Bioinformatics Community SurveyBioGeeks, KCL 24th Feb 2011
William [email protected]
http://eaglegenomics.com/survey
The Bioinformatics Survey• What are the key initiatives in
bioinformatics? • How can these be delivered? • Do they meet operational requirements? • How could they be improved?
• Results will influence development of the next generation of bioinformatics tools;• Guiding policy makers, tool designers and
developers,• Published as an open-access report.
http://eaglegenomics.com/survey
Spoiler AlertBioinformaticians 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.
http://eaglegenomics.com/survey
Company Background Professional services company (bioinformatics);
Founded in May 2008, To make open source/access easier for businesses.
Wide breadth of experience; Balanced knowledge of biology and computer science, From commercial and academic backgrounds.
We build connections and foster collaborations with academic groups.
Delivering a range of successful solutions to a global customer base.
An Open Source Service Company
Consultancy/advice Training Support Installation/Integration Customization Out sourced management
BusinessOpen Community(e.g. Academia) Service Company
ServiceCollaboration
Eagle’s Collaborations with Academia
For Eagle; Credibility Ongoing knowledge transfer
For the academic group; Increased user base (e.g. SMEs) Tangible economic impact
important for funding agencies Collaborative development
contribution of code and documentation Financial rewards
OVER 50 RESPONSES IN A WEEK
CambridgeLondonOther UKOther EuropeUSAOtherUnknown
Biogeeks? Max 11
DemographicIn which sector do you work?
UniversityNon-profitPharmaceuticalAgribiotechBiotechnology
How many others do you manage?
NoneOne2 to 45 to 10Over 10
What is your bioinformatics experience (years)?
NoneOne2 to 45 to 10Over 10
How many bioinformaticians in your organisation?
NoneOne2 to 45 to 10Over 10
University
~ 50%
>5 years
~ 75%
>10 people
~ 50%
None~ 50%
Bioinformatics Areas
%
Gene e
xpres
sion
Genom
ic vari
ation
Compa
rative
geno
mics
Pathw
ay an
alysis
Syste
ms biol
ogy
Epige
netic
s
Gene p
redict
ion
Biomark
er dis
covery
Proteo
mics
Metage
nomics
Metabo
lomics
0
20
40
60
80
100
120
Not anticipatedIn the futureCurrently
The big twoBlockbuster
>70%Mainstream
50-70%
Specialty<50%
Specialty
Areas, Public V. Private
Gene e
xpres
sion
Genom
ic vari
ation
Compa
rative
geno
mics
Pathw
ays
Syste
ms biol
ogy
Epige
netic
s
Gene p
redict
ion
Biomark
er dis
covery
Proteo
mics
Metage
nomics
Metabo
lomics
0
10
20
30
40
50
60
70
80
90
100
PUBLICPRIVATE
%
Mature Emerging Commercialised
Technologies
Meta an
alysis
/integ
ration
Genom
e rese
quen
cing
De nov
o asse
mbly
RNA-seq
Compa
rative
geno
mics/M
SA
Exom
e seq
uenci
ng
Epige
netic
s (ChIP
-chip/
seq)
Microa
rray g
enoty
ping
Proteo
mics/M
ass sp
ec
Microa
rray e
xpres
sion
0
10
20
30
40
50
60
70
80
90
Not anticipatedIn the futureCurrently
%
Integrationwins!
Bad Omission
GWAS old news already?
NGSNGSNGSNGSNGS
The Sequencing Cliff
Bioinformatics Crash Landing?What needs to change?The following must increase:1. Hardware scalability, 2. In-house bioinformaticians, and/or
bioinformatics outsourcing3. Software quality.
Delivery of Bioinformatics
In-ho
use co
mputin
g
Cloud c
ompu
ting
Outsou
rced c
ompu
ting
In-ho
use de
velop
ment
Outsou
rced d
evelo
pmen
t
In-ho
use an
alysis
Outsou
rced a
nalys
is
Open-s
ource
softw
are
Commerc
ial so
ftware
0102030405060708090
100
Not anticipatedIn the futureCurrently
In-house vs. outsourced
2. In-house vs. outsourced
3. Softwarequality
1. Hardwarescalability
%
Different attitudes to delivery?
In-ho
use co
mputin
g
Cloud c
ompu
ting
Outsou
rced c
ompu
ting
In-ho
use de
velop
ment
Outsou
rced d
evelo
pmen
t
In-ho
use an
alysis
Outsou
rced a
nalys
is
Open-s
ource
softw
are
Commerc
ial so
ftware
0
10
20
30
40
50
60
70
80
90
100
PUBLICPRIVATE
In-house vs. outsourced
2. In-house vs. outsourced
3. Softwarequality
1. Hardwarescalability
%
1. Hardware scalability
On desktop PCsOn serversOn clustersOn the cloud
Yes
Yes
No
No
2. In-house Vs. Outsourcing
Respon
se to
chang
e
Data se
curity
Supp
ort co
st
Acces
s to e
xpert
ise
Develo
pmen
t cost
Produ
ct qu
ality
Spee
d of d
elive
ry
Workloa
d scal
abilit
y
Overal
l proj
ect co
st
Overal
l proj
ect ris
k0
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
Stabil
ity/re
liabil
ity
Scien
tific v
alida
tion
Compu
tation
al effi
ciency
Easy
to ins
tall/m
aintai
n
Visua
l repre
sentat
ion
Secur
ity
Integ
ration
Ease
of use
Avail
abilit
y of tr
aining
Commerc
ial su
pport
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
3. Software Quality
Stabil
ity/re
liabil
ity
Scien
tific v
alida
tion
Compu
tation
al effi
ciency
Easy
to ins
tall/m
aintai
n
Visua
l repre
sentat
ion
Secur
ity
Integ
ration
Ease
of use
Avail
abilit
y of tr
aining
Commerc
ial su
pport
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 publishedBioinformaticians 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
Manage
Report
Create
Repo
rtEx
tend
Manage
Share
Reuse
TIMELINE: 100% Bespoke…..…Common Schemas/APIs…..…Content Management Systems
Genome Content Management Systems (G-CMS)
Wor
kflo
w O
rient
ed
Database O
riented
Open Source Proprietary
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