!

be!applicable!to!all!practitioners!regardless!of!scale.
April!24,!2015 6

Working)Group)Summaries

In!the!afternoon,!six!WGs!from!the!pitch!session!met!in!parallel!

to!define!terms!of!reference.!Participants!split!into!WGs!based!

on!individual!interest.!Leadership!of!each!working!group!

emerged organically. These!conversations!were!driven!by!the!

guiding!questions:

• What!problem!will!this!working!group!solve?!

• Who!needs!this!problem!solved?

• What!products!will!you!develop!together!to!solve!the!

problem?!What!will!success!look!like?

The!groups!were!provided!guidelines!and!framing questions!to!

help!in!crafting!their!terms!of!reference.!The!groups!

considered!the!following!questions!as!a!basis:

• What!has!to!be!achieved?

• Who!will!take!part!in!it?

• How!will!it!be!achieved?

• What!is!the!time!frame?

Groups!met!for!ninety!minutes!to!discuss!these!questions!and!

prepared!terms!of!reference to!present!to!the!consortium!as!a!

whole. The!contents!of!the!reports!from!the!groups!are!

illustrated!below!and!in Box!2!– 7.
April!24,!2015 7

Box!2:!Automation!and!Protocol!

Interoperability!Terms!of!Reference

We!will!aim to:!

define!the!minimum!information!set!required!

to!execute!a!protocol!with!results!of!known!

quality

Our!aim is!important!because:

we!need!to!do!this!to!build!on!each!others’!

work. Tools!need!to!have!reproducibility,!

transparency,!portability,!scalability,!

modularity,!abstraction,!and!efficiency.

Our!approach!will!be!to:

• Generate!a!minimum!information!set!for!

appropriate!atomic!lab!operations!

expressed!as!a!controlled!vocabulary

• Generate!a!suite!of!benchmark!

experiments

• Develop!Quality!Metrics

• Demonstrate!benchmarks!on!multiple!

platforms

Box!3:!Flow!Cytometry!Terms!of!Reference

We!will!aim to:!

abolish!the!use!of!relative!fluorescence!units!in!

flow!cytometry!through!adoption!of!simple,!

accessible!(and!established)!calibration!methods.

Our!aim is!important!because:

calibrated!cytometric!measurements!facilitate!

reproducibility!and!generate!performance!

metrics!that improve!data!quality.

Our!approach!will!be!to:

• Draft!documentary!standards!for!calibrated!

flow!cytometry!data

• Develop!an!RFC!for!

presentation/implementation!at!IGEM!

(May/June)

• Establish!connections!for!dissemination!of!

documentary!standards!and!RFC

o BioBricks,!DNA!2.0,!ACS!SynBio,!

Nature!family,!BioConductor.org
April!24,!2015 8

Box!4:!Measurements!for!Regulated!Applications!Terms!of!Reference

We!will!aim to:

identify what!novel!measurements!and!considerations!are!required!for!synthetic!biology!beyond!current!

standards,!best!practices!and!regulations!in!agro/biochemistry/pharma.

Our!aim is!important!because:

products!and!services!need!to!be!accepted!by!federal!and!international!regulations,!customers/industry,!

and!the!public

Our!approach!will!be!to:

• Benchmarking!current!practices!&!regulatory!environment!for!all!products/applications

• Gap!analysis!– understanding!latest!state!of!the!art!for!measurement

• Is!sequencing!adequate!for!measurement!as!a!first!step!– with!NIST!maintaining!standards!of!

known!sequences

• Working!with!Performance!Metrics!WG!– genetic!‘drift’!(mutations!in!growth,!populations,!etc.!over!

the!course!of!production);!secondary!metabolites

• Investigate!viability!of!‘watermarking’!– technically,!implementation!and!public!relations

• Need!to!have!discussion!with!regulators

• “Baselining”!ecosystems!– for!measurement!of!effects!and!‘unnatural’!perturbations

• Digital!Biologic!information!exchange

• Genetic!Drive!– to!manipulate!genetics!of!wild!populations

• Is!a!‘synthetic!biology!spill’!different!than!any!other!biologic/chemical!spill?
April!24,!2015 9

Box!5:!Digital!Biological!Information!Terms!of!Reference

We!will!aim to:!

