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UAMS IT Biomedical Informatics Initiative

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

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  1. UAMS IT Biomedical Informatics Initiative

  2. 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) • …

  3. 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

  4. Vision

  5. 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

  6. 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.

  7. Additional Contributions • Other processes could be enhanced to increase efficiency and reliability • Security • Automation • Common Resource • Sharing

  8. 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?

  9. 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

  10. 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

  11. 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.

  12. Research Communities link website (researchlink.uams.edu)

  13. 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

  14. InsightII Sybyl 3- Structural biology Tools

  15. InsightII

  16. Sybyl

  17. 4- Statistics • R and Bioconductor

  18. 6- Resources and LinksOpen souce tools,tutorials,datasets: http://bic.uams.edu • 5- Databases • BASE(microarray) • PathologyLab(ongoing) • Proteomics: 2-DPAGE and MassSpec(ongoing)

  19. Thanks for listening • Suggestions • Discussions • Create solutions

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