OVium Bioinformatic Solutions
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Transcript of OVium Bioinformatic Solutions
Recommendation of a Strategy
Computational Bio-Discovery
Wolfgang Kraske PhD EE
A scientific paradigm
Bio-Information Networking
Community Tool Services
Model Characterization
Wolfgang F. Kraske, PhD
PhD Electrical Engineering University of Southern California, December 1995Advisor- Irving S. Reed, PhD, Charles E. Powell Professor Emeritus of E.E./C.S.Research- Geometric Algebra for Topological Information RepresentationMS Electrical Engineering University of Southern California, December 1986Research- Microwave Imaging and Signal ProcessingBS Physics/Mathematics-University of Maryland, UMCP, 1982
Computational Bio-Discovery
An Awkward Situation
Cellsin Vivo?
BioinformaticResearchSystem
Computational Bio-Discovery
Overview
Emerging Environment for Bio-Discovery
Community Enterprise and Tools
Model Characterization
Vector/Small Molecule
Sequence
Structure
Pathway
Computational Bio-Discovery
Goal
Establish a breakthrough network environment to promote significant drug discoveries
Integrate tools over network to promote community analysis and discoveryIntegration of Research communities
Integration of internal with external scientific communities
Integration with external patient and lay communities
Computational Bio-Discovery
Network Communities
ClinicalApplications& Research
Internal Biological Informatics Laboratory Algorithmic Definition of Structural Model Characteristics
Wet Laboratory Sequencing and Molecular Data Acquisition
PharmaceuticalResearch &Development
Mathematics andComputer ScienceResearch & Development
External ApplicationComputing Resources
CommunityBio-InformationNetwork Sources
PCR
Mass Spectrometry
Magnetic ResonanceSpectroscopy
Micro-Array
Gel Electrophoresis
Protein RapidTranslation
Southern Blot
X-ray crystallography
Computational Bio-Discovery
Challenge: Tool Integration
Tool Software Accelrys/illumina
MOLMOL/WPDB
UNIO/APSY
DBToolKit
BLAST/ZDOCK
Sequencher/Velvet
Mathlab/Octave/R
HMMER
Enterprise Software O3D/Flash/Flex/JS
Quick-time/MPlayer
Ajax/REST Service
MVC:php/ruby/perl/C#
mySQL/Oracle/MSSQL
Linux/Windows
Sybase/EMC
Centrifugation
Titration
Electron Microscopy
Light Microscopy
IVC Emulsion
Phage Display
Computational Bio-Discovery
Service Architecture Solution
Legend
Mass StorageDatabase ServerEntity ServerTool ServerWeb Content ServerHTTP ServerSocial ServerEthernet/ 100/1000 Base TNetwork SwitchLoad Balance ServerFirewall ServerFiber ChannelRest Server/
CampusLaboratoriesFirewall
REST Server
CampusSwitch
Load Balancing
Internet
Load BalancingFirewall
EntityServersDatabaseServers
MassStorage
NetworkSwitchWeb SegmentData SegmentApplicationSegmentExternalServicesWeb/Session/ToolServers
Scalable Algorithm Solutions
Parallel Language & Algorithm Library
Research Application of Parallel Algorithms
Parallel Algorithm & OS Development
Parallel Algorithm& OS Layer
MPP Clusterw/Algorithm & OS Layer
SMP w/Algorithm
MassStorage
Cloud:
App Engine
EC2/3
Oracle Metro
MS Azure
Web Services
WF Kraske, Voxar-All ATM Distributed Biomedical Visualization:T3D MPP, 8th IEEE Symposium on Computer Based Med Systems, 249, 1995
Dell Xeon Cluster, Message Passing Innterface
MVC Architecture
Fibers
REST-Representation State Transfer
Zend Framework
Ajax XMLHttpRequest
Iterated Software Lifecycle
Requirements
Design
Development
Test
Implementation
Analysis
Deployment
Upgrade orNew Iteration
CoreF1ProtoFn...
