Download - PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Transcript
Page 1: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

PANEL BIO: Are the Current BIO-models

Powerful Enough?

Bionature, Lisbon, Portugal 27 March 2013

Moderator Son Nghiem, Jet Propulsion Laboratory, California Institute of Technology, USA

Panelists •  Hiroshi Toyoizumi, Waseda University, Japan: “Advantage of using applied

probability theory in bio-techonolgy” •  Eduardo dos Santos, Universidade, Brazil: “Are the current models

sufficient to predict the druggable and therapeutic targets that we need?” •  Hesham Ali, University of Nebraska, Omaha, USA: ”Biological Network” •  Son Nghiem, Jet Propulsion Laboratory, California Institute of Technology,

USA: “Malaria Model” © 2013. All rights reserved.

Page 2: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Key Points from Panel •  While bio-research can target specific areas or topics, it

should be carried out as a part of a coordinated system rather than isolated stand-alone effort in order to optimize the value from the research.

•  Bio-modeling should break the traditionally boundary to become extensively interdisciplinary; e.g., to include applied probability theory, computing and internet advances, or satellite observations.

•  A system for bio-information should be developed and sustained with contributions from researchers, institutions, and countries with specific protocols for data formats and policies to serve to common interests of academia, governments, and industries.

•  Diversified funding supports are important to sustain research system.

Page 3: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

PANEL BIO:Are the Current BIO-models

Powerful Enough?

Bionature, Lisbon, Portugal27 March 2013

ModeratorSon Nghiem, Jet Propulsion Laboratory, California Institute of Technology,Son Nghiem, Jet Propulsion Laboratory, California Institute of Technology,

USA

Panelists• Hiroshi Toyoizumi, Waseda University, Japan: “Advantage of using applied

probability theory in bio-techonolgy”

• Eduardo dos Santos, Universidade, Brazil: “Are the current modelssufficient to predict the druggable and therapeutic targets that we need?”

• Hesham Ali, University of Nebraska, Omaha, USA: ”Biological Network”

• Son Nghiem, Jet Propulsion Laboratory, California Institute of Technology,USA: “Malaria Model”

Page 4: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Key Points from Panel• While bio-research can target specific areas or topics, it

should be carried out as a part of a coordinated systemrather than isolated stand-alone effort in order tooptimize the value from the research.

• Bio-modeling should break the traditionally boundary tobecome extensively interdisciplinary; e.g., to includeapplied probability theory, computing and internetapplied probability theory, computing and internetadvances, or satellite observations.

• A system for bio-information should be developed andsustained with contributions from researchers,institutions, and countries with specific protocols fordata formats and policies to serve to common interestsof academia, governments, and industries.

• Diversified funding supports are important to sustainresearch system.

Page 5: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

University of Nebraska at Omaha

Are the Current Bio-models Powerful Enough?

BIOTECHNO 2013 Hesham H. Ali

UNO Bioinformatics Core Facility College of Information Science and Technology

Page 6: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Biomedical Informatics – Where are we?

•  Availability of many large useful database systems; private and public

•  Advances in new technologies as high throughput next generation sequencing

•  Availability of numerous helpful software tools •  Fragmented, in some case isolated, efforts by

computational scientists and bioscientists •  The trendiness of the discipline •  Massive interest from Industry, researchers and the public •  Many advances in Biomedical research

Page 7: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Simple Questions

Where is the cure for cancer? Why don’t we have personalized medicine?

Why is AIDS still misunderstood?

Can effectively be boiled down to: Why hasn’t high-throughput data been

effectively harnessed yet?

Page 8: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Plausible Answers

It is not that easy: –  Complexity of the system –  Complexity of the organisms –  Size of the data (“big data”) –  Search space of inter-data relationships –  Heterogeneity of the data –  Lack of integration of data –  Computing power –  …..

Page 9: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet
Page 10: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

But….