• Standard!means!of!specifying!biological!sequences

• How!DNA!works!in!a!cell!as!specified!via!sequence!annotations!and!molecular!interactions!(context!

dependence)

• Version!control!of!components/parts

• Repositories!of!published!designs!(successful!or!not)

Our!aim is!important!because:

design!standards!need!to!be!extensible!and!flexible.

Our!approach!will!be!to:

• Identify!funding!sources

• Target!common

• Possible!for!NIST!to!facilitate!useQcase!gathering!+!special!issue!discussing!outstanding!standard!

and!software!needs/useQcases

• Participants:

o iGEM!registry!community

o SBOL!community

o DICOMQSB!community

o Biomaterials!Repositories

o Commercial!Entities

o Users!of!software

o Journals
April!24,!2015 10

Box!6:!DNA!Construction!Terms!of!Reference

We!will!aim to:!

create!standards!for!DNA!synthesis,!DNA!assembly!and!DNA!validation,!and!for!easy!information!

exchange!between!DNA!design,!build!and!test.

Our!aim is!important!because:

oligo!fidelity,!ease!of!DNA!assembly,!and!consistency!of!DNA!validation!methods!are!needed!to!

accelerate!progress!in!synthetic!biology.!

Our!approach!will!be!to:

• Oligos:!Standardized!vocabulary,!parameters!and!references

• Source!DNA!(whether!synthesized!or!natural):!Standardized!vocabulary,!parameters!and!references

• DNA!Assemblies:!Standardized!vocabulary,!parameters,!protocols,!to!quantify!the!efficiency!of!DNA!

part!assembly

o How!many!clones!(X)!do!I!need!to!pick!to!get!sequence!validity!of!(Y)%?

o What!does!“sequence!verified/validated!mean”

• BuildQability:!Standardized!error!and!warning!reporting.

• DNA!Functional!Assessment:!Standards!by!which!functional!measurements!(dependent variables)!

can!be!related!to sequence!and!sequence!context!(independent!variables)

• Buildable!while!retaining!function.

• Broadly!disseminated!ways!to!use!open!source!parts!and!assembly!methods.
April!24,!2015 11

Plans)for)next)steps

The!NIST!SBSC!team!committed!to!producing!this!summary!to!

be shared!broadly!to!continue!to!solicit!input!from!synthetic!

biology!stakeholders.!It!was!proposed!that!this!summary!

report!will!be!the!basis!for!a!more!detailed!white!paper!

authored!by!the!consortium!to!describe!SBSC!working!group!

terms!of!reference!as!they!develop!over!the!next!few!months.

Next!steps!were!discussed!for!establishing!consortium!

operations!and!mechanisms!for!communication!and!sharing!

information.!NIST!will!facilitate!and!support!the individual!

working!groups!to!develop!their!terms!of!reference!and!

produce!their!standards.!Moving!forward!there!will!be!fluidity!

in!working!group!membership!and!crossQparticipation!in!

different!working!groups!is!encouraged.!Consortium!

leadership!will!need!to!be!established!to!drive!progress!and!

make!decisions. This!leadership will!consist!of working!group!

leaders!as!well!as!steering!committee!and/or!advisory!board!to!

guide!SBSC!decisions!on!a!broader!scale.

Communication!and!sharing!mechanisms!will!be!developed!for!

the!SBSC.!These!will!include!working!group!email!lists,!cloud!

drives,!and/or!web!forums,!etc.!NIST!will!facilitate!future!

meetings!and!interactions!such!as!faceQtoQface!workshops!and!

conference!calls. The!SBSC!website!will!be!used!to!post!and!

share!information!on!SBSC!activities,!including!this!workshop!

report: http://jimb.stanford.edu/sbsc

We invite all interested parties to join the SBSC!and welcome

any additional feedback on this workshop report.!We thank all

workshop participants for their contributions.

Lukmaan!Bawazer,!Ariel!Hecht,!Jeff!Glasgow,!Noah!Spies,!Jerod!

Parsons,!and!Peter!McLean provided additional notes for this

report!and!facilitation!support.

Box 7:!Performance!Metrics!for!Engineered!

