Us india workshop workshop program v 7.1

US-India Network-enabled Research Collaboration Workshop

Monday
6th December Workshop - day 1

Welcome from Indian hosts
9.00 - 9.10
(N. Mohan Ram Director General, ERNET)

9.10 - 9.20 Lamp Lighting Ceremony

Introduction to the Workshop - background, objectives and what we want to achieve from the workshop
9.20 - 9.30
Jim Williams, Indiana University & TransPac

Welcome from Marjorie Lueck, Office of International Science and Engineering, National Science Foundation and introduction of
9.30 - 9.45
Video address and announcement by Subra Suresh, Director, National Science Foundation

Welcome from Indiana Universtiy
9.45 - 9.55
Brad Wheeler, Vice President for Information Technology and CIO, Indiana University

Theme Addess
9.55 - 11.10
Shri. Shashi Kant Sharma, Secretary, DIT, GOI

Address by Guest of Honour
10.10 - 10.20
Shri. Kapil Sibal, Hon,ble Minister for Communications & IT, GOI

10.20 - 10.30 Vote of Thanks - Dipak Singh, Director, ERNET

10.30 - 11.00 Morning Tea

Technology, Cyberinfrastructure, Networks and Advanced Communication Systems
Session Chair: S.Ramakrishnan, former Director General, Centre for Developmentof Advanced Computing (CDAC)

The aim of this session is to present the network infrastructure that is available to researchers today or will be will be available to researchers in the relatively near term (1-2 years). This session should
prepare the researchers for their sessions regarding the required Cyberinfrastructure for their network-enabled collaborations. These are short talks <10mins each). Reference material (urls, printed
material) should be avialable to supplement the overviews.

Current and evolving R&E network infrastructures in India
11.00 - 11.10
Prof. S.V.Raghvan , Scientific Secretary to the Principal Scientific Advisor, Govt of India

India's National Knowledge Network (NKN)
11.10 - 11.20
Dr B K Gairola, Director General, National Informatics Centre (NIC), Govt of India

ERNET
11.20 - 11.30
N Mohan Ram, Director General, ERNET India

TBD
11.30 - 11.40
Gulshan Rai, CERT-In, India
current and evolving R&E network infrastructures in the US
11.40 - 11.50
Ana Preston, Internet2

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Taj - High-Performance Networking Facilitating US-India Science Collaboration
11.50 - 12.00
Greg Cole, GLORIAD/TAJ
Abstract: The Global Ring Network for Advanced Applications Development (GLORIAD) and its ‘Taj’ expansion is constructed from many fiber-optic trans-oceanic and trans-continental links encircling the
northern hemisphere and connecting universities, schools and national laboratories around the world at the highest network speeds possible today. Literally millions of scientists, educators and students
have used this infrastructure to cooperate in ways unimagined only a few years ago. The bandwidth is sufficient to transmit entire libraries of information in seconds, permit thousands of simultaneous
video-conferences for distance learning or shared seminars, and enable the sharing of expensive scientific instrumentation. Created to foster increased Science, Engineering and Education cooperation, it
today enables sharing of the most advanced science and research in the world.

The talk will briefly describe the GLORIAD/Taj program with a focus on US-India efforts to build global Cyber Infrastructure through a highly federated, distributed, decentralized model – based on open
network exchange points and community-shared links and services. The ‘Taj’ expansion of GLORIAD is building another ring of light around the northern hemisphere. A new link to India is being extended
also to Egypt and Singapore (and later to Vietnam) with a 1Gbps circuit being provided by Taj partners, Tata Communications (a $6M contribution). This will create the first direct US-India Science and
Education network connecting with India’s own National Knowledge Network (NKN). Additionally, Taj is improving connectivity with China, building major capacity across the northern Polar Regions with
NORDUnet partners and providing new services from Europe to India, to Egypt, Singapore and Vietnam and Korea and broader Asia.

TransPAC3
12.00 - 12.10
Jim Williams, Indiana University
Abstract: The ACE (America Connects to Europe) and TP3 (TransPac3) infrastructure, when combined with existing infrastructure made available by our partners in the US, Asia and Europe, will provide
a necessary high-performance communication and collaboration tool for scientists, educators and students around the world as they struggle with the complex problems presented by the world today.

