Slide 1

“The World's 1st
Ultra High throughput Genomics Data Platform”

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Slide 2

Introductions
Robert George Hercus – CTO/MD
Over 30 years IT experience
Pioneered many large-scale IT
projects
“Language of Biology” basis of
Synamatix

Synamatix 1 of 4 companies in
group: Linguamatix, Neuramatix
and Viramatix
Interests: Linguistics, Genomics,
Artificial Intelligence, Neuronal
Networks

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Slide 3

What we are NOT….what we ARE..
NOT ABOUT:
Data content
Flat file, hierarchical or Relational Databases
Replacement of existing browser/mapping tools: e.g.EnsEMBL
Just a Blast alternative……..
Applications – IP is within SynaBASE

ARE ABOUT:
NEW CONCEPT: Proprietary pattern based approaches to construct
1st “structured-network data system” for biological data
ITERATION, SPEED and EXTENSIBILITY: enable single data system
for a wide array of biological data – enabling enterprise wide
capability
Providing tools, Know-how and Technologies to assist in
understanding and ultimately defining the “language” of
biological data – FUNCTIONAL GENOMICS

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Slide 4

Intelligence… not
brute force
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Slide 5

Syntax and Semantics

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Slide 6

Synamatix

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Slide 7

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Slide 8

Basis of IP – Human Brain>SynaBASE
This is
SynaBASE:
Identifies
and learns
patterns
without
human
supervision
or training
sets.
Synabase
maintains
patterns &
their
relationships

Highly
efficient
data
structures
and
relationships
between
data
elements
are
constructed

Copyright © 2004 Synamatix sdn bhd (538481-U)

Applications
becomes
more
accurate and
efficient as
more data is
added


Slide 9

A structural database for genomics data, SynaBASE*

*patents pending
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Slide 10

4
unique features
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Slide 11

1. Patterns and structures
Finds, Stores, Relates & Structures
PATTERNS,
not FLAT FILES

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Slide 12

What makes Synamatix UNIQUE - 1
What do we
know about
data ?

There is no evolutionary need to
preserve non-functional sequence
patterns
Evolution requires the
conservation of patterns which are
at least functionally equivalent, or
functionally better

Similarity
of DATA
Common PATTERNS and
functionality

Significant patterns and their
relationships are extended and
maintained by SynaBASE

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Slide 13

A conventional flat-file database

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Slide 14

SynaBASE * - A structured network database

*patents pending
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Slide 15

2. Significance and Frequency
SynaBASE automatically learns and
maintains the significance of patterns and
data

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Slide 16

Significance
Fixed length K-mers are inappropriate

The elephant and the giraffe walked up the mountain
A graph showing Frequency of “string (word)” patterns
in a sentence does not reflect meaning

The elephant and the giraffe walked up the mountain
A graph showing Probabilities of predicting Precessor and Successor
characters (string Significance) reflects true meaning

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Slide 17

HUMAN Placental ribonuclease inhibitor
FREQUENCY

SIGNIFICANCE

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Slide 18

3. Scale and Speed
Unique method for structuring data leads to
Ultra-high-throughput applications becoming routinely accessible

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Slide 19

What makes Synamatix UNIQUE - 3
All Eukaryotes

All Prokaryotes

Proteomics

All genomes!!
Human

Any data

VirusAll

Protein Interactions

Array data

proteomes!!
Mouse

Multiples….

Array analysis

Text

Phylogenetics

Sequence data
Non-Sequence data

3rd Party

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Slide 20

Multi-genome scalability – flat file db
10
Genome 10 – 99.9%
9
Genome 9 – 99.9%
8
Genome 8 – 99.9%
7

Size of database

Genome 7 – 99.9%
6
Genome 6 – 99.9%
5
Genome 5 – 99.9%
4
Genome 4 – 99.9%
3
Genome 3 – 99.9%
2
Genome 2 – 99.9%

1
Genome 1
2

4
6
Number of Human genome copies
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8

10


Slide 21

Multi-genome scalability – SynaBASE
10
9
8
7

Size of database

6
5
4

Genome 10 – 99.9%
Genome 9 – 99.9%
Genome 8 – 99.9%
Genome 7 – 99.9%

Genome 6 – 99.9%
Genome 5 – 99.9%

3

Genome 4 – 99.9%

2

Genome 3 – 99.9%
Genome 2 – 99.9%

1

Genome 1

2

4
6
Number of Human genome copies
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8

10


Slide 22

Analysis speed scales at logn base 2
Speed milliseconds
1000
900

Conventional
800
700
600
500
400
300
200

100

1 10

100

Size of database giga bp
Copyright © 2004 Synamatix sdn bhd (538481-U)

1000


Slide 23

What makes Synamatix UNIQUE - 4
Massively Parallel Single
Molecule Sequencing analysis

Real-time Proteomics

Comparative genomics

Probe design / testing
Personalised medicine

Clinical Diagnostics

Ultra High Throughput (UHT)
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Slide 24

Architecture
3rd party
Applications

SUITE

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Slide 25

Architecture
Users
Custom /
Windows
Applications
Linux

Linux
Itanium

Java

C++

Application
SUITE
Servers

WWW Interface

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Slide 26

Summary
Unique pattern network dB
Maintains patterns and their relationships
Able to derive Significance from data “a priori”
Self learning mechanism
Accuracy

Developed world’s 1st genomics platform capable
of addressing demanding new applications:
Scalable and efficient ultra volume storage
Ultra-high-throughput genome analysis
Personalised medicine and the $1000 genome

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