Strains!Terms!of!Reference

We!will!aim to:!

assemble!a!reference!collection!of!strains,!

parts,!and!conditions!for!the!validation!of!

bioprocesses

Our!aim is!important!because:

there!is!an!opportunity!to!facilitate!sharing!of!

data!and!parts!between!cooperating!groups!to!

improve!biomanufacturing!efficiency

Our!approach!will!be!to:

• Build!buyQin!to!the!consortium!by!having!a!

minimal!demonstration!of!productivity!

using!the!reference!collection!

• Design!a!minimally!viable!datasheet!that!

demonstrates!the!utility!of!comparing!

bioprocesses

• Consider!analytic!validation!techniques!

(RNAQseq,!metabolomics,!etc.)!and!who!

would!do!the!validation; Include!all!the!

stakeQholders:!metabolic!engineering!

companies,!toll!fermenters,!analytic!

manufacturers,!academia!at!large

• Establish!a!milestone!timeline
Appendix"A:"Workshop"Participants

1

Name Organization

Evan Appleton Boston!University

David Bachinksy Molecular!Creativity

Tom Baer Stanford!University

Peter Bajcsy NIST!Information!Technology!

Laboratory

Maxwell Bates Autodesk

Lukmaan Bawazer NISTQJIMB

Jacob Beal Raytheon!BBN!Technologies

Aaron Berliner Autodesk!Research

Swapnil Bhatia Boston!University

Andrew Bond Gen9

Roel Bovenberg DSM

Patrick Boyle Ginkgo!Bioworks

James Brown UK!Synthetic!Biology!Leadership!

Council

Skyler Brungardt MachinaBio

Evren Cakir GenoFAB

Gisela Canales SGIQDNA

Will Canine Opentrons

Marcus Carr Riffyn,!Inc.

Javier Carrera Stanford!Bioengineering

Daniel Chadash Genome!Compiler

Matthew Chang National!University!of!Singapore

Chiu Chau OpenTrons

Erika Check!Hayden Nature

Siyuan Chen Twist!Bioscience

Mac Cowell Genefoo

John Cumbers SynBioBeta

Kim de!Mora iGEM!Foundation

Jed Dean Zymergen

Douglas Densmore Boston!University

Connor Dickie Synbiota!Inc.

Philip Dormitzer Novartis!Influenza!Vaccines

Omri Drory Genome!Compiler

Bill Efcavitch Molecular!Assemblies

Susan Ehrlich

Drew Endy Stanford!&!BioBricks

Steven Evans Dow!AgroSciences

Micheal Fero TeselaGen!Biotechnology

Paul Freemont Imperial!College!London

Emma Frow Arizona!State!University

Michal Galdzicki Arzeda!Corp

Timothy Gardner Riffyn, Inc.

Jeff Glasgow NIST

Traci Haddock iGEM

Emily Hatas Pacific!Biosciences

Ariel Hecht NIST

Matthew Henry Dow!AgroSciences

Andrew Hessel Autodesk!Inc

Nathan Hillson Joint!BioEnergy!Institute

Max Hodak Transcriptic

Jim Hollenhorst Agilent!Technologies

Louise Horsfall University!of!Edinburgh

Karen Ingram Cut/Paste/Grow

Barbara Jasny Science/AAAS

Richard Johnson Global!Helix!LLC

Linda Kahl BioBricks!Foundation

Richard Kitney Imperial!College!London

Fred Kittler Firelake

Eric Klavins University of!Washington

Daniel Kleinbaum Emerald!Therapeutics!Inc

Tom Knight MIT

Todd Kuiken Woodrow!Wilson!Center

Steve Laderman Agilent!Technologies,!Inc

Dae!Hyun Lee University!of!Washington

Sara Lefort Stanford!University
Appendix"A:"Workshop"Participants

2

Joshua Lerman Amyris

Kevin LeShane Lattice!Automation

Cory Li OpenTrons

Sheng LinQGibson NIST

Laurie Locascio NIST

Aleksandra Małyska MIT

Matthew Mattozzi Wyss!Institute,!Harvard!University

Joseph McAuliffe DuPont!Industrial!Biosciences

Peter Mclean NIST/Stanford

Amor Menezes University!of!California,!Berkeley

Jeremy Minshull DNA2.0

Sarah Munro NISTQJIMB

Matt Munson NIST

Vivek Mutalik LBNL

Chris Myers University!of!Utah

Chris Myers University!of!Utah

Joel Myerson Agilent!Technologies

Ernst Oberortner Joint!Genome!Institute!(JGI)!Q

Lawrence!Berkeley!National!Labs!