This investment will enable increased educational interactions between faculty experts and students in different parts of the world. It will also enable communication of all types among researchers,
educators and students worldwide. By understanding more about how people in other countries work, think, and feel, we will ultimately understand more about ourselves, and they about us, and how we
all fit into global civil society.

US National Science Foundation International Network Programs relevant to India
12.10 - 12.20
Kevin Thompson, NSF
The World Bank's Role in catalysing Advanced Networks for Learning and Knowledge Dissemination
12.20 - 12.30
Michael Foley, World Bank, South Asia Region
TEIN3
12.30 - 12.40
Dai Davies, DANTE, UK (Remote presentation)

Identifying key issues, challenges, obstacles, opportunities
12.40 - 12.55 associated with the new network infrastructures
Panel Session and participant Interactive process led by session chair - S.Ramakrishnan

12.55 - 14.00 Lunch



Geosciences, Climate Change, Weather Prediction and Observing Systems
14.00 - 14.05 Session Chair: Chaitan Baru, San Diego Supercomputer Center (SDSC), University of California, San Diego
overview by session chair including collaboration and funding opportunities

14.05 - 14.25 Fostering India and US Geoscience Collaboration through iGEON: A cyber infrastructure for Geo Scientists
Dr. Rajeev Wankar, Department of Computer and Information Sciences, University of Hyderabad
Abstract: Geographic information analysis often requires the use of simulation, optimization, and statistical methods that are computationally intensive, particularly when they are applied to large, realistic
problems. One of the large Grid research projects, GEON, concentrates on geo-specific applications that make use of Grid resources was designed by the team at San Diego Supercomputing Centre
(SDSC) at University of California. In order to cater the scientific need of the Geo Scientists of India an iGEON India node has been deployed at Centre for Simulation Modelling and Design (CMSD) at
University of Hyderabad, with Point of Presence (PoP) nodes at Pune, Rajamundhry and Jammu. In India, geo scientists have done lot of data collection for many years. Unfortunately we don’t have an
open repository of the data. The information, if collected and stored at a central location may be of immense importance and can be used for scientific analysis later. Further, Hyderabad is blessed with
many National Laboratories and various uncensored data sets can be collected and kept in this central repository for further analysis. Grid portals are emerging as a highly convenient mechanism for
providing the scientific community with a familiar and simplified interface to the Grid and Grid services. GIS portals organize content and services such as directories, search tools, community information,
support resources, data, and applications. They provide capabilities to query metadata records for relevant data and services and link directly to the online sites that host content services. Irrespective of
place of repository and form, content can be visualized as maps and can be used in geographic queries and analyses. This requires high transmission bandwidth between the client and the server
locations. We at the University of Hyderabad have design portal for scientist from both countries India and US to register geo data sets of different types, analyze and view online. Conversion of the
topological map to digital form is one of the most complex problems in computer science. If this problem is solved than it would be one of the most important contributions. Several efforts have already
been made by researchers from the image processing area to develop efficient methods for this conversion and as of now there is no open source software available which does this conversion. We are
perusing this study and if successful will provide this service on the GEON portal.

In this talk we will cover issues related to developing such cyber infrastructure (hardware, software and network bandwidth related) for Geo Scientists and answer queries.

Environmental Networks and Cloud Computing: Opportunities for Collaboration
14.25 - 14.45
Chaitan Baru. San Diego Supercomputer Center (SDSC), University of California, San Diego
Abstract: Datasets in the areas of environmental science, geosciences, and ecology may reside locally to where they have been collected, i.e. either in India or US. Linking these data via common
services and portal-based interfaces will require addressing concerns regarding data ownership, integrity, and provenance, while also optimizing access to data. We will discuss opportunities for
collaboration in shared access to such data in the context of two projects: the Tropical Ecology, Assessment and Monitoring (TEAM) Network (http://teamnetwork.org) and GEON
(http://www.geongrid.org). The TEAM network is a collaboration among Conservation International, Wildlife Conservation Society, Smithsonian Institution and the Missouri Botanical Gardens for monitoring
a collection of forested sites across the tropics in order to study the impacts of global climate change and land-use change on ecosystem services and biodiversity. We will present an overview of the
cyberinfrastructure of the TEAM network and opportunities for collaboration for sites in India. Second, building upon collaborations over the past few years between the Center for Modeling, Simulation,
and Design (CMSD) and the University Center for Earth and Space Sciences (UCESS) at the University of Hyderabad and SDSC in the GEON (Geosciences Network) project, we will describe
opportunities for experiments to examine the Core/Edge model for cloud computing, in which the Core consists of large, shared-nothing clusters and the Edge optimizes data access in the network.



