robots are team members, too!

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The Genome Sequencing Operations group at the Broad Institute rely on JIRA to manage laboratory operations and instilled a high level of collaboration and communication between lab techs, project managers, and even robots! Learn how these robots use REST APIs to become active collaborators in a number of JIRA projects, and how you can integrate your own external applications to automate your interactions with JIRA in exciting and useful ways.

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Page 1: Robots are Team Members, Too!

Friday, June 15, 12

Page 2: Robots are Team Members, Too!

100000s samples10000s QC data points1000s of knowledge documents1000s small equipment pieces1000s sequencing runs100s of technology development projects100s instruments (sequencing & robots)100s of experiments100s of people (resource mgmt)10s of beta tests from vendors

We track lots of things:

Friday, June 15, 12

Page 3: Robots are Team Members, Too!

100000s samples10000s QC data points1000s of knowledge documents1000s small equipment pieces1000s sequencing runs100s of technology development projects100s instruments (sequencing & robots)100s of experiments100s of people (resource mgmt)10s of beta tests from vendors

We track lots of things:

Friday, June 15, 12

Page 4: Robots are Team Members, Too!

100000s samples10000s QC data points1000s of knowledge documents1000s small equipment pieces1000s sequencing runs100s of technology development projects100s instruments (sequencing & robots)100s of experiments100s of people (resource mgmt)10s of beta tests from vendors

$$$$We track lots of things:

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Page 5: Robots are Team Members, Too!

100000s samples10000s QC data points1000s of knowledge documents1000s small equipment pieces1000s sequencing runs100s of technology development projects100s instruments (sequencing & robots)100s of experiments100s of people (resource mgmt)10s of beta tests from vendors

or

$$$$We track lots of things:

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Page 6: Robots are Team Members, Too!

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Page 7: Robots are Team Members, Too!

The Broad Institute of MIT and HarvardGenome Sequencing Platform

Jim Meldrim and John Stalker

Robotsare Team Members Too!

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Page 8: Robots are Team Members, Too!

Established 2004 - Eli and Edythe Broad

Joint CollaborationMITHarvard UniversityAffiliated HospitalsBeth Israel Deaconess Medical Center

Brigham and Women’s Hospital

Children’s Hospital

Dana-Farber Cancer Institute

Massachusetts General Hospital

The Broad Institute

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Page 9: Robots are Team Members, Too!

Programs (Science)Chemical BiologyMedical and Population GeneticsCell CircuitsEpigenomicsGenome Sequencing and AnalysisCancerInfectious DiseasesMetabolismPsychiatric Disease

OrganizationPlatforms (Technology)

Genome SequencingBiological SamplesChemical BiologyGenetic AnalysisImagingMetabolite ProfilingProteomicsRNAiTherapeutics Discovery and Development

Friday, June 15, 12

Page 10: Robots are Team Members, Too!

Programs (Science)Chemical BiologyMedical and Population GeneticsCell CircuitsEpigenomicsGenome Sequencing and AnalysisCancerInfectious DiseasesMetabolismPsychiatric Disease

OrganizationPlatforms (Technology)

Genome SequencingBiological SamplesChemical BiologyGenetic AnalysisImagingMetabolite ProfilingProteomicsRNAiTherapeutics Discovery and Development

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Page 11: Robots are Team Members, Too!

Genome Sequencing Background

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Page 12: Robots are Team Members, Too!

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Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

1st Human Genome2001$3 billion

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Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

1st Human Genome2001$3 billion

AutomatedSequencing ABI3730 / Tphi

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Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

1st Human Genome2001$3 billion

AutomatedSequencing ABI3730 / Tphi

Next GenSequencing Illumina GA

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Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

1st Human Genome2001$3 billion

AutomatedSequencing ABI3730 / Tphi

Next GenSequencing Illumina GA

Current SofA Illumina HiSeq

Friday, June 15, 12

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amples

 (cop

y)

Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

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ulative  Num

ber  o

f  Sam

ples

Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

Friday, June 15, 12

Page 19: Robots are Team Members, Too!