(LBNL)

Kenneth Oye MIT

Megan Palmer Stanford

Vanya Paralanov NIST!Materials!Measurement!

Laboratory

Jerod Parsons NISTQJIMB

Morgan Paull Stanford!Bioengineering

Matt Percival Riffyn,!Inc.

Kashef Qaadri Biomatters

Carlo Quinonez MachinaBio

Randy Rettberg iGEM

Melissa Rhoads Lockheed!Martin

Ingmar RiedelQKruse Stanford!University

Ryan Ritterson UCSF

Veronica Rocha Amyris!and!ASTM!E62!(Liaison!subQ

committee)

Nicholas Roehner Boston!University

David Ross NIST!Materials!Measurement!

Laboratory

Lexie Ross Center!for!International!Security!

and!Cooperation!(CISAC)

Hans Roubos DSM

Marc Salit NISTQJIMB

Karl Sanford DuPont!Industrial!Biosciences

Mary Satterfield NIST

Herbert Sauro University!of!Washington

Leona Scanlan National!Institute!of!Standards!&!

Technology!(NIST)

Markus Schmidt Biofaction

Dorothy Silverman Autodesk

William So FBI

Noah Spies NIST/Stanford

Ram Sriram NIST

Wesley Straub Twist!Bioscience

Elizabeth Strychalski DARPA,!NIST

Anu Thubagere Caltech

Thomas Treynor Zymergen,!Inc.

Noël van!Peij DSM

Lili Wang NIST

Sean Ward Synthace!Ltd

Arnie Wernick Wernick!&!Associates

Dave Whelan Nancy!J!Kelley!&!Associates

Adison Wong National!University!of!Singapore

Enoch Yeung Caltech

Wen!Shan Yew National!University!of!Singapore
Appendix(B:(NIST(workshop(framing(slides(

1(

Synthe=c(Biology(Standards(

Consor=um(KickBoff(Workshop(

March(31,(2015(

Sarah(Munro,(MaK(Munson,(&(Marc(Salit(

GenomeBScale(Measurements(Group(

JIMB(–(Joint(Ini=a=ve(for(Metrology(in(Biology(

Material(Measurement(Laboratory(

Sponsored)by)the)ABMS)Affiliate)Program)

Synthe=c(Biology(Standards(

Consor=um(KickBoff(Workshop(

March(31,(2015(

Sarah(Munro,(MaK(Munson,(&(Marc(Salit(

GenomeBScale(Measurements(Group(

JIMB(–(Joint(Ini=a=ve(for(Metrology(in(Biology(

Material(Measurement(Laboratory(

Sponsored)by)the)ABMS)Affiliate)Program)

Open,(public(mee=ng(

(((@SynBioStandards,(#sbsc(

NIST,(seVng(the(standards(

America(lives(by...(

• U.S.(Department(of(

Commerce(

• Advance((

measurement(science,(

standards,(and(

technology(

• NonBregulatory(

• Convening(power(

NIST,(founded(to(meet((

na=onal(standards(needs(

•(((

Ar=cle(I,(Sec=on(8:(The(

Congress(shall(have(the(power(

to...fix)the)standard)of)weights)

and)measures)

Na#onal'Bureau'of'Standards'

established'by'Congress'in'1901'

• Eight(different(“authorita=ve”(values(

for(the(gallon(

• Electrical(industry(needed(standards(

• American(instruments(sent(abroad(

for(calibra=on(

• Consumer(products(and(construc=on(

materials(uneven(in(quality(and(

unreliable

NBS'became'NIST'in'1988'
Appendix(B:(NIST(workshop(framing(slides(

2(

We(all(need(standards(

to(put(out(fires(or(enable(engineering(feats(

Thousands(of(NIST(Standards(

MM16-A

Vol. 26 No. 29 

Replaces MM16-P 

Vol. 25 No. 19 

Use of External RNA Controls in Gene 

Expression Assays; Approved Guideline

This document provides protocols supporting the use of external RNA controls in 

microarray and QRT-PCR-based gene expression experiments, including preparation of 

control transcripts, design of primers and amplicons, quality control, use in final 

experimental or clinical test application, and analysis and interpretation of data obtained. 

