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