•  Her2+ BC –  20-25% of breast cancers – Normal treatment: Herceptin

•  Eventually stops working if cancer comes back

•  T-DM1 Drug – Trojan horse drug –  3 extra months of improvement – Lack of usual side effects

Page 11: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Personalized Medicine

Page 12: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Methods •  54yr old male volunteer •  Plasma and serum used for testing •  14 month time course •  Complete medical exams and labs at each meeting

(20 time points total) •  Extensive sampling at 2 periods of viral infection:

–  HRV (human rhinovirus) – common cold –  RSV (respiratory synticial) - bronchitis

Page 13: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Time-course summary 726 days total HRV - red RSV - green Fasting - blue Lifestyle change: ↑exercise, took ibuprofen daily, ↓sugar intake

Page 14: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Deep Dynamic Omics Analysis

•  Transcriptome: RNA-Seq of 20 time points –  2.67 billion paired end reads –  19,714 isoforms for 12,659 genes tracked

•  Proteome: Quantification of 6,280 proteins –  14 time points via TMT and LC/MS

•  Metabolome: 1,020 metabolites tracked during viral infections –  miRNA analysis also during HRV infection

Page 15: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Techniques Used

•  Summary of techniques used: –  Sample collection –  HRV and RSV detection –  Whole-genome sequencing –  Whole-exome sequencing –  Sanger-DNA sequencing –  Whole-transcriptome sequencing: mRNA-Seq –  Small RNA sequencing: microRNA-Seq –  Serum Shotgun Proteome Profiling –  Serum Metabolome Profiling –  Serum Cytokine Profiling –  Autoantibodyome Profiling –  Telomere Length Assay –  Genome Phasing –  Omics Data Analysis

Page 16: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Team Count: 41

Page 17: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Data Generation vs. Integration/Analysis

•  New technologies lead to new data: –  Competition to have the latest technology –  Focus on storage needs to store yet more data

•  Bioinformatics community needs to move from a total focus on data generation to a blended focus of measured data generation (to take advantage of new technologies) and data analysis/interpretation/visualization

•  How do we leverage data? Integratable? Scalable? •  From Data to Information to Knowledge to Decision

making

Page 18: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

“Big Data”

Image Source: http://api.ning.com/files/O6-JQcfS6sxRuZ8I2i5nJVa59xL-krT-a6UqeoLNaHwL2w-JSR-Cy56PmikOywRQgy2gDfYxLAb0Hs*VFr8IePv5QFBJdhDH/BigData.001.jpg

Page 19: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Data versus Knowledge

•  With high throughput data collection, Biology needs ways not only to store data but also to store knowledge (Smart data)

•  Data: Things that are measured •  Information: Processed data •  Knowledge: Processed data plus meaningful relationships

between measured entities Power of graph modeling

Page 20: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Data-Driven Decisions

•  With high throughput data collection, Biology needs ways not only to store data but also to store knowledge (Smart data)

•  Data: Things that are measured •  Information: Processed data •  Knowledge: Processed data plus meaningful relationships

between measured entities •  Decision Support

Page 21: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

A Potential Major Change

•  Data driven research vs. Hypothesis driven research

http://www.genome-engineering.com/from-hypothesis-to-data-driven-research.html

Page 22: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Systems  Biology  Approach    

•  Realistic  and  Innovative:    –  Networks  model  relationships,  not  just  elements  –  Discover  groups  of  relationships  between  genes  and  gene  products  

•  Validation  and  Discovery  Aspects  –  Examine  changes  in  systems  

•  Normal  vs.  diseased  •   Young  vs.  old  •  Stage  I  v.  State  II  v.  Stage  III  v.  Stave  IV  

Page 23: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Systems  Biology  

•  Holist  view  of  the  system  –  Ability  to  zoom  in/out  to  view  critical  system  components  

•  Past:  Reductionist  biology  –  Find  a  gene/protein  of  interest    – Examine  under  different  conditions  

•  Systems  biology:  examine  an  entire  system  at  different  conditions  

Page 24: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Biological  Networks  