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ome

0K

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20K

30K

40K

50K

60K

70K

80K

Cum

ulative  Num

ber  o

f  Sam

ples

Cost  of  Sequencing  a  Mammalian  Genome  over  time  and  compared  to  Moore's  LawGenome  sequencing  cost  data  courtesy:  Wetterstrand  KA.  DNA  Sequencing  Costs:  Data  f rom  the  NHGRI  Large-­Scale  Genome  Sequencing  Program  Available  at:  www.genome.gov/sequencingcosts.  Accessed5/9/2012

LCSET-11st JIRA tracked libraries

5/17/2010

Friday, June 15, 12

Page 20: Robots are Team Members, Too!

Genome Sequencing101

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Page 21: Robots are Team Members, Too!

Genome Sequencing 101

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Page 22: Robots are Team Members, Too!

Cell

Nucleus

Genome Sequencing 101

Friday, June 15, 12

Page 23: Robots are Team Members, Too!

Genome Sequencing 101

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Page 24: Robots are Team Members, Too!

Genome Sequencing 101

1 2 3 4 5

6 7 8 9 10 11 12

13 14 15 16 17 18

19 20 21 22

X YFriday, June 15, 12

Page 25: Robots are Team Members, Too!

Genome Sequencing 101

1 2 3 4 5

6 7 8 9 10 11 12

13 14 15 16 17 18

19 20 21 22

X Y

Mom

Pop

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Page 26: Robots are Team Members, Too!

Genome Sequencing 101

X Y

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Page 27: Robots are Team Members, Too!

Genome Sequencing 101

JIRA is in our DNA!Friday, June 15, 12

Page 28: Robots are Team Members, Too!

Genome Sequencing 101

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Genome Sequencing 101

DNA (Deoxyribonucleic acid)

• Two intertwined molecules - Double Helix

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Page 30: Robots are Team Members, Too!

Genome Sequencing 101

DNA (Deoxyribonucleic acid)

• Two intertwined molecules - Double Helix

• Described in 1953 by James Watson and Francis Crick

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Page 31: Robots are Team Members, Too!

Genome Sequencing 101

DNA (Deoxyribonucleic acid)

• Two intertwined molecules - Double Helix

• Described in 1953 by James Watson and Francis Crick

• Carries the genetic code - the instructions for life

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Page 32: Robots are Team Members, Too!

Cytosine

Adenine Thymine

Guanine

Genome Sequencing 101

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Page 33: Robots are Team Members, Too!

Genome Sequencing 101

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Page 34: Robots are Team Members, Too!

Genome Sequencing 101

TGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGT

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Genome Sequencing 101TGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGT

3 Billion Bases Long!

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Genome Sequencing 101TGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGT

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Genome Sequencing 101TGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGT

Normal

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Page 38: Robots are Team Members, Too!

Genome Sequencing 101TGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGTGGTACACAGTACGTACTCTGTGACGT

Normal

TGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGTTGCAGCAATGCTGAGCGCTAGCGAGGTACACAGTACGTACTCTGTGACGT

Tumor

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Page 39: Robots are Team Members, Too!

Lab Process Trackingwith

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Page 40: Robots are Team Members, Too!

Outside the Genome Sequencing Platform

Our Process“The Players”

?

Scientist

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Page 41: Robots are Team Members, Too!

Outside the Genome Sequencing Platform

Our Process“The Players”

?

Scientist

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Page 42: Robots are Team Members, Too!

Outside the Genome Sequencing Platform

Our Process“The Players”

?

Scientist

Cancer HIV E. Coli Ice Core

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Page 43: Robots are Team Members, Too!

Outside the Genome Sequencing Platform

Our Process“The Players”

?

Scientist

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Page 44: Robots are Team Members, Too!

Our Process“The Players”

?