Potential for expanded exchange of earth observation satellite data for climate, weather and environmental studies
14.45 - 15.05
Chris Elvidge, National Geophysical Data Centre, NOAA

Abstract: Both India and the USA have robust earth observation programs designed to meet national requirements in weather prediction, tracking crop growth, environmental analyses, and climate
research. ISRO earth observation missions span a wide gamut of spatial resolutions, spectral ranges and repeat cycles, ranging from the high spatial resolution observations made by the Cartosat series,
radar imaging collected by RISAT-2, moderate resolution multispectral observations from Resourcesat, ocean color observations from Oceansat-2, to the geostationary imaging for weather collected by
the INSAT series. The US program includes the geostationary weather satellite series (GOES), kilometer scale global multispectral imaging systems such as MODIS and the to be launched VIIRS, the
moderate resolution multispectral Landsat series, and others. The earth observation systems of the two nations are largely complementary. For instance, both countries operate geostationary weather
satellites, but these cover different geographic regions. Other systems, like Oceansat-2 and MODIS collect data at comparable spatial resolutions, but with different spectral band sets and at different
times of day. At present the quantity of earth observation satellite data being shared between India and the USA is relatively small. In the past there simply was not sufficient bandwidth to routinely deliver
large volumes of near real time satellite data between the two countries. Given the high cost associated with building, launching and operating these systems there is a good rationale for increasing the
volume of data exchanges. With the advent of high bandwidth links such as TransPac2 and Gloriad the physical obstacles for data exchange are vastly reduced. It is now feasible to expand both the
volume of earth observation data exchanged and the number of scientific collaborations on high priority topics between India and the USA.

The presentation will be of interest to a general audience, though the subject matter will be best appreciated by remote sensing scientists from ISRO and universities.
Relevant web linkages include: http://www.ngdc.noaa.gov/dmsp/dmsp.html http://www.ngdc.noaa.gov/dmsp/download.html http://www.ipo.noaa.gov/
http://www.ipo.noaa.gov/index.php?pg=viirs http://www.class.ncdc.noaa.gov/saa/products/welcome http://www.isro.org/satellites/allsatellites.aspx http://www.nrsc.gov.in/

15.05 - 15.25
Satellite and ground observing systems for climate change studies –requirement for network enabled research collaboration
KVS Badarinath, Head of the Atmospheric Sciences Division, National Remote Sensing Agency, Hyderabad
Abstract: India is densely populated, industrialized and in the recent years has witnessed an impressive economic development. Aerosols over and around India not only affect the Indian monsoon but
also the global climate. The growing population coupled with revolution in industry has resulted in higher demands for energy and transport. With more and more urbanization the usage pattern of fossil
and bio-fuels are leading to changes in aerosol properties, which may cause changes in precipitation and can decelerate the hydrological cycle. Over urban areas of India aerosol emissions from fossil
fuels such as coal, petrol and diesel oil dominate. Furthermore, the Indian subcontinent exhibits different land characteristics ranging from vegetated areas and forests to semiarid and arid environments
and tall mountains. India experiences large seasonal climatic variations, which result in extreme temperatures, rainfall and relative humidity. These meteorological and climatic features introduce large
variability in aerosol optical and physico-chemical characteristics at spatial and temporal scales. The availability multi-sensor data sets from different current and future satellite missions makes it possible
to undertake near-real-time analysis of geophysical variables required for studies related to climate change. In addition to using remote sensing data collected by Indian satellites, we expect to draw on US
satellite data from current sensors and sensors to be launched in the next several years such as NPP (2011 launch) and LCDM (2012 launch). Necessary cyber infrastructure for data transfer and network
enabled research collaboration will enhance the studies related to climate change. With continuous improvements in the remote sensing platforms and data programs, there is an increased the availability
of satellite image data for analysis of climate, agriculture, environment in different spatial, radiometric and temporal resolutions. The general practice is to order data on web and then download through
File Transfer Protocol (FTP). With this approach the data will be made available to an analyst with a certain time lag and it is not possible to monitor climate related parameters in real time. A grid based
computational infrastructure with high speed internet connectivity allows direct and secured access to the data. The applications like MATLAB , SAS , ARCVIEW can directly access this data and the
analyst can produce the results as soon as the data is made available on to the site.