A guideline for global application developed through the Clinical and Laboratory 

Standards Institute consensus process. 

Improvement of Quality in Publication of Experimental

Thermophysical Property Data: Challenges, Assessment Tools,

Global Implementation, and Online Support

Robert D. Chirico,a,* Michael Frenkel,a Joseph W. Magee,a Vladimir Diky,a Chris D. Muzny,a

Andrei F. Kazakov,a Kenneth Kroenlein,a Ilmutdin Abdulagatov,a Gary R. Hardin,a William E. Acree, Jr.,b

Joan F. Brenneke,c Paul L. Brown,d Peter T. Cummings,e Theo W. de Loos,f Daniel G. Friend,g

Anthony R. H. Goodwin,h Lee D. Hansen,iWilliam M. Haynes,g Nobuyoshi Koga,jAndreas Mandelis,k

Kenneth N. Marsh,lPaul M. Mathias,m Clare McCabe,e John P. O’Connell,n Agilio Padua, ́ o Vicente Rives,p

Christoph Schick,q J. P. Martin Trusler,r Sergey Vyazovkin,s Ron D. Weir,t and Jiangtao Wuu

a

Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305-3337, United States b

Department of Chemistry, University of North Texas, NT Station, Box 305070, Denton, Texas 76203, United States

c

Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States

d

Rio Tinto Technology and Innovation, 1 Research Avenue, Bundoora, Victoria 3083, Australia

e

Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States

f

Department of Process and Energy, Engineering Thermodynamics, Delft University of Technology, Leeghwaterstraat 44,

2628 CA Delft, Netherlands

g

National Institute of Standards and Technology, Boulder, Colorado 80305-3337, United States

h

Schlumberger Technology Corporation, 150 Gillingham Lane, MD150-2, Sugar Land, Texas 77478, United States

i

Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States

j

Department of Science Education, Graduate School of Education, Hiroshima University, 1-1-1 Kagamiyama, 739-8524,

Higashi-Hiroshima City, Japan

k

Department of Mechanical and Industrial Engineering, University of Toronto, 5 King’s College Road, Toronto, Ontario, Canada M5S 3G8 l

School of Mechanical and Chemical Engineering, University of Western Australia, Crawley 6009, Australia

mFluor Corporation, 3 Polaris Way, Aliso Viejo, California 92698, United States

n

Department of Chemical Engineering, Virginia Commonwealth University, 102 Engineers’ Way, Charlottesville,

Virginia 22904-4741, United States

o

Laboratoire de Thermodynamique (CNRS & UBP), UniversitéBlaise Pascal, 24 avenue des Landais, 63177 Aubiere, France ̀ p

GIR-QUESCAT, Departamento de Química Inorganica, Universidad de Salamanca, 37008-Salamanca, Spain ́ q

Institute of Physics, Universitat Rostock, Wismarsche Str. 43-45, 18051 Rostock, Germany ̈ r

Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom

s

Department of Chemistry, University of Alabama at Birmingham, 901 S. 14th Street, Birmingham, Alabama 35294, United States

t

Department of Chemistry and Chemical Engineering, Royal Military College of Canada (RMCC), PO Box 17000 STN Forces,

Kingston, K7K 7B4, Canada

u

Center of Thermal and Fluid Science, School of Energy and Power Engineering, Xi’an Jiaotong University, No. 28,

Xianning West Road, Xi’an 710049, China

ABSTRACT: This article describes a 10-year cooperative effort between the U.S. National

Institute of Standards and Technology (NIST) and five major journals in the field of

thermophysical and thermochemical properties to improve the quality of published reports of

experimental data. The journals are Journal of Chemical and Engineering Data, The Journal of

Chemical Thermodynamics, Fluid Phase Equilibria, Thermochimica Acta, and International

Journal of Thermophysics. The history of this unique cooperation is outlined, together with an

overview of software tools and procedures that have been developed and implemented to aid

authors, editors, and reviewers at all stages of the publication process, including experiment

Received: June 14, 2013

Accepted: July 26, 2013

Published: September 6, 2013

continued...