Outside the Genome Sequencing Platform

Scientist

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Page 45: Robots are Team Members, Too!

Our Process“The Players”

?

Outside the Genome Sequencing Platform

Scientist

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Page 46: Robots are Team Members, Too!

Our Process“The Players”

?

Outside the Genome Sequencing Platform

Scientist

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Page 47: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

?Project

Manager

Outside the Genome Sequencing Platform

Scientist

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Page 48: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

?Project

Manager

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 49: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

?Project

Manager

Outside the Genome Sequencing Platform

Scientist

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Page 50: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Coordinator

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 51: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Coordinator

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 52: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Coordinator

Outside the Genome Sequencing Platform

Scientist

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Page 53: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Coordinator

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 54: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Coordinator

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 55: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Outside the Genome Sequencing Platform

Scientist

Technician

Coordinator

Friday, June 15, 12

Page 56: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Outside the Genome Sequencing Platform

Scientist

Technician

Coordinator

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Page 57: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Coordinator

Outside the Genome Sequencing Platform

Scientist

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Page 58: Robots are Team Members, Too!

Shearing

Coordinator

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 59: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

Page 60: Robots are Team Members, Too!

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC

Outside the Genome Sequencing Platform

Scientist

Friday, June 15, 12

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Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 62: Robots are Team Members, Too!

Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 63: Robots are Team Members, Too!

Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling

Outside the Genome Sequencing Platform

Friday, June 15, 12

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Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 65: Robots are Team Members, Too!

Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 66: Robots are Team Members, Too!

Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Data!

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 67: Robots are Team Members, Too!

Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Data!

Analyst

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 68: Robots are Team Members, Too!

Scientist

Our Process“The Players”

Projects Group

Lab Operations

?Project

Manager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Data!

Analyst

Outside the Genome Sequencing Platform

Friday, June 15, 12

Page 69: Robots are Team Members, Too!

Our ProcessShearing

LC

Pooling

Sequencing

“The Workflow”

Friday, June 15, 12

Page 70: Robots are Team Members, Too!

Our Process“The Workflow”

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 71: Robots are Team Members, Too!

Our Process“The Workflow”

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 72: Robots are Team Members, Too!

Our Process“The Workflow”

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 73: Robots are Team Members, Too!

Our Process“The Workflow”

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 74: Robots are Team Members, Too!

Our ProcessCustom Fields

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 75: Robots are Team Members, Too!

Our ProcessCustom Fields

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 76: Robots are Team Members, Too!

Friday, June 15, 12

Page 77: Robots are Team Members, Too!

Friday, June 15, 12

Page 78: Robots are Team Members, Too!

#summit12

You can take any business process, even something

thats far removed from ‘typical’ (like genome

sequencing) and boil it down to a workflow.

Friday, June 15, 12

Page 79: Robots are Team Members, Too!

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 80: Robots are Team Members, Too!

Shearing

LC

Pooling

Sequencing

Friday, June 15, 12

Page 81: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

Friday, June 15, 12

Page 82: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

Friday, June 15, 12

Page 83: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

Friday, June 15, 12

Page 84: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

Friday, June 15, 12

Page 85: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 86: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 87: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 88: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 89: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 90: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 91: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 92: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 93: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

Friday, June 15, 12

Page 94: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

“Flowcell Tracking”

CREATE

Friday, June 15, 12

Page 95: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

“Flowcell Tracking”

CREATE

Friday, June 15, 12

Page 96: Robots are Team Members, Too!

Sequencing

Strip Tube Setup Flowcell Setup Sequencing

REST

“Crazy Robots”

“Flowcell Tracking”

CREATE TRANSITION & UPDATE

Friday, June 15, 12

Page 97: Robots are Team Members, Too!

#summit12

Integrate and automate your business processes with

JIRA using RESTful web services.

Friday, June 15, 12

Page 98: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 99: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 100: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 101: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 102: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 103: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 104: Robots are Team Members, Too!

