Transcript Document

LiveBASE, the Bioinformatics
Application SuitE
Introduction:
Mission Statement
Leading Provider of
Business Process Integration
Solutions for
Life Science Industry
BPI for Life Sciences
Data
Management
Databases
Web Contents
22 Nov 2002, Computerworld
Legacy Systems
(e.g. HR, CRM, Analytical)
KM Tools
Application
Management
Knowledge
Management
Equipment
Process System
Features of LiveBASE
EMBOSS
IBM DiscoveryLink
LiveBASE
LION SRS
LiveQuest
Connectors
• 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
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
An application of LiveBASE:
Genomics and Proteomics Studies
Sequence Modification
Search for Regulatory Sites
fuzznuc: pattern matching
merger: join two sequences
revcomp: make a complementary strand
chromatogram
DNA
Suggest Coding Regions
abiview: convert ABI chromatogram to a sequence in AGCT
getorf: ORF extraction
cpgreport: infer CpG islands
chips: codon usage
wobble: 3-base periodicity
Sequence Similarity
search many sequences：
(BLAST, FASTA)
Translation
pair wise：
water, needle, seqmatchall
multiple：
emma + (clustalW)
translate: tranlation to amino acids
Protein Functions
Phylogenetics
Pasimony, Distance Matrices
Protein Properties
motif search：
fuzzpro, patmotifs
motif search, specialized：
digest: restriction enzyme sites
sequence-feature extraction：
antigenic, pepcoil, sigcleave, tfscan
physical-chemical properties：
iep: isoelectric point
charge: charge plot
pepwindow: average hydropathy
secondary-structure prediction：
garnier
An application of LiveBASE:
ABIView for Chromatograph viewing
An application of LiveBASE:
Genomics and Proteomics Studies
Sequence Alignment
Protein Function Analysis
Translation & Site Searching
Protein Property Analysis
Technologies of KOOPrime:
KOOPrime Solutions
HIGH THROUGHPUT
SCREENING
GENOMICS,
PROTEOMICS LAB
MGT AND ANALYSIS
LiveBASE
LiveXchange
LiveQuest
LiveIDEA
LIVEPORTAL
KOOPLATFORM
LiveLINKS
PRE-CLINICAL
TRIAL SYSTEM
CLINICAL TRIAL
SYSTEM
KOOP-EDUCATION
SYSTEM
TISSUE
REGISTRY
HEALTH TRACKING
SYSTEM
HOSPITAL HL7
EXCHANGE
Different modes of
deployment
LiveBASE Lite
(APBioBox)
Individual
LiveBASE Enterprise
Classroom
Based
Enterprise
Wide
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