Bio-Informatics & High Performance Computing (HPC) for...

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Bio-Informatics & High

Performance Computing (HPC)

for Realization & Advancement

of Precision Agriculture

Kudang B. Seminar

e-mail: [email protected]

Head of Bio-informatics Engineering Laboratory Fateta IPB

Honorary Member of AFITA

Member of ASICTA

Honorary Member HIPI

Member of PERTETA

The creation and

development of

advanced

information and

computational

techniques for

solving problems

in biology

https://www.osc.edu/press/ohio_supercomputer_center_ralph_regula_s

chool_to_power_choose_ohio_first_bioinformatics

http://www.babraham.ac.uk/our-research/science-

services/bioinformatics/

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The use of super computers and parallel

processing techniques for solving complex

computational problems

1. Fundamental Concepts

"I think the next century will be the century of complexity"

Stephen Hawking (January 2000), The Newton Professor of Physics at Cambridge:

George Rzevski: www.rzevski.net

http://www.rzevski.net/

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http://www.necsi.edu/projects/mclemens/cs_char.gif

What is Complexity?

It consists of a large number of diverse components

engaged in unpredictable interaction (Variety and Uncertainty)

Its global behaviour emerges from the interaction of

local behaviours of its components (Emergence)

It self-organises to accommodate unpredictable external or internal events and therefore its global behaviour is “far from equilibrium” or “at the edge of chaos” (Adaptability and Resilience)

It co-evolves with its environment (Irreversibility)

George Rzevski: www.rzevski.net



http://www.rzevski.net/

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Dramatic Change!

Biology has changed

dramatically and high-

throughput experimental

methods such as produce

masses of data.

Superlinear Grow &

Challenging Problems

The bioinformatics

databases grow

superlinearly!

The masses of data

led to numerous

challenging

bioinformatics

problems &

solutions http://www.benjaminwicks.com/portfolio/

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Big Data Analysis & Optimism Tens of thousands of ESTs (Expressed

Sequence Tags) available for study

Most methods to study message

distributions are low throughput AND

time consuming

“Genomics” necessitates the large scale

study of gene expression

Optimism: Biology is finite…

~30,000 human genes; ~1000 protein superfamilies

…but computers speeds keep increasing => HPC

Future Extension of Bio-informatics

Genotype

Data

Phenotype

Data

Gographical

Indication

Data

Integrated

Data

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Why Integration is needed?

Genotype: genetic constitution of an

individual organism

Phenotype: expressed physical traits of

an individual organism.

Geographical indication (GI): specific

characters (signature) of an individual

organism that correspond to a specific

geographical location or origin.

Relating Genotype & Phenotype Data

Leaf Tuber

Chromosome

DNA

Genotype

data

Phenotype

data

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cDNA Collections (Libraries)

• Various tissues are collected from the plant,

and messages are extracted

Leaf

Messages

Tuber

Messages

Unifying GI,Phenotype,

Genotype Data

Genotype +

Phenotype

Data

Origin

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What about

Precision Agriculture (PA)?

An agricultural system that provides precise

treatments to all agribusiness chain from

upstream (onfarm) to downstream (off farm).

agribusiness

chain

from

Field

To

Table

Complex behavior & attributes

Why is Precision Agriculture hard?

Non-Life

Systems

Life Systems

Simple behavior & attributes

Involve genetics Do not involve genetics

Autonomous Non-autonomous

CNC BDA

(Computer Numerical Control) (Biosistem-Derived Algorithm)

Fuzzy control Genetic algorithm

Photosynthetic algorithm

Immune system algorithm

Expert system

Finite Element System Fractals

Pattern recognition

Artificial Neural Network

Adaptive System

Ant Colony Algorithm

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General Model of

Precision Agriculture

Bio-Process

Control System

Complex

Computation &

Decision Making

Bio-Products

Related Values

Timely &

Conditionally

Valuable Data

Environment

Related Values

Tecnology

for specific

bioproducts

Agro-products

Gerhard Schiefer. 2014. Transparency for Sustainability: Food chain challenge & Future Internet opportunities, AFITA Conference 2014.

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Food Chain/Network


Tools for

making

transparency

& precision

work?


Tools for Transparency &

Precision Support

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ICT Cloud to Support PA

Gerhard Schiefer. 2014. Transparency for Sustainability: Food chain challenge & Future Internet opportunities, AFITA Conference 2014.`

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Linking production with Consumers



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Plant Health Monitoring and Control

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Tomato Grading

Grading Technology

Precision Agriculture (Off Farm): Minimizing Loss in Tomato Ketchup Supply Chain

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THE DEVELOPMENT OF IDENTIFICATION SYSTEM AND GENOME ANALYSIS

SINGLE NUCLEOTIDE POLYMORPHISM UNTUK PEMULIAAN

SOYBEAN PLANT

Tim Peneliti:

Dr. Wisnu Ananta Kusuma (Ilmu Komputer, IPB)

Dr. Agus Buono (Ilmu Komputer, IPB)

Dr. Ir. I Made Tasman (BB Biogen)

Habib Rijzaani (BB Biogen)

Mukhlis Hidayat, M.Kom (Matematika, Unsyiah)

Research Contributions

•Creation of superior strains

• Utilization of genomic analysis for

breeding

•Utilization of information

technology to support the analysis of

genomic-based breeding

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Kudang B. Seminar Herry Suhardiyanto

UIJI Seminar, 23-25 July 2011, Ehime University

Dept. of Mechanical & Biosystem Eng. Bogor Agricultural University

The Supervised Multi-Agent Systems for Greenhouse-Based Crop

Industry

A Large Scale Crop Production Plant

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Concurrent Engineering for Environment and Plant Control

USER

U S E R I N T E R F A C E

USER’S PREFERENCE SELECTION MODULE

Modes of

control

Parameters of control

Optimality Criteria

Control Knowledg

e

Supervisory Control Engine

Crop Knowledg

e

Climatic Knowledge

I/O Knowledg

e

Greenhouse Controllers

Greenhouses



Array of Controller

s

SUPERVISORY AGENT

Supervised

Agents

CONCLUDING REMARKS (1)

The role of bio-informatics & HPC is

becoming very crucial and strategic to the

realization and advancement of precision

agriculture (PA).

intergrating and interelating the knowledge

of genotype, phenotype and GI will be very

useful for formulating and establishing better

paradigms, solutions and tools for better &

smarter agricultural system particularly in

Indonesia

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Collaborative & interdisciplinary research

can be extended coherently towards

better & competitive agriculture

production through PA & bioinformatics

There have been many applications of

bioinformatics for agriculture, partcularly

food production but there are more

challenging research & applications due to

biosystem diversity & complexity

CONCLUDING REMARKS


The applications of bioinformatics heavily

rely on the advancement of HPC (High

Performance Computing Technology) &

that of superintelligent computations.

The development & use of bio-derived

computational algorithms will be more

aggresive due to nature of bio-systems.

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THANK YOU

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