“Flowcell Tracking”

Friday, June 15, 12

Page 105: Robots are Team Members, Too!

“Flowcell Tracking”

6wk  Ave Week  Filter49

Cluster  AmpResult Total  Lanes

%  of  Lanes  (CA)

Lanes  Reimb.  (CA)

%Reimburseable  

(CA)

Pass

Cluster  Amp  Fail

Grand  Total 12100%487

7.02%1235%171

0.00%065%316

Amp  Fails  for  FC's  Created:  11/27/2011  -­  12/3/2011

Week  16 Week  17 Week  18 Week  19 Week  20

0

50

100

150

Value 62

52

8

34

2

131

76

32

54

18

Amp  Fail  History  6  weeks

Measure  NamesTotal  Lanes

Cluster  Amp  Fails

Sequencing  Result Total  Lanes

%  of  Lanes  (SEQ)

Lanes  Reimb.  (SEQ)

%Reimburseable  

(SEQ)  NEW

Pass

Sequencer  Fail

Grand  Total 10100%327

100%103%10

0%097%317

Seq  Fails  for  FC's  Started:  11/27/2011  -­  12/3/2011

Week  16 Week  17 Week  18 Week  19 Week  20

0

50

100

150

Value

016 16 16

0

129

6248 46

10

Seq  Fail  History  6  weeks

51%

16%

1 Too  sparse

2 Too  sparse

3 Too  sparse

4 None

5 Too  sparse

6 Too  sparse

7 Too  sparse

8 None

C096UACXX

Fail  Category Reworked? Designation  Comments FLOWCELL JIRA  Issue Fail  Mode #  of  Lanes  FailedCA N FAST  TRACK:  Library  QC D0EN9ACXX FCT-­2715 ICs  only

LCSet  849  &  866 C096DACXX FCT-­2706 Too  dense

LCSet  913  1000G  WGS  Phase  2 D0EAUACXX FCT-­2719 Too  sparse

LCSET  913  1000G  WGS  Phase  2 D0ECRACXX FCT-­2722 Too  sparse

LCSETs  866  &  850 C096WACXX FCT-­2711 Too  dense

Y Check  volume  of  Normalized  to  make  sure  there  is  enough  left  LCSE.. C095FACXX FCT-­2704 ICs  only

LCSET  863  (mouse  prostate  WEx)  and  LCSET  805  (Ciliopathies  WE.. C096UACXX FCT-­2717 Too  sparse

LCSET-­814:  Lung  CIP  and  Melanoma  CIP  WGS C09A7ACXX FCT-­2735 No  Amp

TLC:  Prokaryotic  RNA,  dUTP  Tetrahymena,  WNV  &  HIV  Nugen,  180.. D0EL9ACXX FCT-­2709 Too  sparse

SEQ N LCSETs  807  &  810 D0ED1ACXX FCT-­2718 Images  Out  Of  Focus

Y (TLC)  CLL  RNA-­Seq  dUTP  cDNA D0EVTACXX FCT-­2730 Images  Out  Of  Focus

1

2

8

8

1

8

6

4

6

1

8

Flowcell  Fail  List  for  FC's  Created  or  Started:  Null  -­  Null

Flowcell Fail Report

Friday, June 15, 12

Page 106: Robots are Team Members, Too!

Dev JIRAElectronic Lab Notebook

&Project Management

Friday, June 15, 12

Page 107: Robots are Team Members, Too!

Collaborator

Outside the GSP

Our ProcessInnovating

Projects Group

Lab Operations

ProjectManager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Friday, June 15, 12

Page 108: Robots are Team Members, Too!

Collaborator

Outside the GSP

The ProblemProjects Group

Lab Operations

ProjectManager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Friday, June 15, 12

Page 109: Robots are Team Members, Too!

Electronic notebooks:A new leaf7 January 2005 - Jim Giles

experimental protocols are continually changing....

redesigning the pages of e-note-books, and adding

fields and tables, usually entails modifying the

structure of the underlying database.

nature

Friday, June 15, 12

Page 110: Robots are Team Members, Too!