Review

pubs.acs.org/jced

© 2013 American Chemical Society 2699 dx.doi.org/10.1021/je400569s | J. Chem. Eng. Data 2013, 58, 2699−2716

Reference((

Data(

Reference(Methods(

&(Documentary(Standards(

Reference(

materials(

Our(team(has(built(standards...(

• Whole(Human(

Genome(Reference(

Materials(

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RNA(SpikeBin(Controls(

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External(RNA(Controls(Consor=um(was((

ini=ated(by(industry(to(put(out(a(fire...(

• Irreproducible(gene(

expression(

measurements(

• NIST(hosted(ERCC(to(

develop(solu=ons(

– RNA(spikeBin(controls(

– Documentary(standards(

– Sofware(for(

standardized(analysis(

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Appendix(B:(NIST(workshop(framing(slides(

3(

ERCC:(answering(the(call(for((

reproducible(gene(expression(results(

What(products(will(you(develop(

together(to(solve(the(problem?(

What(will(success(look(like?(

What(is(the(problem?(

Who(needs(this(problem(

solved?(

Irreproducible(gene(expression(

measurements(across(

technology(plaiorms(

Technology(developers,(clinical(

labs,(government,(academia,(

industry(

RNA(spikeBin(controls,((

analysis(sofware,(and(

documentary(standards(used(by(

everyone(

GIAB:(suppor=ng(the(future(of((

precision(medicine(

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So(you’ve(sequenced(my(

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technology(developers,(

government,(academia,(industry(

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reference(materials,(reference(

data,(analysis(methods,(

performance(metrics,(and(

documentary(standards(used(by(

everyone(

We(work(with(our(customers(

• Whole(Human(

Genome(Reference(

Materials(

– Genome(in(a(BoKle(

Consor=um((GIAB)(

• Sequence(library(for(

RNA(SpikeBin(Controls(

– External(RNA(Controls(

Consor=um((ERCC)(

Industry,(

Government,(

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Professional(Socie=es,(

Technology

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Synthe=c(Biology(Standards(Consor=um

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Reference(Data(

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Consor=um(

Needs(focused(

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PublicBPrivateBAcademic(

Global(

Voluntary(

jimb.stanford.edu/sbsc(
Appendix(B:(NIST(workshop(framing(slides(

4(

1 This!paper!is!a!working!version.!Please!contact!the!authors to!provide!feedback.!

For!the!most!recent!version!of!this!strategic!action!plan,!visit!http://synbioleap.org

A"Vision"for"a"Synthetic"Biology"Standards"

Consortium Michal"Galdzicki,"University"of"Washington,"mgaldzic@uw.edu

Sarah"Munro,"National"Institute"of"Standards"and"Technology,"sarah.munro@nist.gov

Patrick"Boyle,"Ginkgo"BioWorks,"patrick@ginkgobioworks.com

Jeff"Ubersax,"Amyris,"jeff.ubersax@gmail.com

Synthetic"Biology"LeAP"Strategic"Action"Plan

Version"2:"March"18,"20131

Synopsis

The!promise!of!synthetic!biology!to!be!instrumental!in!improving!global!quality!of!life!and!economic!security!

can!not!be!realized!if!there!is!not!a!concerted!effort!to!transform!synthetic!biology!innovations!into!useful,!

safe,!and!affordable!products.!As!synthetic!biology!continues!to!develop,!growing!numbers!of!government!and!

nonCgovernment!organizations!have!focused!on!how!synthetic!biology!could!be!used!to!responsibly!improve!

global!quality!of!life!while!considering!environmental!and!health!safety!issues.!The!development!of!

measurement,!performance,!and!safety!standards!for!synthetic!biology!by!a!multiCstakeholder!consortium!

could!be!the!most!effective!way!of!ensuring!the!responsible!development!and!wide!acceptance!of!this!

technology.

