Bioinformatics Service Core

seaurchininterpreterInternet and Web Development

Dec 7, 2013 (3 years and 8 months ago)

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The

Indiana

University

School

of

Medicine

(IUSM)

Bioinformatics

Service

Core

started

in

2007

in

the

Center

for

Computational

Biology

and

Bioinformatics
.

Sean

Mooney

(Department

of

Medical

and

Molecular

Genetics)

leads

the

informatics

infrastructure

and

projects

for

the

Core

while

Lang

Li

(Division

of

Biostatistics)

leads

the

analytical

services
.


We

are

an

IUSM

and

an

Indiana

Clinical

and

Translational

Sciences

Institute

(IndianaCTSI)

approved

service

core
.

We

have

been

operating

for

2

years

serving

basic

and

clinical

researchers

through

web

application

development,

data

analysis,

graphic

design,

and

more
.

Through

our

diverse

resources

and

personnel,

a

mature

development

environment,

and

our

dynamic

project

scope

we

are

able

to

serve

a

diverse

set

of

researchers

with

rapid

development

and

quality

solutions

to

many

biological,

clinical,

and

informatics

problems
.



























































































































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OVERVIEW

RESOURCES

RESEARCH CONTRIBUTION HIGHLIGHT

LIST OF SERVICES

QUALITY CONTROL AND ASSURANCES

CONTACT INFORMATION

Our

projects

include

web
-
based

data

analysis

tools,

commercial

web

sites,

cross
-
institutional

sites,

and

collaborative

workspaces
.

We

easily

adapt

to

provide

novel

features

for

clients

and

are

able

to

develop

efficiently

even

on

new

frameworks

(i
.
e
.

Joomla)

and

provide

professional

quality

graphic

design
.

Example Sites

Bioethics

Library
-

IU School of
Medicine

http://bioethics.iupui.edu/


Academic Association

of Biologics
Manufacturers

http://aabmonline.org/


Indiana Clinical

and Translational
Sciences Institute

http://indianactsi.org/

Preferred

Platforms

Platform

Linux/Apache/MySQL/PHP



Although
we also support sites in Python, Perl,
Java and ColdFusion

Framework

CakePHP


MVC

programming in PHP.
Also use Drupal and Joomla.


Workflows

Python and/or

Perl

As

with

all

projects

in

the

Core,

each

project

is

executed

by

a

staff

member

with

updates

and

results

reviewed

by

a

faculty

researcher
.

Analysis

generally

results

in

a

report

containing

a

verbal,

laymen

explanation

of

the

data,

the

analysis

algorithms,

and

further

publication
-
ready

text

as

the

client

requests
.

The

report

also

contains

images

portraying

the

data

set,

visually

answering

questions

posed

by

the

client

or

staff

member,

and

publication

quality

images

where

applicable
.

Lastly

the

report

is

returned

with

any

intermediate

or

interesting

data

set

(i
.
e
.

specific

gene

lists

applicable

to

a

given

microarray

experiment,

pathway

details,

et

cetera
)
.


Analytical

consulting

for

many

high
-
through

data

platforms

have

been

matured

enough

for

routine

analysis

services,

such

as

micoarray,

proteomics,

SNP

array,

pharmacogenetics,

sequence
-
analysis

/

next
-
generation

sequencing,

molecular

/

physiological

static

/

dynamics

network

models,

text

mining
.

Most

of

the

work

flows

have

been

built

within

BioConductor
.

Metabolomics

is

the

only

area

that

needs

further

development
.


In

order

to

facilitate

analysis

of

these

high
-
throughput

data

sets

the

Core

has

licensed

several

pieces

of

software
.

Pathway

Studio

(
http
:
//www
.
ariadnegenomics
.
com/
)

and

Ingenuity

Pathway

Analysis

(IPA,

http
:
//www
.
ingenuity
.
com
)

are

used

for

understanding

data

in

a

systems

biology

context
.