Going paperless:The digital lab25 January 2012 - Jim Giles

The greatest challenge... is not to create a

tool that can do everything, but one that... is fundamentally easy to use.

nature

Friday, June 15, 12

Page 111: Robots are Team Members, Too!

Collaborator

Outside the GSP

The ProblemProjects Group

Lab Operations

ProjectManager

Technician

Shearing

Coordinator

LC Pooling Sequencing

Friday, June 15, 12

Page 112: Robots are Team Members, Too!

Outside the GSP

The ProblemProjects Group

Lab Operations

Technician

Shearing

Coordinator

LC Pooling Sequencing

Friday, June 15, 12

Page 113: Robots are Team Members, Too!

Outside the GSP

The ProblemProjects Group

Lab Operations

Technician

Shearing

Coordinator

LC Pooling Sequencing

Friday, June 15, 12

Page 114: Robots are Team Members, Too!

The Solution

Friday, June 15, 12

Page 115: Robots are Team Members, Too!

Outside the GSP

The ProblemProjects Group

Lab Operations

Technician

Shearing

Coordinator

LC Pooling Sequencing

Friday, June 15, 12

Page 116: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Friday, June 15, 12

Page 117: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

!

Friday, June 15, 12

Page 118: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

We need a better “Shearing” protocol

Friday, June 15, 12

Page 119: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

We need a better “Shearing” protocol

Story

Friday, June 15, 12

Page 120: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Friday, June 15, 12

Page 121: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Idea

Friday, June 15, 12

Page 122: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Idea

Experiment

Friday, June 15, 12

Page 123: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Idea

Experiment

Friday, June 15, 12

Page 124: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Idea

Experiment

We need to get new BOM to Materials Group

Friday, June 15, 12

Page 125: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Idea

Experiment

Task

Friday, June 15, 12

Page 126: Robots are Team Members, Too!

InnovationDEV JIRA

Shearing

Story

Issue Types

Experiment

Idea

Experiment

Task

Friday, June 15, 12

Page 127: Robots are Team Members, Too!

InnovationDEV JIRA

Story

Issue Types

Experiment

Idea

Task

Experiment

Friday, June 15, 12

Page 128: Robots are Team Members, Too!

InnovationDEV JIRA

Story

Issue Types

Experiment

Idea

Task

Custom Link Type

Is Parent of

Is Child of

Experiment

Friday, June 15, 12

Page 129: Robots are Team Members, Too!

InnovationDEV JIRA

Story

Issue Types

Experiment

Idea

Experiment

Task

Custom Link Type

Is Parent of

Is Child of

Friday, June 15, 12

Page 130: Robots are Team Members, Too!

InnovationDEV JIRA

Story

Issue Types

Experiment

Idea

Experiment

Task

Custom Link Type

Is Parent of

Is Child of

structure.almworks.commarketplace.atlassian.com/34717

Structures

Friday, June 15, 12

Page 131: Robots are Team Members, Too!

Innovation DEV JIRAStory - Umbrella issue equivalent to a “project”

Issue Types

Experiment - Question aimed at improving a process

Idea - Seed for a Story or Experiment

Task - Something that needs to be done

Friday, June 15, 12

Page 132: Robots are Team Members, Too!

Innovation DEV JIRAStory - Umbrella issue equivalent to a “project”

Issue Types

Experiment - Question aimed at improving a process

Idea - Seed for a Story or Experiment

Task - Something that needs to be done

Document - Reference material, scientific article etc

Friday, June 15, 12

Page 133: Robots are Team Members, Too!

Innovation DEV JIRAStory - Umbrella issue equivalent to a “project”

Issue Types

Experiment - Question aimed at improving a process

Idea - Seed for a Story or Experiment

Task - Something that needs to be done

Document - Reference material, scientific article etc

Process Change - Note that something changed on a certain date

Friday, June 15, 12

Page 134: Robots are Team Members, Too!