15.25 - 15.50 Afternoon Tea



Astronomy, Astroinformatics and Astrophysica
15.50 - 15.55 Session Chair: Dr Dipankar Bhattacharya, Inter University Centre for Astronomy & Astrophysics(IUCAA)

Virtual Observatory - India
15.55 - 16.15
Professor Ajit Kembhavi, Inter University Centre for Astronomy & Astrophysics(IUCAA)
Vast quantities of astronomical data can now be accessed through data archives and other sources. The data can be in highly processed form, presented as ready-to-use tables, or as processed images
and spectra. Data on the same set of objects can be available over a wide range of wavelengths, which facilitates multiwavelength studies. The focus has therefore shifted from processing of raw data and
images using a variety of techniques, to the scientific analysis of the processed data products. The data to be analyzed may involve only a few to several tens of objects, which have to be subjected to
detailed statistical studies, aided by advanced visualization. Or the data could be vast, and perhaps even be spread over archives in more than one location, making it difficult to get it to the user's end for
analysis. These and other situations call for appropriate tools for visualization and sifting of the data, for advanced statistical analysis and related tasks. Several sophisticated but easy to use tools for such
analysis have been developed in recent years in the framework of Virtual Observatories.

I will describe come important tools developed by the Virtual Observatory India project, the major data bases that are maintained by the project at IUCAA, and how the project benefits from Indo-US
collaborations and data exchanges, and plan and requirements for the future.
Astronomy With Massive Data Streams
16.15 - 16.35 Dr. Ashish Mahabal, CalTech (remote)
Abstract: A decade and a half ago, digital sky surveys pushed astronomy in the Terascale regime. Today, a new generation of digital synoptic sky surveys cover large areas of the sky repeatedly, looking
for moving objects or variable and transient phenomena. This trend is moving us rapidly towards the Petascale regime: while the typical raw data rates today are ~ 0.1 TB/night, they will increase by at
least 2 orders of magnitude within a decade or so, with the next generation of sky surveying instruments, e.g., LSST in the optical, or SKA and its prototypes in radio. The addition of the time dimension
enables exciting new science, ranging from the Solar system to cosmology, but it also adds considerably to the challenges of knowledge extraction. In order to extract maximum amount of science from
these massive data streams, the data have to be analyzed, new phenomena identified, classified, and followed up in (near-)real time, and with a minimum human intervention. Since the instruments, the
data assets, the computational assets, and the scientists are geographically distributed, this imposes significant requirements for the network infrastructure.
We will describe the current work on some of these issues, and the possibilities for the future.

Transient Sources
16.35 - 16.50 Sajeeth Philip, Inter University Centre for Astronomy & Astrophysics(IUCAA)
16.35 - 16.50 With the advent of synoptic surveys the detection of transients is now possible. These are objects that have never been seen before. These events open up a completely new dimension of astronomy with
new science possible from the solar system to cosmology. Surveys of the near future will detect tens of thousands of transients per night making it necessary for distributed and intense computing
encompassing all wavelengths to ensure that the meaningful subset of these objects get followed up. We will describe the details of this as well about some tools useful in determining the classes of these
fascinating objects.

16.50 - 17.00 Identifying key issues, challenges, obstacles, opportunities from Day 1 for action plan

17.00 - 17.30 A conversation with Marjorie Lueck, Office of International Science and Engineering, about National Science Foundation collaborative opportunities
17.30 - 18.30 Drinks, nibbles and Demonstrations (Nightime Lights, Climate Change, National Library of Medicine Resources)