•  A  biological  network  represents  elements  and  their  interactions  

•  Nodes  à  elements  •  Edges  à  interactions  

•  Can  represent  multiple  types  of  elements  and  interactions  

Page 25: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet
Page 26: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Treated  mice  Control  

Bender  et  al.  2008  .  Neuro  Biol  Aging  29(9):1404-­‐11  

Page 27: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Case  Study:  Aging  

Young  

Midage  

Page 28: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Razzaque,2009.  Nat.  Rev.  Endocrin.  5:611-­‐619  

Page 29: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Chateau  et  al.  2010.  Aging      

Validation  

Page 30: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Razzaque  ,  2009.  Am  J  Physiol  Renal  Physiol.  296(3):F470-­‐6.    

Page 31: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Function?  

Page 32: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Working in the Cloud

•  Cloud computing is Web-based processing and storage. Software and equipment are offered as a service over the Web. –  Data and applications can be

accessed from any location –  Data and applications can easily be

shared through a common platform –  Clouds need not be public; companies

can introduce private cloud computing solutions

Page 33: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

¢  Flexible availability of resources

¢  Opportunity for developers to easily push their applications

¢  Targeted advertising

¢  Easy Software Upgrades for customers �  Example: Webmail

Cost Reduction & Convenience

Cloud

Multinational Corporations

Government Offices

Small Business

Homes

Page 34: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Private Clouds

•  Core facilities need to acquire private infrastructure-level virtual cloud technology. Best vendor for such technology is VMware. The Bioinformatics Core facility at UNO uses VMware vSphere Enterprise.

•  Public Clouds like Amazon EC2, RackSpace cannot be used in all cases due to various restrictions put forth by regulations (e.g. HIPAA data locality requirement). Such public clouds could only be used as a scalable platform for already anonymized data.

•  Private Virtual Cloud is on-premise solution allowing all the benefits of virtualization technology both from an administrative and end-user perspective.

Page 35: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Security Hardened OS Template

•  Virtual layer allows launching servers/machines from a template tested and hardened by the designated Security Office of the organization.

•  Easier to isolate security issues on a virtual

machine, resolve the issue on a clone of the virtual machine and deploy clone back to production environment.

Page 36: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Proposed Model

Page 37: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Are the current models sufficient to predict the druggable and

therapeutic targets that we need?

Eduardo Campos dos [email protected]

Page 38: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Issues in new drug development

basic discovery research government andphilanthropic organizations

funded mainly by

late-stage development pharmaceutical companies and venture capitalists

funded mainly by

Gap:proof of concept

Cancer treatment- hard targets- to attack cancer cells but to leave healthy cells largely untouched

Neglected diseases - low investment - acquirement of drug resistance

Challenging areas

Challenging paradigm

Page 39: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Drawback: virtual screening needsto know the protein structure(x-ray crystallography or theoretical by homology)

Current methods

How to find potential therapeutic targets?- druggable- disease related- specificity

The Druggable Genome- estimates: not much more (based on current small-molecule drug design)- do not consider future breakthroughs in medicinal chemistry or biology

Page 40: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Advantage of Using Applied Probability Theoryin Bio-tenchonolgy

Hiroshi Toyoizumi

Waseda University

Biotechno2013 (Lisbon)

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 1 / 4

Page 41: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Advantage of Using Applied Probability Theory

Why math for Bio?

Bio: real, complex, interesting

Math: virtual, simple, beautiful

Business: real, complex, practical

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 2 / 4

Page 42: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Advantage of Using Applied Probability Theory

Why math for Bio?

Bio: real, complex, interesting

Math: virtual, simple, beautiful

Business: real, complex, practical

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 2 / 4

Page 43: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Advantage of Using Applied Probability Theory

Why math for Bio?

Bio: real, complex, interesting

Math: virtual, simple, beautiful

Business: real, complex, practical

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 2 / 4

Page 44: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Bio→ Math→ Business

Erlang-B formula

Bio: Population

Math: Birth and Death process (Random Walk)

Business: Erlang-B formula for designing telephone networks;

B =ρN/N !∑Nk=0 ρ

k/k!, (1)

where ρ = λ/µ.