The

IPA

license

purchased

allows

the

Core

to

use

the

tool

for

analysis

and

also

sub
-
license

it

within

the

School

of

Medicine



making

IPA

far

more

affordable

for

research

labs
.

For

those

labs

purchasing

an

IPA

license,

the

core

offers

training

and

a

first

line

of

support
.

Supported Analysis

Proteomics

Microarray

SNP Arrays

Pharmacogenetics
/Correlative
-
Studies

Sequence analysis/next

generation sequencing

Metabolomics

Molecular/physiological

static/d
ynamics

network models

Text mining

Database access

Custom built tools



Data

Analysis




Biomedical

Data

Management




Graphic/Web

Design




Consulting




Community

&

Training




Tool

Access

We

are

completely

soft

funded
.

That

means

all

of

our

service

projects

are

billable
.

For

short

projects

(less

than

150
-
200

hours),

we

bill

hourly

at

$
50
/hr
.

For

longer

term

projects,

we

bill

as

a

percent

of

effort

of

a

Core

staff

member
.

Each

project

is

led

by

a

Core

staff

member

who

is

responsible

for

‘spec’ing

the

project,

making

sure

the

project

is

completed

on

time

within

budget

and

then

billed
.

While

a

staff

member

manages

the

project,

each

project

generally

has

faculty

oversight

to

ensure

the

science

behind

the

project

is

sound
.


Internally,

we

track

projects/code

with

TRAC
.

We

have

evaluated

many

tools

for

tracking

projects

including

BaseCamp,

dotProject,

Drupal

extensions,

Document

Management,

Wiki’s,

etc
.

We

built

Laboratree

to

manage

documents

and

messaging
.

We

have

built

web
-
based

tools

to

support

other

projects

on

campus,

such

as

the

Consortium

for

Breast

Cancer

Pharmacogenetics
.


Service

cores

in

various

disciplines

are

being

initiated

in

medical

schools

and

universities

across

the

country

with

the

intention

of

serving

principal

investigators

through

many

services

including

microarray

experiment

execution,

data

analysis,

visualization,

and

software

development
.

We

present

the

development

of

the

Bioinformatics

Core

at

Indiana

University

School

of

Medicine,

lessons

learned,

and

best

practices

implemented
.


We

present

example

projects

with

a

simple

explanation

of

core

operations,

and

lessons

learned

in

establishing

new

projects,

collaboration,

project

development,

and

advertising
.

We

also

discuss

practices

we've

adopted

in

development,

analysis,

and

technology
.


The

challenge


One

of

the

primary

challenges

facing

informatics

service

units

on

medical

school

campuses

is

providing

service

to

small

day
-
to
-
day

activities

as

well

as

meeting

the

significant

challenge

of

cyber
-
infrastructure

that

is

large

national

informatics

networks
.

Campuses

need

to

invest

heavily

in

adopting

to

large

informatics

networks

(such

as

caBIG,

BIRN,

etc),

however,

there

is

often

few,

if

any

resources

to

actually

invest

in

this

infrastructure
.



Projects


Examples

of

projects

we

have

undertaken

include

development

of

web
-
based

tools,

databases,

analytical

pipelines

and

analytical

consulting

services
.




Funding


The

Core

was

established

with

startup

funds

provided

by

the

Center

for

Computational

Biology

and

Bioinformatics
.

Our

continued

operation

is

funded

by

ongoing

hourly

and

percent

effort

projects
.



Future


We

hope

to

continue

to

aid

basic

and

clinical

researchers

through

existing

and

novel

services

in

the

future
.

We

recognize

several

areas,

including

large

scale

data

integration/

annotation,

online

collaboration

spaces,

and

rapid

genotyping,

as

areas

of

future

service
.

We

seek

future

clients

and

projects

by

presenting

our

mission

and

passed

work

at

faculty

meetings,

seminars,

conferences,

and

events

throughout

our

campus
.




Bioinformatics Service Core