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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) 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 not here to do: Tell investigators how to conduct research Take over investigators’ data Purchase $$$$ of computers and software 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 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? 1/10/2007 Information Systems Integration Diagram – Dec. 2006 Renal Ent. Scheduling O/P Scheduling EPF Tumor Registry Cold Feeds I/P EMR Clin Docum. Eligibility ADT ADT O/P EMR Logician ADT, Results OBGyn BirthNet Omnicell ADT ADT OR Mgmt Emergency Charges ADT eChart ADT Healthquest ADT, Orders PM/3.0 ADT Transplant Acuity/Staffing ADT Results Ultrasound Imaging ADT Bed Mngmt Charges Integration Engine Results Orders ADT, Blood Gas Cardiology/CVL Orders Results ADT SoftPath LAB ADT Bloodbank Clin Lab Anat. Path Micro Charges Charges Charges Orders, Status, Results StemLab BMT Serve RAD Lab, Rx, OR data Pharmacy Charges Results: AP, Lab,Hemocare SoftMed ADAMS/MMDB MediPac 3.0 Med Rec Abstr Budget Pyxis Transcription PACS Charges, Orders Charges Charges ADT Charges & Refunds Physician Access Mediq MCPG SMS Billing Contract Mgmt MedTeach HSS Encoder EIS Healthquest ADT/Charges Library RA Posting ABN Compli Billing AR & Patient Refunds TrendStar Student Info Systems Orders ADT Infection Con. Transcription SAP GL, HR, MM OTG Document Imaging ADT, Orders Payments UB92 Processor Claims APC PostLink 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 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 3- Structural biology Tools InsightII Sybyl 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