Biosciences Working Group Update

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Dec 4, 2013 (3 years and 9 months ago)

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Biosciences Working Group Update

Wilfred W. Li, Ph.D.,
UCSD, USA

Habibah Wahab, Ph.D.,
USM, Malaysia

You
-
Qiang Song, Ph.D,
HKU, PRC


Hosted by HKU

Hong Kong, PRC, March 2
-
4, 2010


PRAGMA: model for international
collaboration in Technology and Science

Broadening Impact of Technology

Engaging Future Generations


PRIME Student 2009: Jessica Hsieh, USM

Scientific Drivers and Use Cases: Influenza A Virus

http://www.reactome.org/

http://www.wikipedia.org



http://library.thinkquest.org/05aug/01479/prevention1.html


Harris et al, PNAS, 2006

2009 H1N1 Pandemic Influenza

Source: http://flutracker.rhizalabs.com/


Cumulative cases
represented in
Google Map as of 21
Apr, 2010


WHO: 18769 deaths
to date


US: 4642 deaths;
480230 total cases


Malaysia: 74 deaths,
6463 total cases


China: 650 deaths;
124300 total cases



Postpandemic
period as of Aug
2010


0.5~1% death rate,
similar to seasonal flu


Targets younger and
healthy individuals,
different from
seasonal flu (90% >
65 years older)



WHO Status Update

Week 17 (Apr 19, 2009) to Week 13 (Apr 3, 2010)

http://www.who.int/csr/disease/swineflu/laboratory23_04_2010/en/index.html

Transparent access of applications on Avian Flu
Grid through middleware

CNIC Duckling Portal

Konkuk/Kukmin

Glyco
-
M*Grid

NBCR CADD

Relaxed Complex Scheme and Ensemble based Virtual Screening
Contributed to HIV Integrase Inhibitor Development



Exploration of the structural basis for this unexpected result … suggests an
approach to the development of integrase inhibitors with unique resistance profiles.



D. Hazuda et al.,
Proc. Natl. Acad. Sci. USA

(Aug. 2004), refers to Schames, et al. (2004).


Discovery of unexpected binding site in HIV
-
1 Integrase using MD and AutoDock:

Schames, … & McCammon,
J. Med. Chem.

(released on web, early 2004)

February, 2006


Phase III Clinical Trials

February, 2007


Name announced:


Isentress (raltegravir)

October, 2007


FDA

fast track


approval

New Class of HIV Drugs: Merck & Co.

MK
-
0518


Source: A. McCammon

Ensemble
-
based Virtual Screening with Relaxed Complex Scheme

NAMD2

Amber

NCI Diversity Set: 3.3 MB, 2000 compounds;

Required at each site

ZINC subset: 200,000. A few hundred MB

Multiple targets: HA, NA subtypes

Each target: 30~50 MD snapshots, 1~2 MB each

AutoDock4

Simulation Data: hundreds of GB

Docking Data: hundreds of MB

Total data to date: ~5 TB in long term storage.

Each experiment is about 1 Petaflops accumulative in computation cost.

Source: Amaro

Advances in Computing Infrastructure Enables Complex Simulations

of Biomolecular Systems

Amaro & Li, CTMC, 2010

Opal 2 for SaaS

Condor pool

TeraGrid/PRAGMA Grid

PBS/SGE Clusters

Globus

Opal Application Services

Opal App

MGLTools

Kepler

Opal WS: Transparent Access Layer for Applications

Grid/Cloud Resources

CADD

Vistrails

Taverna

Condor

CSF4

Opal Plugins for Popular Workflow Software

14

CADD: Opal Web Services for Biomedical Applications


Ren et al, NAR 2010,
Web Server Issue


http://cadd.nbcr.net



Modules supporting
MD simulation and
analysis, Virtual
Screening, Docking,
Visualization


Project management
under development

Opal MetaService: Transparent Access
to Workflows and Applications

Social Networks and Collaborative Environment

Social Network Site

Number of Users

Features

API Examples

Google

170 million (Gmail)

Google Integrated
Suite of Tools

Google Apps Engine

LinkedIn

65 million

Professional

Huddle/Zoho Office
Online

Twitter

100 million

Short MMS/SMS

TwitPic

Google Wave

100,000 X 7?

Upload any file

Google Wave Robot

Facebook

500
million+

Social network

Facebook Apps

Are these too big to fail?

Utility Computing finally?


