This presentation includes an intro to bioinformatics with an emphasis on human genome re-sequencing and how Hadoop and Neo4j can be used together to open striking possibilities.

1. {GraphConnect NYC}
Hadoop and Graph Databases
(Neo4j): Winning Combination for
Bioinformatics
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

2. Hadoop + Neo4j = Bioanalytics Win
Open Software Integrators
●
Jonathan Freeman
@freethejazz
Founded January 2008 by Andrew C. Oliver
○ Durham, NC
Revenue and staff has at least doubled every year since
2009.
●
New office (2012) in Chicago, IL
○ We're hiring associate to senior level as well as UI Developers
(JQuery, Javascript, HTML, CSS)
○ Up to 50% travel (probably less), salary + bonus, 401k, health,
etc etc
○ Preferred: Java, Tomcat, JBoss, Hibernate, Spring, RDBMS,
JQuery
○ Nice to have: Hadoop, Neo4j, MongoDB, Ruby a/o at least one
Cloud platform
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

3. Hadoop + Neo4j = Bioinformatics Win
Questions to answer
●
●
●
●
uhh, bioinformatics?
What is Hadoop? Why is it a good fit?
And Neo4j? Why the combination?
I want this now! How do I do it?!?!
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}
Jonathan Freeman
@freethejazz

4. {Hadoop + Neo4j = Bioinformatics Win}
Bioinformatics
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

5. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
“
dynamic
information processing
system
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

6. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Life
http://www.labtimes.org/labtimes/issues/lt2011/lt07/lt_2011_07_26_29.pdf
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

7. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
● Storing/Retrieving Biological Data
● Organizing Biological Data
● Analyzing Biological Data
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

8. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Biological Data
● amino acid sequences
● nucleotide sequences
● protein structures
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

9. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
●
●
●
●
●
Genetic sequence analysis
Tracing biological evolution
Analysis of gene expression
Studying mutations in cancer
Predicting protein structure and
function
● Molecular Interaction
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

10. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
●
●
●
●
●
Genetic sequence analysis
Tracing biological evolution
Analysis of gene expression
Studying mutations in cancer
Predicting protein structure and
function
● Molecular Interaction
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

11. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Full Human Genome Sequencing Then
13 Years
$2,700,000,000
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

12. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Full Human Genome Sequencing Then
1 Day
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}
$5,000

13. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
http://www.genome.gov/images/content/cost_per_genome_apr.jpg
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

14. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
So what are we
waiting for?
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

15. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

16. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
well, the thing
about that…
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

17. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

18. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

19. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
...
ATTCCAGGAGTATTGACACCAT...
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

20. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

21. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

22. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

23. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
AGGATTACCAGGA
CAAAGGATT
TTACCAGGATACCAG
TGACAA
AAGGATTAC
GATACCAGTA
CAAGGATT
GTGACAA
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

24. {Hadoop + Neo4j = Bioinformatics Win}
Hadoop
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

25. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Infrastructure for distributed computing
HDFS
MapReduce
A distributed file system.
An implementation of a
programming model for
processing very large data sets.
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

26. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
…
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

27. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

28. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

29. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Infrastructure for distributed computing
HDFS
MapReduce
A distributed file system.
An implementation of a
programming model for
processing very large data sets.
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

30. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
AGGATTACCAGGA
CAAAGGATT
TTACCAGGATACCAG
TGACAA
AAGGATTAC
GATACCAGTA
CAAGGATT
GTGACAA
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

31. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
...
ATTCCAGGAGTATTGACACCAT...
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

32. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
1000 CPU hours
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

33. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
3 hours
$85
OSS
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

34. {Hadoop + Neo4j = Bioinformatics Win}
And Neo4j?
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

35. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

36. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
MATCH (snp)<-[:INFLUENCED_BY]-(conditions)
WHERE snp.id = “rs1234”
RETURN conditions;
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

37. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
MATCH (p)-[:GENOME_CONTAINS]->(snp)
(snp)<-[:INFLUENCED_BY]-(conditions)
WHERE p.name = “Jonathan Freeman”
RETURN conditions;
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

38. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
MATCH (p)-[:GENOME_CONTAINS]->(snp)
(snp)<-[:INFLUENCED_BY]-(conditions)
WHERE c.name = “Parkinsons”
RETURN p;
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

39. {Hadoop + Neo4j = Bioinformatics Win}
How can I haz?!?!?!1
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

40. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Step 1: Get local copies
● Hadoop: http://www.neo4j.org/download
● Neo4j: http://hadoop.apache.org/releases.html#Download
● Batch Importer: https://github.com/jexp/batch-import
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

41. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Step 2: Familiarize yourself with the languages
●
●
●
MapReduce: http://hadoop.apache.org/docs/r0.18.3/mapred_tutorial.html
Pig: http://pig.apache.org/docs/r0.12.0/start.html
Hive: https://cwiki.apache.org/confluence/display/Hive/GettingStarted
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

42. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Step 3: Find a dataset
●
●
Typical starter data: http://www.gutenberg.org/
Amazon’s public data sets: http://aws.amazon.com/publicdatasets/
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

43. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Step 4: Start Playing!!!
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

44. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Step 5: Take Hadoop to the cloud
● http://aws.amazon.com/elasticmapreduce/
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

45. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Doing this in production?
http://blog.xebia.com/2012/11/13/combining-neo4j-and-hadoop-part-i/
http://blog.xebia.com/2013/01/17/combining-neo4j-and-hadoop-part-ii/
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

46. {Hadoop + Neo4j = Bioinformatics Win}
Thank You
@freethejazz
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}

47. Hadoop + Neo4j = Bioinformatics Win
Jonathan Freeman
@freethejazz
Image Attribution:
Sand Timer: http://bit.ly/HyCAgy
Money: http://bit.ly/1e4lhS6
Scraggly DNA drawings: Jonathan Freeman :)
{Open Software Integrators} { www.osintegrators.com} {@osintegrators}