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 3 / 4

Page 45: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Bio→ Math→ Business

Erlang-B formula

Bio: Population

Math: Birth and Death process (Random Walk)

Business: Erlang-B formula for designing telephone networks;

B =ρN/N !∑Nk=0 ρ

k/k!, (1)

where ρ = λ/µ.

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 3 / 4

Page 46: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Bio→ Math→ Business

Erlang-B formula

Bio: Population

Math: Birth and Death process (Random Walk)

Business: Erlang-B formula for designing telephone networks;

B =ρN/N !∑Nk=0 ρ

k/k!, (1)

where ρ = λ/µ.

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 3 / 4

Page 47: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Physics→ Math→ Business

Brownian MotionPhysics: Random Movement of Particles

Math: Brownian Motion dB(t) = µB(t)dt+ σdW (t).

Business: Black-Scholes Equation P = e−rtE[(B(t)−K)+].

-20 20 40 60

-80

-60

-40

-20

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 4 / 4

Page 48: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Physics→ Math→ Business

Brownian MotionPhysics: Random Movement of Particles

Math: Brownian Motion dB(t) = µB(t)dt+ σdW (t).

Business: Black-Scholes Equation P = e−rtE[(B(t)−K)+].

-20 20 40 60

-80

-60

-40

-20

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 4 / 4

Page 49: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Physics→ Math→ Business

Brownian MotionPhysics: Random Movement of Particles

Math: Brownian Motion dB(t) = µB(t)dt+ σdW (t).

Business: Black-Scholes Equation P = e−rtE[(B(t)−K)+].

-20 20 40 60

-80

-60

-40

-20

[email protected] Using Applied Probability Theory Biotechno2013 (Lisbon) 4 / 4

Page 50: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal, 27 March 2013

Panelist: Son Nghiem

Jet Propulsion Laboratory California Institute of Technology,

Pasadena, California, USA

Malaria Model and Ringed Seal Research

© 2013 California Institute of Technology. Government sponsorship acknowledged.

Page 51: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Malaria Model

Global distribution of dominant or potentially important malaria vectors (Kiszewksi et al., 2004).

Idealized puddle model (Lunde et al., 2013).

Page 52: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Malaria Model

(a) Left panel: Soil moisture change (SMC) across Africa [Nghiem, 2009] measured by QuikSCAT with the vertical polarization along ascending orbits on 10/16/ 2009. The color scale represents backscatter change in dB, and volumetric SMC in % with the Lonoke rating. Data gaps between orbits are seen in dark bands on land. High SMC is observed in an extensive pattern (yellow areas) across South Africa curving northward to Botswana, Namibia, Zambia, and Mozambique, with a wet region seen in Madagascar. (b) Right panel: SMC across Ethiopia measured by Oceansat-2 on 5/7/2012. Here we use data only from ascending orbit in this example (all orbits can be used so that the orbit data gaps are small).

!"#$%&$'()*+,-.+/+-$0+)12)+

Page 53: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Arctic Ringed Seal Research

What if seals come out too early due to early snow melt on sea ice?

Death by predation Death by melt/freeze

-4

-2

0

2

4

6

8

4/1/2000 4/16/2000 5/1/2000 5/16/2000 5/31/2000 6/15/20000

0.2

0.4

0.6

0.8

1

QuikSCAT diurnal radar signature (dB)Fraction of visible seal population

Result from Prudhoe Bay ringed seal survey (2000)

2 dB threshold 50% visible seals

Qu

ikS

CA

T D

iurn

al S

ign

atu

re (

dB

)

Frac

tio

n o

f V

isib

le S

eal

Kelly and Nghiem, IGARSS, 2004

Page 54: PANEL BIO: Are the Current BIO-models Powerful Enough?...PANEL BIO: Are the Current BIO-models Powerful Enough? Bionature, Lisbon, Portugal 27 March 2013 Moderator Son Nghiem, Jet

Contact

[email protected]