LiveBASE, the Bioinformatics Application SuitE

Introduction: Mission Statement Leading Provider of Business Process Integration Solutions for Life Science Industry

BPI for Life Sciences Application Management Knowledge Management Data Management Databases Web Contents Legacy Systems (e.g. HR, CRM, Analytical) EquipmentProcess System KM Tools 22 Nov 2002, Computerworld

Features of LiveBASE Integrate databases and applications Integrate public domain and commercial systems that visualize DNA sequences, proteins, etc. Include connectors to manage data formats Run applications from legacy Operating Systems LiveQuest Connectors EMBOSS IBM DiscoveryLink LION SRS LiveBASE

How LiveBASE Works Drag-and-drop applications to form process Personalize Process Schedule and Execute

Features of LiveBASE Distributed and parallel computing Applications can be distributed across geographical boundaries Applications can be run in parallel Allow interactive or fully automated processing Process can be stopped halfway to receive inputs from users Include Viewer for images, XML, structures, movies, etc. Process can be automated if default values for applications are filled

A Demo of LiveBASE Open Workflow Open Bubblelist Link Bubble Insert Bubble

An application of LiveBASE: Genomics and Proteomics Studies chromatogram DNA Sequence Modification Sequence Similarity Search for Regulatory Sites Suggest Coding Regions Translation Protein Properties merger: join two sequences revcomp: make a complementary strand abiview: convert ABI chromatogram to a sequence in AGCT search many sequences ： (BLAST, FASTA) pair wise ： water, needle, seqmatchall multiple ： emma + (clustalW) fuzznuc: pattern matching getorf: ORF extraction cpgreport: infer CpG islands chips: codon usage wobble: 3-base periodicity motif search ： fuzzpro, patmotifs sequence-feature extraction ： antigenic, pepcoil, sigcleave, tfscan Protein Functions translate: tranlation to amino acids motif search, specialized ： digest: restriction enzyme sites physical-chemical properties ： iep: isoelectric point charge: charge plot pepwindow: average hydropathy secondary-structure prediction ： garnier Phylogenetics Pasimony, Distance Matrices

An application of LiveBASE: ABIView for Chromatograph viewing

An application of LiveBASE: Genomics and Proteomics Studies Sequence Alignment Translation & Site Searching Protein Function Analysis Protein Property Analysis

KOOPLATFORM LIVEPORTAL Technologies of KOOPrime: KOOPrime Solutions HIGH THROUGHPUT SCREENING GENOMICS, PROTEOMICS LAB MGT AND ANALYSIS HOSPITAL HL7 EXCHANGE CLINICAL TRIAL SYSTEM KOOP-EDUCATION SYSTEM HEALTH TRACKING SYSTEM PRE-CLINICAL TRIAL SYSTEM TISSUE REGISTRY LiveBASE LiveLINKS LiveXchange LiveQuest LiveIDEA

Different modes of deployment IndividualClassroom Based Enterprise Wide LiveBASE Lite LiveBASE Enterprise (APBioBox)

Why LiveBASE? All for One and One for All!  End-to-end Integration and Automation  Support EMBOSS, MS Excel and other tools  Distributed Computing to manage compute workload  Connectors to support BLAST, EMBL and other formats  Open-ended to integrate more tools  Reduce learning curve  Set of processes for jump-start  Sample Data/Files as inputs for processes  Knowledge based  Visual drilling interfaces facilitate top-down learning