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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