computing in the age of the $1000 genome
DESCRIPTION
A look at trendsTRANSCRIPT
Biomarkers for Pharmacogenomics
Right doseRight drugRight patientRight time
PERSONALIS
ED MEDIC
INE
Biomarkers for Plant Breeding
Discovering Biomarkers in Sequence
Genotype;
Genome/exome resequencing,
Genome Wide Association Studies (GWAS).
Gene expression;
RNA-Seq,
Expression Quantative Trait Loci (eQTL).
Epigenetic;
ChIP-Seq, Bisulfide-Seq, sequence capture,
Epigenetic GWAS (eGWAS).
Metagenomic.MISSIN
G HERITA
BILITY
Bioinformatics Areas
%
Gene
expr
ession
Genom
ic v
aria
tion
Compa
rativ
e ge
nom
ics
Path
way
ana
lysis
Syst
ems bi
olog
y
Epig
enet
ics
Gene
pred
ictio
n
Biom
arke
r disco
very
Prot
eom
ics
Met
agen
omics
Met
abol
omics
0
20
40
60
80
100
120
Not anticipated
In the future
Currently
The big twoBlockbuster
>70%Mainstream
50-70%
Specialty<50%
Specialty
Areas, Public V. Private
Gene
expr
ession
Genom
ic v
aria
tion
Compa
rativ
e ge
nom
ics
Path
way
s
Syst
ems bi
olog
y
Epig
enet
ics
Gene
pred
ictio
n
Biom
arke
r disco
very
Prot
eom
ics
Met
agen
omics
Met
abol
omics
0
10
20
30
40
50
60
70
80
90
100
PUBLICPRIVATE
%
MatureEmerging Commercialised
Sequencing Technology
Capillary Sequencing
Array sequencing
1998
20052006
2010
2010201?
Sequence Cost
Read Length
Quality
$1000
OPT-ICAL
AMPL-IFIED
ELECT-RICAL
AMPLI-FIED
OPT-ICAL
SINGLE MOL
ELECT-RICAL
SINGLE MOL
Turner – the Deluge
“Data tsunami”
“Tidal wave of data”
The Sequencing Cliff
$1000 genome~$0.01 Mbase (30x coverage)
Bioinformatics Crash Landing?
What needs to change?
The following must increase:
1. Hardware scalability,
2. In-house bioinformaticians, and/or bioinformatics outsourcing
3. Software quality.
1. Hardware scalability
On desktop PCsOn serversOn clustersOn the cloud
Yes
Yes
No
No
2. In-house Vs. Outsourcing
Respo
nse
to cha
nge
Data
secu
rity
Supp
ort c
ost
Acce
ss to
exp
ertis
e
Devel
opm
ent c
ost
Prod
uct q
ualit
y
Spee
d of
del
iver
y
Wor
kloa
d sc
alab
ility
Overa
ll pr
ojec
t cos
t
Overa
ll pr
ojec
t risk
0
10
20
30
40
50
60
70
80
90
100
Outsourced betterNeitherIn-house better
%
In-house wins overall
Outsource wins in scalability
3. Software Quality
Stab
ility
/relia
bilit
y
Scie
ntifi
c va
lidat
ion
Compu
tatio
nal e
fficien
cy
Easy
to in
stal
l/mai
ntai
n
Visu
al re
pres
enta
tion
Secu
rity
Inte
grat
ion
Ease
of u
se
Avai
labi
lity
of tr
aini
ng
Comm
ercial
sup
port
0
20
40
60
80
100
120
IrreleventUsefulImportant
%
Technical attributes win
Technical attributes win
Technical attributes win
Usability attributes lose
Usability attributes lose
Usability attributes lose
BUT…CAN THIS APPROACH SCALE?
Bioinformaticians like to;
• Develop their own solutions,
• Using open-source software,
• That’s stable, reliable, and published
Bioinformaticians don’t like to;
•Outsource, or use commercial software,
•Develop user-friendly, supported software.
Is this the Answer?
“Genome Content Management is the set of processes and technologies that support the creating, managing, and reporting of genomic data.”
Create
Man
ag
e
Report
Create
Report
Ext
end
Manage
Share
Reuse
TIMELINE: 100% Bespoke…..…Common Schemas/APIs…..…Content Management Systems
An Open Source Service Company
Consultancy/advice Training Support Installation/Integration Customization Out sourced management
BusinessOpen Community(e.g. Academia)
Service Company
ServiceCollaboration
And Finally
• The survey closes at the end of march,
• Those that participated, thanks!
• Those that did not, please participate!
• Tell your friends! Tell your enemies!
• We will run it again next year; suggestions?
http://eaglegenomics.com/survey
Genome Content Management Systems (G-CMS)
Wo
rkfl
ow
Ori
ente
d
Datab
ase Orien
ted
Open Source Proprietary