I."Strategic"vision

The!synthetic!biology!community!has!grown!to!a!critical!mass!of!industry,!academic,!and!government!

members!and!a!consortium!of!these!partners!dedicated!to!developing!measurement!standards!for!the!field!

could!have!high!impact.!Effective!development!of!any!new!technology!requires!accurate!measurement!

standards!to!assess!product!and!process!performance,!reliability,!and!safety.!A!consortium!could!unify!the!

shared!interest!of!the!public!and!the!synthetic!biology!community!for!development!of!standards!that!enable!

the!responsible!application!of!the!technology!to!serve!the!public!good.!These!standards!could!facilitate!

communication!by!providing!a!shared!language!for!discussions!about!product!and!technology!performance!

across!institutional!and!disciplinary!boundaries.!They!could!also!reduce!the!barrier!to!entry!and!increase!the!

rate!of!innovation!of!product!development!using!synthetic!biology!by!providing!a!shared!community!resource!

open!to!all.!It!is!likely!that!some!of!these!standards!already!exist!in!the!field!and!are!not!shared!and!must!be!

redeveloped!by!each!new!entrant!into!the!synthetic!biology!field.!By!providing!the!field!with!a!shared!

language!of!measurements!and!standards,!a!consortium!could!foster!responsible!innovation!in!the!field.

Today’s(plan(

• Workshop(framing((

• Working(group(pitches(and(discussion(

• Working(group(narra=veBbuilding(

• Working(group(stories(

• Plans(for(next(steps( Break(at(10:30(am(

Lunch(at(12:30(pm(

Break(at(2:30(pm(

Adjourn(at(4:30(pm(

Dynamic(array(of(Working(Groups(

Automa=on(and(

Protocol(

Interoperability(

DNA((

Construc=on(

Digital(Biological(

Informa=on(

DNA(

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Measurements(for(

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Applica=ons(

Performance(

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Engineered(Strains(

Flow(Cytometry( Others,(as(they(

arise(

• Each(working(group(to(

develop(story,(success(

measures(

• Consor=um(as(host(

– StandardsBseVng(

environment(

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arise(

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informa=on(

standards(

DNA((

Construc=on(

Metrics(beyond(cost(

per(base(

Describe(gene=c(

func=on(and(

context(

Guidance(

documents,(best(

prac=ces(

Calibra=on(

standards(and(

protocols(

Authen=ca=on(and(

iden=fica=on(

standards((

Systema=c(

approaches(for(

strain(comparison(

Your(thoughts(

here...(
Appendix(B:(NIST(workshop(framing(slides(

5(

Problems(and(products(

Did(I(build(a(

beKer(

organism?(

Who(made(

this(DNA?(

Are(my(

experiments(

portable?(

MAC(address/

DOI(system(

for(DNA(

Methods((to(

compare(

organisms(

Protocol(

Interchange(

Database(

Working(groups(should((

answer(these(ques=ons(

What(problem(will(this(working(group(solve?(

Who(needs(this(problem(solved?(

What(products(will(you(develop(together(to(

solve(the(problem?(What(will(success(look(like?(

((

How(we(operate(

• You(get(out(of(it(what(you(put(into(it

• NISTBhosted(

– not)funded)

• Technology(agnos=c(

• DecisionBmaking(

– ConsensusBbased(

– DataBdriven(

• Leadership(group(as(a(steering(body(

How(we(operate(

• You(get(out(of(it(what(you(put(into(it

• NISTBhosted(

– not)funded)

• Technology(agnos=c(

• DecisionBmaking(

– ConsensusBbased(

– DataBdriven(

• Leadership(group(as(a(steering(body(

“No(proprietary(informa=on(will(be(shared(at(the(workshop.”(

FRN)#2015H06839)(SBSC)is)a)preHcompeOOve)space))

Our(inten=on(is(that(SBSC(standards(are(free(to(prac=ce.(
Appendix(B:(NIST(workshop(framing(slides(

6(

Charge(to(the(Workshop(

• Establish(working(groups((WGs)(

– Answers(to(“3(Ques=ons”(

– WG(terms(of(reference(

– WG(leadership,(structure,(and(opera=on(

• Iden=fy(ini=al(poriolio(of(work(

– We(hope(to(get(2B3(concrete(projects(with(12B18(

month(deliverables(

Working)Group)Terms(of(Reference(

• This)is)a)bulleted)describing)the)specifics)of)how)this)will)get)done)

• ((

• ((

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