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UAMS IT Biomedical Informatics Initiative. Motivation: Scattered resources. 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)

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Uams it biomedical informatics initiative

UAMS IT Biomedical Informatics Initiative


Motivation scattered resources
Motivation: Scattered resources

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)


Objectives

  • 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



Vision1
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
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
Additional Contributions

  • Other processes could be enhanced to increase efficiency and reliability

    • Security

    • Automation

    • Common Resource

    • Sharing


Data collection analysis
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?


Information Systems Integration Diagram – Dec. 2006

1/10/2007

O/P EMR

Logician

Ent. Scheduling

Renal

EPF

ADT

WebChart

Viewer

ADT,

Results

O/P

Scheduling

Tumor

Registry

OBGyn -

BirthNet

Omnicell

Cold

Feeds

ADT

ADT

I/P EMR

Clin Docum.

Eligibility

OR Mgmt

Emergency

Charges

ADT

ADT

eChart

Transplant

Acuity/Staffing

Healthquest

PM/3.0

ADT

Ultrasound

Imaging

ADT,

Orders

ADT

Results

ADT

Bed Mngmt

ADT

Charges

Integration Engine

ADT,

Results

Results

Orders

Blood Gas

ADT,

Orders

ADT, Orders

RAD

Orders,

Status, Results

Results

ADT

Lab, Rx,

OR data

Orders

Cardiology/CVL

StemLab

BMT Serve

SoftPath

LAB

Clin Lab

Anat. Path

Micro

ADT

Infection Con.

Pharmacy

Bloodbank

ADT

PACS

Transcription

Charges

Results: AP,

Lab,Hemocare

Charges,Orders

SoftMed

Transcription

Charges

Pyxis

ADAMS/MMDB

Charges

Charges

Charges

Charges

ADT

Charges & Refunds

SAP GL, HR, MM

MediPac 3.0

Med Rec Abstr

Physician

Access

Mediq

Budget

MCPG

SMS Billing

OTG Document

Imaging

MedTeach

Contract Mgmt

HSS Encoder

EIS

Healthquest

Billing

APC

PostLink

ABN Compli

ADT/Charges

TrendStar

AR & Patient Refunds

Student Info

Systems

UB92 Processor

Library

Payments

Payments

Payments

RA Posting

Claims


Data storage retrieval and sharing
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
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.



In house Bionformatics tools

Nucleotide analysis

  • 1- Sequence,pattern and structure analysis Tools

  • SeqWeb

    • Tools in Seqweb:

      • Comparison ,

      • Database Searching,

      • Evolution,

      • Mapping,

      • Pattern Recognition,

      • Primer Selection,

      • Protein Analysis,

      • Nucleic Acid,

      • Secondary Structure,

      • Translation

Phylogeny

Whole Genome Search

Protein and proteomic analysis

2- Bioinformatics Tools in Apple Cluster


InsightII

Sybyl

3- Structural biology Tools




4 statistics
4- Statistics

  • R and Bioconductor


6 resources and links open souce tools tutorials datasets http bic uams edu
6- Resources and LinksOpen souce tools,tutorials,datasets: http://bic.uams.edu

  • 5- Databases

  • BASE(microarray)

  • PathologyLab(ongoing)

  • Proteomics: 2-DPAGE and MassSpec(ongoing)


Thanks for listening
Thanks for listening

  • Suggestions

  • Discussions

  • Create solutions


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