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The Best of Both Worlds: Speeding Up Drug Research with MongoDB & Oracle (Genentech)
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Transcript of The Best of Both Worlds: Speeding Up Drug Research with MongoDB & Oracle (Genentech)
Speeding Up Drug Research with MongoDB
Introducing MongoDB
into an RDBMS Environment
Doug Garrett
• Genentech Research and Early Development (gRED)
Bioinformatics and Computational Biology (B&CB)
Software Engineer
gRED: Disease and Drug Research
Bioinformatics Customers: Scientists
Most of All: Patients
Bioinformatics: Not Your Typical IT
MongoDB
• Not just about big dataMongoDB has a flexible schema
• Not just about new systemsMongoDB easily integrates with RDBMS
• Not just about softwareIt’s about saving lives
Time to Introduce New Genetic TestW
eeks
Drug Development Process
9
NewDrug
Drug Development Process
10
NewDrug
Drug Development Process
11
NewDrug
New Mouse Model - Genetic Testing
File (csv)
J. Colin Cox Sept. 2013 Presentation
Growth In Genetic Testing(t
hou
san
ds)
Samples
Genotypes
6 months 3 months
6 months 3 months
6 months 3 months
Varies by Genetic Test
Case Study: New Genetic Test Instrument
20
New Instrument!
Impact?
Bio-RadCFX384
ABI7900HT
Case Study: New Genetic Test Instrument
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New Instrument!
Impact?
DB Schema? No Impact
Project? 3 weeks
Bio-RadCFX384
ABI7900HT
Going Live…
22
Failure Mode
Failure Mode
Synch MongoDB with RDBMS
db.NewRdbmsMongoId .find().forEach(function(doc){ db. TestResults .update({'_id':doc._id}, {'$inc':{useCount:1}})})
db. db. TestResults.remove({'useCount':0});
But Wait! There’s More…
• Flexible data collection
Load CSV to MongoDB
"_id" : ObjectId(“…."),“plate_wells” : [ { "Well" : "A01", "Sample" : "308…", … }]
Add Fields to CSV
"_id" : ObjectId(“…."),“plate_wells” : [ { "Well" : "A01", "Sample" : "308…", … "New1" : "New Value" }]
Future – What If…
Avoiding the typical “Catch 22”:
1.Is it worth collecting the data?
2.What is the value of the data?
3.Need the data to find the value
Future Analytics
MongoDB Aggregation Framework
RMatlab
MongoDB Aggregation Framework
40% Discount Thru July 4Use Code: mdbdgcf
Under Discussion
CSV
JSON
XML
Other
Lab Instruments
GovernmentAgencies
Third PartySources
MongoDB
Load to RDBMS
Process Directly
MongoDB
• Not just about big dataMongoDB has a flexible schema
• Not just about new systemsMongoDB easily integrates with RDBMS
• Not just about softwareIt’s about saving lives
“You better do it fast”
For my Father
Who I hope would have enjoyed this talk