UAMS IT Biomedical Informatics Initiative

Sites at UAMS containing references to or people who perform bioinformatics services

http://www.cor.uams.edu/bioinformatics.asp (Center or Ortho. Research- Larry Suva)

http://bioinformatics.uams.edu/ (Bioinformatics Center-Tom Kieber-Emmons)

http://brin.uams.edu/bioinformatics.asp (INBRE - Larry Cornett)

http://microarray.uams.edu/services.htm (Microarray Core)

http://myeloma.uams.edu/lambertlab/ (Myeloma Institute- John Shaughnessy)

http://www.acnc.uams.edu/- (Arkansas Children’s Nutrition Center)

http://www.uams.edu/biostat/ (Biostatistics- Radha Nagarajan)

http://intranet.uams.edu/it/Bioinformatics/ (IT- Umit, Rinku, Ted)

…

Motivation: Scattered resources

What we are here to do: Address the needs of investigators by

Fostering a collaborative environment Locating software and hardware resources Developing interfaces for those resources

What we are not here to do: Tell investigators how to conduct research Take over investigators’ data Purchase $$$$ of computers and software

Objectives

Vision

Vision

Our vision is to identify, map, and interface existing and projected

information, content and services supporting research.

Diagnostic ,therapeutics and vaccines

Target discovery

Biological Research

Knowledge Generation

Data tailored,visualization and annotation

Data Storage,Queries,management

Some areas where we can contribute

Existing hardware/software resources, such as: Data collection,

Data analysis,

Data storage (both long and short term),

Data retrieval,

Data sharing.

In addition, support or take responsibility for the following areas.

Database design, Data mining, Artificial intelligence

Web development (page, portal, or access)

Distributed computing, Grid, and Security

etc.

Additional Contributions

Other processes could be enhanced to increase efficiency and reliability Security Automation Common Resource Sharing

Data Collection & Analysis

How is data currently collected?

What software and hardware are being used?

Would the researchers prefer an alternative?

Commercial, freeware and open source options

More secure and efficient environment

Are others on campus using same or similar?

I/P EMRClin Docum.

Ent. Scheduling

Integration Engine

HealthquestPM/3.0

Omnicell

SAP GL, HR, MM

TrendStar

Bloodbank

SoftPathLAB

Clin LabAnat. Path

MicroSoftMed

TranscriptionPyxis

Pharmacy

RAD

MCPGSMS Billing

Healthquest

Billing

ADT

ADT ADT, Orders Results

Results

ADT, Orders

Results: AP, Lab,Hemocare

ADT, Orders Orders,

Status, Results

Transcription

ADT

Charges

Charges & Refunds

ADT

ADT

Charges

PhysicianAccess

OBGyn -BirthNet

TumorRegistry

OR Mgmt

O/PScheduling

Transplant

Budget

ADT

ADT

Charges

Charges,Orders

Eligibility

PACS

Orders

ADT

ADT,Results

Renal

MedTeach

O/P EMRLogician

ADT

UltrasoundImaging

Mediq

Charges

Blood Gas

ADT,

Results

1/10/2007

Orders

Infection Con.

Lab, Rx,OR data

OTG DocumentImaging

Charges

Library

Information Systems Integration Diagram – Dec. Information Systems Integration Diagram – Dec. 20062006

RA PostingUB92 Processor

PaymentsClaims

Charges

EPFADT

Charges

Charges

MediPac 3.0Med Rec Abstr

HSS Encoder

Cardiology/CVL

ABN Compli

Contract Mgmt

ResultsADT

APCPostLink

AR & Patient Refunds

eChart

ADT

Acuity/Staffing

Student InfoSystems

WebChart

Viewer

ADT

ColdFeeds

StemLabBMT Serve

ADAMS/MMDB

Emergency

Bed Mngmt

ADT/ChargesEIS

PaymentsPayments

Data Storage, Retrieval and Sharing

Short and long term storage Local drive vs. network vs optical

Database vs Windows folders

Data sharing Database/Network folders/SharePoint

Security Data accessible only to those who need it

Benefits of IT Bioinformatics Support

Much data collection and analysis is repetitious. Automation can decrease the time required as well as limit the opportunities for error.

Well written interfaces for software increase their utility and provide opportunity for alternative analysis (i.e. exploration and discovery).

Hard drives fail, even new ones. Storing data in a secure database reduces risk of lost data and allows for secure viewing and/or sharing.

Creating a centralized infrastructure by means of utilizing available and planned resources.

Increase productivity.

Research Communities link website (researchlink.uams.edu)

In house Bionformatics tools

1- Sequence,pattern and structure analysis Tools

SeqWebTools in Seqweb:

Comparison ,Database Searching, Evolution, Mapping,Pattern Recognition,Primer Selection, Protein Analysis,Nucleic Acid, Secondary Structure, Translation

Nucleotide analysis

Protein and proteomic analysis

Phylogeny

Whole Genome Search

2- Bioinformatics Tools in Apple Cluster

InsightII Sybyl

3- Structural biology Tools

InsightII

Sybyl

4- Statistics

R and Bioconductor

5- Databases

BASE(microarray)

PathologyLab(ongoing)

Proteomics: 2-DPAGE and MassSpec(ongoing)

6- Resources and Links

Open souce tools,tutorials,datasets: http://bic.uams.edu

Thanks for listening

Suggestions

Discussions

Create solutions