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

21

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