Innovation DEV JIRAStory - Umbrella issue equivalent to a “project”

Issue Types

Experiment - Question aimed at improving a process

Idea - Seed for a Story or Experiment

Task - Something that needs to be done

Document - Reference material, scientific article etc

Process Change - Note that something changed on a certain date

Troubleshooting - Group effort to diagnose a problem

Friday, June 15, 12

Page 135: Robots are Team Members, Too!

Innovation DEV JIRAStory - Umbrella issue equivalent to a “project”

Issue Types

Experiment - Question aimed at improving a process

Idea - Seed for a Story or Experiment

Task - Something that needs to be done

Document - Reference material, scientific article etc

Process Change - Note that something changed on a certain date

Troubleshooting - Group effort to diagnose a problem

HotPot Topic - Agenda item for group weekly meeting

Friday, June 15, 12

Page 136: Robots are Team Members, Too!

WorkflowExperiment

Experiment - Question aimed at improving a process

Hypothesis

Observe

Analyze

Report

Friday, June 15, 12

Page 137: Robots are Team Members, Too!

ExperimentHypothesis

Observe

Analyze

Report

Friday, June 15, 12

Page 138: Robots are Team Members, Too!

ExperimentHypothesis

Observe

Analyze

Reportwww.valiantys.com

marketplace.atlassian.com/1076698

Exocet

Friday, June 15, 12

Page 139: Robots are Team Members, Too!

Custom FieldsExperiment

Hypothesis

Observe

Analyze

Report

Custom Fields

Summary - A question that needs answering

Hypothesis - More formal phrasing of that question

Experimental Design - How did you do it

Materials and Methods - What did you use

Results - What did you learn

Conclusions - What are the next steps

Friday, June 15, 12

Page 140: Robots are Team Members, Too!

Grouping ThingsVersions

Illumina v1.0

Ion v3.0

Friday, June 15, 12

Page 141: Robots are Team Members, Too!

Grouping ThingsVersions

Illumina v2.0

Ion v3.0

Friday, June 15, 12

Page 142: Robots are Team Members, Too!

Grouping ThingsVersions

Illumina v3.0

Ion v3.0

Friday, June 15, 12

Page 143: Robots are Team Members, Too!

Grouping ThingsComponents

Illumina

Ion

Shearing

Shearing

Components = Functional Areas

Pooling

Pooling

Friday, June 15, 12

Page 144: Robots are Team Members, Too!

Grouping ThingsComponents

Illumina

Ion

Shearing

Shearing

Pooling

Pooling

Automation

Friday, June 15, 12

Page 145: Robots are Team Members, Too!

Grouping ThingsComponents

Illumina

Ion

Shearing

Shearing

Pooling

Pooling

Materials

Friday, June 15, 12

Page 146: Robots are Team Members, Too!

Friday, June 15, 12

Page 147: Robots are Team Members, Too!

Friday, June 15, 12

Page 148: Robots are Team Members, Too!

Friday, June 15, 12

Page 149: Robots are Team Members, Too!

#summit12

JIRA is flexible enough to mirror our particular style

of Project Management.