OPAL

as

resource

manager

of

CSF
4


CSF
4

allocate

service

instances

of

OPAL

for

jobs

17

17

New OPAL
-
CSF4 Cloud model

PRAGMA 19 workshop, Changchun, Jilin, China, Sep.13
-
15, 2010.

2


4 March 2010


PRAGMA 18, San Diego

18


Nornisah Mohamed, USM

Integrating Visualization Workflows using

Real
-
time bioMEdical data Streaming and visualization (RIMES)

Kevin Dong, CNIC


Biomedical CLOUD
Resource Manager
(
edu
.
sdsc
.
nbcr
.
opal
.
manager
.
CSFJobManager
)
Service Manager
Scheduling
:
Workflow Job
Array Job
AutoDock
NAMD
OPAL
2
CSF
4
User Interface
Grid Sites
MetaScheduler

generate RSL files
Grid Resources
Input
/
Ouput Files
:
StageIn and StageOut
VM Replication Experiment

http://goc.pragma
-
grid.net/wiki/index.php/VC
-
replication
-
2

SDSC VM hosting server

AIST VM hosting server

AFG VM

(original)

AFG VM

(copy)



VM hosting server:


Rocks 5.3 Xen roll



Avian Flu Grid VM



Rocks VM



Globus/SGE



Autodock



Replication updates



hostname and IP



Compute nodes



Network configurations



Globus configuration



SGE configuration

NBCR VM hosting server

AFG VM

(copy)

Lau, Haga and Date

ViewDock TDW

Other Examples of Continued Software Development
at Member Institutions



Drugscreener
-
G


KISTI, Korea


Grid Enabled Virtural Screening Service


ASGC,
Taiwan


CADD Pipeline


NBCR, USA


WISDOM project


CNRS, EU


Glyco
-
M*Grid


Kookmin & Konkuk U, Korea



Meeting the New Challenges


Virtualization


What does it mean to us?


Virtual machines, CSF server, Gfarm server and virtual
clusters


Production environment


Where is it? What form
should it take?
--

EC2, VC replication


Collaboration


How to stay in touch better, PRIME,
MURPA, research in general?

PRAGMA 20: Look Around Session


Arry Yanuar, University of
Indonesia



Molecular Dynamics
Simulation of disordered
regions the RGK
-
family of
small GTPase revealed no
GTPase activity


Simulation often suffered
from communication failure


Request: Application service
for GROMACS in PRAGMA?

GDP

GTP

GDP

Pi

GAP

GEF

GDP

GDI

GTP

Effector

Small

GTPase

Small

GTPase

Small

GTPase

Downstream signal

Inactive

Active

Look Around 2


Suntae Hwang


South Korea Kookmin
University


MGrid Service on
Nationwide Consortium
of Supercomputing
Infrastructure (PLSI) in
Korea


Features: IP free,
virtualized resource
selection


LoadLeveler

PLSI

MGrid

Look Around Session


Day 2
-


NBCR CADD Pipeline
Demonstration


CADD for Computer Aided
Drug Discovery, Based upon
the Vision workflow platform.


Nadya Williams


Requested features:


Ability to track data
provenance


Ability to run workflow
using own cluster


Potential collaboration


Alzheimer’s Disease
-
HKU





Look Around


KISTI BioWorks


Bioworks workflow
environment for
Bioinformatics and Virtual
Cell applications in Systems
Biology


Seok Jeong Yu


Features:


Client server architecture


Uses Java Web Start
technology


Allows users to share, edit
and execute workflows


Will add PSExplorer
(parameter space explorer)


Not ready for release yet


Looking ahead


NBCR/SDSC and KISTI: co
-
development of
Opal Plugin for Bioworks; scholastic exchange


UCSD and HKU: Use CADD pipeline in
Alzheimer’s Disease Research


KISTI and HKU: Use Bioworks in Alzheimer’s
Disease Research


UCSD and University of Indonesia: Security
requirement for proprietary compound library
and Opal services

Looking Ahead


PRAGMA Resources:


More application services? Amber? Virtual Machines?


How can one replicate application services at own site? Is
this necessary?


Data resource? Gfarm
-
iphone bridge is cool. Can we
actually share data securely this way?


PRAGMA Institute? More hands on training on applications
such as CADD for local participants?


Nimrod/K 2.0 for parameter sweep in Sapporo, Japan


Opal App for Biomedical Services


Leveraging Google App
Engine and Social Network Infrastructure


Duckling Portal with Opal 2.4 support