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.
2. We track lots of things:
100000s samples
10000s QC data points
1000s of knowledge documents
1000s small equipment pieces
1000s sequencing runs
100s of technology development projects
100s instruments (sequencing & robots)
100s of experiments
100s of people (resource mgmt)
10s of beta tests from vendors
Friday, June 15, 12
3. We track lots of things:
100000s samples
10000s QC data points
1000s of knowledge documents
1000s small equipment pieces
1000s sequencing runs
100s of technology development projects
100s instruments (sequencing & robots)
100s of experiments
100s of people (resource mgmt)
10s of beta tests from vendors
Friday, June 15, 12
4. We track lots of things:
$$$$
100000s samples
10000s QC data points
1000s of knowledge documents
1000s small equipment pieces
1000s sequencing runs
100s of technology development projects
100s instruments (sequencing & robots)
100s of experiments
100s of people (resource mgmt)
10s of beta tests from vendors
Friday, June 15, 12
5. We track lots of things:
$$$$
100000s samples
10000s QC data points
1000s of knowledge documents
1000s small equipment pieces
1000s sequencing runs
100s of technology development projects
100s instruments (sequencing & robots)
or
100s of experiments
100s of people (resource mgmt)
10s of beta tests from vendors
Friday, June 15, 12
7. Robots
are Team Members Too!
Jim Meldrim and John Stalker
The Broad Institute of MIT and Harvard
Genome Sequencing Platform
Friday, June 15, 12
8. The Broad Institute
Established 2004 - Eli and Edythe Broad
Joint Collaboration
MIT
Harvard University
Affiliated Hospitals
Beth Israel Deaconess Medical Center
Brigham and Women’s Hospital
Children’s Hospital
Dana-Farber Cancer Institute
Massachusetts General Hospital
Friday, June 15, 12
9. Organization
Programs (Science) Platforms (Technology)
Chemical Biology Genome Sequencing
Medical and Population Genetics Biological Samples
Cell Circuits Chemical Biology
Epigenomics Genetic Analysis
Genome Sequencing and Analysis Imaging
Cancer Metabolite Profiling
Infectious Diseases Proteomics
Metabolism RNAi
Psychiatric Disease Therapeutics Discovery and Development
Friday, June 15, 12
10. Organization
Programs (Science) Platforms (Technology)
Chemical Biology Genome Sequencing
Medical and Population Genetics Biological Samples
Cell Circuits Chemical Biology
Epigenomics Genetic Analysis
Genome Sequencing and Analysis Imaging
Cancer Metabolite Profiling
Infectious Diseases Proteomics
Metabolism RNAi
Psychiatric Disease Therapeutics Discovery and Development
Friday, June 15, 12
12. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
50K
$100,000
Running Sum of Samples (copy)
Cost per Genome
40K
$10,000
30K
$1,000
20K
$100
10K
$10
0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
13. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
50K
$100,000
Running Sum of Samples (copy)
Cost per Genome
1st Human Genome
40K
$10,000
2001
$3 billion
30K
$1,000
20K
$100
10K
$10
0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
14. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
50K
$100,000
Running Sum of Samples (copy)
Cost per Genome
1st Human Genome
40K
$10,000
2001
$3 billion
30K
$1,000
20K
$100
Automated 10K
$10
Sequencing
ABI3730 / Tphi 0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
15. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
50K
$100,000
Running Sum of Samples (copy)
Cost per Genome
1st Human Genome
40K
$10,000
2001 Next Gen
$3 billion
$1,000
Sequencing 30K
Illumina GA
20K
$100
Automated 10K
$10
Sequencing
ABI3730 / Tphi 0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
16. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
50K
$100,000
Running Sum of Samples (copy)
Cost per Genome
1st Human Genome
40K
$10,000
2001 Next Gen
$3 billion
$1,000
Sequencing 30K
Illumina GA
20K
$100
Automated Current SofA 10K
$10
Sequencing Illumina HiSeq
ABI3730 / Tphi 0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
17. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
50K
$100,000
Running Sum of Samples (copy)
Cost per Genome
40K
$10,000
30K
$1,000
20K
$100
10K
$10
0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
18. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
Cumulative Number of Samples
$100,000 50K
Cost per Genome
40K
$10,000
30K
$1,000
20K
$100
10K
$10
0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
19. 20.. 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
$100,000,000
80K
$10,000,000
70K
$1,000,000 60K
Cumulative Number of Samples
$100,000 50K
Cost per Genome
40K
$10,000
30K
$1,000
LCSET-1
1st JIRA tracked libraries
20K
$100 5/17/2010
10K
$10
0K
$1
April
April
April
April
April
April
April
April
April
April
June
June
June
June
June
June
June
June
June
June
August
August
August
August
August
August
August
August
August
August
December
October
October
October
October
October
October
October
October
October
February
February
February
February
February
February
February
February
February
February
Cost of Sequencing a Mammalian Genome over time and compared to Moore's Law
Genome s equencing c ost d ata c ourtesy: Wetterstrand KA. D NA Sequencing Costs: D ata f rom the NHGRI Large-Scale Genome Sequencing Program Available at: www.genome.gov/sequencingcosts. Accessed
5/9/2012
Friday, June 15, 12
29. Genome Sequencing 101
DNA (Deoxyribonucleic acid)
• Two intertwined molecules - Double Helix
Friday, June 15, 12
30. Genome Sequencing 101
DNA (Deoxyribonucleic acid)
• Two intertwined molecules - Double Helix
• Described in 1953 by James Watson and Francis Crick
Friday, June 15, 12
31. 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
Friday, June 15, 12
40. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Friday, June 15, 12
41. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Friday, June 15, 12
42. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Cancer HIV E. Coli Ice Core
Friday, June 15, 12
43. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Friday, June 15, 12
44. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Friday, June 15, 12
45. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Friday, June 15, 12
46. Outside the Genome Sequencing Platform
? Our Process
“The Players”
Scientist
Friday, June 15, 12
47. Outside the Genome Sequencing Platform Projects Group
? Our Process
Project “The Players”
Manager
Scientist
Friday, June 15, 12
48. Outside the Genome Sequencing Platform Projects Group
? Our Process
Project “The Players”
Manager
Scientist
Friday, June 15, 12
49. Outside the Genome Sequencing Platform Projects Group
? Our Process
Project “The Players”
Manager
Scientist
Friday, June 15, 12
50. Outside the Genome Sequencing Platform Projects Group
? Our Process
Project “The Players”
Manager
Scientist
Lab Operations Coordinator
Friday, June 15, 12
51. Outside the Genome Sequencing Platform Projects Group
? Our Process
Project “The Players”
Manager
Scientist
Lab Operations Coordinator
Friday, June 15, 12