Friday, June 15, 12

Page 150: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

0

500

1000

1500

2000

2500

3000

3500

4000Cum

ulative  Activity

DEV  JIRA  Activity

DEV  JIRA  ActivityActivity

Friday, June 15, 12

Page 151: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

0

50

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200

250

300

350

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450

500

550

600

650

Cum

ulative  Activity

Story

Idea

Experiment

Document

ActionDocument

Experiment

Idea

Story

Friday, June 15, 12

Page 152: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

0

50

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Cum

ulative  Activity

Story

Idea

Experiment

Document

ActionDocument

Experiment

Idea

Story

Friday, June 15, 12

Page 153: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

20

40

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80

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Cum

ulative  Activity

weiand

voltaire

tfennell

tcasse

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima

nlennon

nicol

mcoyne

mcoole

mattlee

lisaz

lisatran

lisag

lholmes

leonmlaurena

lambiase

kompella

kelliher

kathleen

julozoa

jgrimsby

jfostel

jboch

jabreu

haon

grandboi

gottardi

ginav

fviloria

frerefrederiq

eupsall

eryan

emsalls

drobbins

dperrin

dionne

desmet

delorey

cwalsh

crwalls

costello

connollychrisf

celie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

anavidi

alyssar

alvintam

alexallalecw

aholling

acheney

SDodge

QYuJStalker

DEV  JIRA  User  Activity5/30/2012  1:52:32  PM

UserJStalker

QYu

SDodge

acheney

aholling

alecw

alexall

alvintam

alyssar

anavidi

andrew

atzou

barry

bhurhula

biasella

bminie

bourzgui

candido

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsby

Friday, June 15, 12

Page 154: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

20

40

60

80

100

120

140

160

180

200

220

240

Cum

ulative  Activity

weiand

voltaire

tfennell

tcasse

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima

nlennon

nicol

mcoyne

mcoole

mattlee

lisaz

lisatran

lisag

lholmes

leonmlaurena

lambiase

kompella

kelliher

kathleen

julozoa

jgrimsby

jfostel

jboch

jabreu

haon

grandboi

gottardi

ginav

fviloria

frerefrederiq

eupsall

eryan

emsalls

drobbins

dperrin

dionne

desmet

delorey

cwalsh

crwalls

costello

connollychrisf

celie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

anavidi

alyssar

alvintam

alexallalecw

aholling

acheney

SDodge

QYuJStalker

DEV  JIRA  User  Activity5/30/2012  1:57:30  PM

UserJStalker

QYu

SDodge

acheney

aholling

alecw

alexall

alvintam

alyssar

anavidi

andrew

atzou

barry

bhurhula

biasella

bminie

bourzgui

candido

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsby

Friday, June 15, 12

Page 155: Robots are Team Members, Too!

Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

weiand

voltaire

tfennell

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima nicol

mcoyne

mcoole

mattlee

lisaz

lisag

lholmes

leonmlaurena

kompella

kelliher

kathleen

julozoajboch

grandboi

gottardi

ginav

fviloria

frerefrederiq

emsalls

desmet

cwalsh

crwallscelie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

alyssar

alvintam

alecw

acheney

SDodge

QYuJStalker

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsbyFriday, June 15, 12

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ulative  Activity

weiand

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tfennell

tcasse

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima

nlennon

nicol

mcoyne

mcoole

mattlee

lisaz

lisatran

lisag

lholmes

leonmlaurena

lambiase

kompella

kelliher

kathleen

julozoa

jgrimsby

jfostel

jboch

jabreu

haon

grandboi

gottardi

ginav

fviloria

frerefrederiq

eupsall

eryan

emsalls

drobbins

dperrin

dionne

desmet

delorey

cwalsh

crwalls

costello

connollychrisf

celie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

anavidi

alyssar

alvintam

alexallalecw

aholling

acheney

SDodge

QYuJStalker

DEV  JIRA  User  Activity5/30/2012  1:57:30  PM

UserJStalker

QYu

SDodge

acheney

aholling

alecw

alexall

alvintam

alyssar

anavidi

andrew

atzou

barry

bhurhula

biasella

bminie

bourzgui

candido

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsby

Friday, June 15, 12

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Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

