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

KnowledgeManagement

DataManagement

Databases Web Contents

Legacy Systems(e.g. HR, CRM, Analytical)

Equipment Process 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-dropapplications

to form process

PersonalizeProcess

Schedule andExecute

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

OpenWorkflow

OpenBubblelist LinkBubble

InsertBubble

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 plotpepwindow: 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 AnalysisProtein Property Analysis

KO

OP

LAT

FO

RM

LIVE

PO

RT

AL

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

Individual Classroom 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