Iterated Weekly Functional Roll out
Agile and eXtreme programming processes
I Jacobson, G Booch, J Rumbaugh, Unified Software Development Process, Addison Wesley 1999
Use Case Management
SoftwareDevelopment
Programmer
Program
Test &Validation
Evaluator
Use Case
Project Manager
ResourceManagement
Report
Report
Planning
Stakeholder
Control
Conceptual Model
Sequence: Linear
Small Molecule: Node
Structure: Spatial
Pathway: Time & Space
Allometric Scaling
The 4th dimension of life (Evolution/Temporal Development)
Evolution maximizes external surface area versus internal efficiency to yield a one quarter scaling of fractal dimension(size invariant property)ie Protein folding, capillary & mitochondria formation
Conventional EuclideanBiological (Fractal)
LengthLA1/2V1/3M1/3la1/3v1/4M1/4
AreaL2AV2/3M2/3l3aV3/4M3/4
VolumeL3A3/2VMl4a3/2vM
GB west, RH Brown, BJ Enquist, The Forth Dimension of Life, Science 1677, 284, 1999
WF Kraske, Analysis & Segmentation of Higher Dimensional Data Sets, SPIE Press 264, IS12, 1995
Computational Bio-Discovery
Scale Free Versus Random
Random Network
Scale-Free Network
Scale Free Interaction characterizes the natural (Organic) behavior of : Metabolic signaling pathways
Internet links
Bioinformatic Analysis Algorithms
Protein Interactome
Knockout of Proteins Eliminates Temporal Communicationbetween Processes
Knockout of Scaffold Proteins Eliminate Structure
NATURE | doi:10.1038/nature02555 |www.nature.com/nature
NATURE | doi:10.1038/nature02555 |www.nature.com/nature2004, pp 1-6
Iterative Construction of
Deterministic Scale-Free Networks
Peripheral Nodes with 4 Links
Hub Nodes with 6 Links
A. Barbasi, Linked, Penquin Books, pp. 232-237, 2003
Level 0
Level 1
Level 2
Hub Nodes with 15 Links
Model Based Algorithms
Algorithms are easily programmed and distributed on parallel computing architecturesTrivially distributed on an SMP architecture
Optimally distributed on an MPP architecture
Use fractional dimension models to analyze biomedical data setsMarkov field analysis
Cluster measures to establish hierarchical structure
Regular statistical characterization
MEJ Neuman, SH Strogatz, DJ Watt, Random Graphs with arbitrary degree distributions & applications, Physical Review E, 64, 026118-1, 2003
Kinase Pathway Analysis
Receptor Tyrosine Kinases EGFR(ErbB1/HER1-4)Inhibited by Irressa/Tarceva
Internalized by Herceptin
VEGFR (Tumor)
FGFR
Insulin Receptor (CD220)
Nonreceptor Tyrosine Kinases Bcr-Abl
Inhibited by GleevacSerine Threonine Kinases
P38- MAPK
Cyclin dependent Kinases
Flavopinridol HIV Treatment
Indirubin Chinese Herbal
Transcription & Translation
Hox Algorithm VarietiesHox Clock
Protein Micro-Array Analysis
Pathway Studio Interpret gene expression and other high throughput data
Build, expand and analyze pathways
Find relationships among genes, proteins, cell processes and diseases
Draw publication-quality pathway diagrams
BioConductor- analysis of single channel Affymetrix and two or more channel cDNA/Oligo micro-arrays based on theR statistical package
Pathway analysis for model organisms BIND: Bio-molecular Interaction Network
Database KEGG
Science Signaling
Prolexys HyNet protein-protein
Interaction database
Probe-target hybridization
Development up to present
Multidimensional Markov field analysis is a standard algorithm for sequence analysis, signal processing and multidimensional image processing
I have programmed a variety of multi-scale and multi-dimensional algorithms on Cloud and MPP architecture with great success
A Gelman,J Hill, Data Analysis Using Regression & Multilevel/Hierarchical Models, Cambridge University Press, 2008
Further Topics for Algorithms
Incorporation of RNAi Regulation of Transcription/ Translation, Epigenic Activation and Translational Coding Cycles
Agent Based Organization and Processing to Develop and Execute Processing SystemsNeural Networks
Genetic Algorithms
Swarm Algorithms
Applications in Phylogeny, Developmental Biology, Social Psychology
CD Manning,P Ragahavan, H Shutze, Introduction to Information Retrieval, Cambridge University Press, 2008
J Augen, Bioinformatics in the Post Genomic Era, Addison-Wesley, 2005
P Baldi, S Brunak, Bioinformatics The Machine Learning Approach, MIT, 2001
Translation Codon
Human Kinome
Montage Pictures
Montage Pictures
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