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80

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240

Cum

ulative  Activity

weiand

voltaire

tfennell

tcasse

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima

nlennon

nicol

mcoyne

mcoole

mattlee

lisaz

lisatran

lisag

lholmes

leonmlaurena

lambiase

kompella

kelliher

kathleen

julozoa

jgrimsby

jfostel

jboch

jabreu

haon

grandboi

gottardi

ginav

fviloria

frerefrederiq

eupsall

eryan

emsalls

drobbins

dperrin

dionne

desmet

delorey

cwalsh

crwalls

costello

connollychrisf

celie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

anavidi

alyssar

alvintam

alexallalecw

aholling

acheney

SDodge

QYuJStalker

DEV  JIRA  User  Activity5/30/2012  1:52:32  PM

UserJStalker

QYu

SDodge

acheney

aholling

alecw

alexall

alvintam

alyssar

anavidi

andrew

atzou

barry

bhurhula

biasella

bminie

bourzgui

candido

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsby

Friday, June 15, 12

Page 158: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

20

40

60

80

100

120

140

160

180

200

220

240

Cum

ulative  Activity

weiand

voltaire

tfennell

tcasse

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima

nlennon

nicol

mcoyne

mcoole

mattlee

lisaz

lisatran

lisag

lholmes

leonmlaurena

lambiase

kompella

kelliher

kathleen

julozoa

jgrimsby

jfostel

jboch

jabreu

haon

grandboi

gottardi

ginav

fviloria

frerefrederiq

eupsall

eryan

emsalls

drobbins

dperrin

dionne

desmet

cwalsh

crwalls

costello

connollychrisf

celie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

anavidi

alyssar

alvintam

alexallalecw

aholling

acheney

SDodge

QYuJStalker

delorey

DEV  JIRA  User  Activity5/30/2012  2:32:33  PM

UserJStalker

QYu

SDodge

acheney

aholling

alecw

alexall

alvintam

alyssar

anavidi

andrew

atzou

barry

bhurhula

biasella

bminie

bourzgui

candido

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsby

Friday, June 15, 12

Page 159: Robots are Team Members, Too!

Oct  1,  10 Dec  1,  10 Feb  1,  11 Apr  1,  11 Jun  1,  11 Aug  1,  11 Oct  1,  11 Dec  1,  11 Feb  1,  12 Apr  1,  12 Jun  1,  12

20

40

60

80

100

120

140

160

180

200

220

240

Cum

ulative  Activity

weiand

voltaire

tfennell

tcasse

tamason

steelmansogoloff

skim

shoangsheflersfisher

sdookranscott

schauvin

schanner

rjohnson

rhegarty

rdazaptrang

nyima

nlennon

nicol

mcoyne

mcoole

mattlee

lisaz

lisatran

lisag

lholmes

leonmlaurena

lambiase

kompella

kelliher

kathleen

julozoa

jgrimsby

jfostel

jboch

jabreu

haon

grandboi

gottardi

ginav

fviloria

frerefrederiq

eupsall

eryan

emsalls

drobbins

dperrin

dionne

desmet

delorey

cwalsh

crwalls

costello

connollychrisf

celie

carsten

candido

bourzguibminie

biasellabhurhula

atzou

andrew

anavidi

alyssar

alvintam

alexallalecw

aholling

acheney

SDodge

QYuJStalker

DEV  JIRA  User  Activity5/30/2012  1:52:32  PM

UserJStalker

QYu

SDodge

acheney

aholling

alecw

alexall

alvintam

alyssar

anavidi

andrew

atzou

barry

bhurhula

biasella

bminie

bourzgui

candido

carsten

celie

chrisf

connolly

costello

crwalls

cwalsh

delorey

desmet

dionne

dperrin

drobbins

ebevil

emsalls

eryan

eupsall

frederiq

frere

fviloria

ggiannou

ginav

gottardi

grandboi

haon

jabreu

jboch

jfostel

jgrimsby

Friday, June 15, 12

Page 160: Robots are Team Members, Too!

#summit12

If you can describe a business process -- even genome

sequencing -- you can model it in JIRA.

Friday, June 15, 12

Page 161: Robots are Team Members, Too!

Thank you!

JIRA TeamAmy BiasellaJohn Walsh

Genomics PlatformSheila FisherNiall Lennon

All our Users!

Friday, June 15, 12