Bioinformatics Community SurveyBioGeeks, KCL 24th Feb 2011

William Spoonerwhs@eaglegenomics.com

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