19.00 - 21.00 Workshop Dinner - with String Quartet playing from Cleveland, Ohio, US - and performances by local Indian Dance Troupe
During the dinner, and to celebrate our coming together for this workshop, there will be performances locally by Indian dancers and a remote performance by a string quartet from the Cleveland Institute of
Music - a premiere U.S. conservatory.. The Vera Quartet is thrilled to be performing one of their favorite pieces for the audience in India. Anne-Sophie LaCharite-Roberge, first violin, is a Senior from
Quebec, Canada. Michelle Abraham, second violin, is an Artist Diploma student from Connecticut. Caitlin Lynch, viola, is an Artist Diploma student from Oregon. Katie Tertell, cello, is a 2nd year
Masters student from Virginia. The quartet has been together for two years and participates in the Intensive String Quartet program at CIM
Performing: String Quartet Number Three in A Major, Op.41; 4th Movement – Finale: Allegro Molto Vivace – Quasi Trio; by Robert Schumann (1810-1856)



Tuesday
7th December Workshop - day 2
Cyberinfrastructure for Medical Research
Morning
Session Chair: Anil Srivastava

9.00 - 9.10 overview by session chair including collaboration and funding opportunities

caBIG Cooperation for Cancer Care
9.10 - 9.50 Dr. Hemant Darbari, Executive Director, Centre for Development of Advanced Computing (C-DAC) and
Dr. George Komatsoulis, Deputy Director, NCI Center for Biomedical Informatics and Information Technology (NCI CBIIT)

Abstract: Cancer exacts a heavy economic and social toll broadly across the globe, striking people of all ages and socioeconomic statuses. The World Health Organization (WHO) estimates that in 2004
nearly 730,000 citizens of India and 575,000 citizens of the United States died of cancer. Indeed, ongoing improvements in the treatment of communicable disease and enhancements in standards of living
in India are likely to increase the number of deaths due to non-communicable diseases such as cancer. Recognizing the important role that biomedical informatics technology can play to increase
efficiency and to drive discoveries in cancer research, HHS/NIH/NCI created the Center for Biomedical Informatics and Information Technology (CBIIT) to develop interoperable health information
technology (HIT) to support research and care delivery for cancer. The primary instantiation of HHS/NIH/NCI’s HIT program is the cancer Biomedical Informatics Grid or caBIG®, a program designed to
create a world wide web of cancer research and care. The Centre for the Development of Advanced Computing (C-DAC) is an element of the Ministry of Information Technology, Government of India. The
Medical Informatics Group of C-DAC has been active in the areas of ICT in healthcare, Telemedicine, EHR/EMR, Imaging and cutting edge computing and delivery/deployment infrastructure such as
Distributed systems and Grid. Recognizing that each organization produces unique capabilities, and determined to maximize our respective nation’s investments in health IT, CBIIT and C-DAC are
collaborating to create an Indo-US Cancer Research Grid (IUCRG) that will benefit scientists in both India and the US.

The Indo-US Cancer Research Grid will leverage the specialized capabilities of both organizations. Basic connectivity, data discovery and semantics and security infrastructure will utilize caBIG technology
(dubbed caGrid) that is derived from the standard Globus toolkit (http://www.globus.org), with each partner contributing specialized capabilities. For caBIG, this includes interoperable information systems
that support a variety of capabilities including clinical trials management, biospecimen collection, in vivo imaging and life sciences research. C-DAC brings expertise in high-performance computing
(particularly in the area of computational genome analysis and advanced molecular simulations), software development and enhancement and “Integrative Medical Informatics” which includes R&D for
promotive, preventive and curative healthcare, as well as advanced artificial intelligence capabilities for natural language processing and translation.
Early areas of cooperation cover a wide spectrum of activities ranging from linking US and Indian biomedical IT resources, support for machine translation of biomedical terminologies into many Indian
languages to support for clinical trials that utilize Complementary and Alternative Medicine (CAM) techniques such as Ayurvedic medicine. Over the longer term, we hope to engage in joint development of
technology such as non-invasive medical instruments for early detection of Cancer from pulse morphology pattern/s, advanced simulation technology and analytics associated with next-generation DNA
sequencing data.

In summary, two programs from the Indian and US Government propose to utilize the internet2 cyberinfrastructure to improve cancer outcomes in both countries by facilitating collaborations between
researchers in both countries.



Complementing Epidemiological and Clinical Research with Bioinformatics Applications
9.50 - 10.10
Dr Sheela Godbole, National AIDS Research Institute (NARI), Indian Council of Medical Research
Abstract:The talk will focus on the experiences at National AIDS Research Institute [NARI] in utilization of informatics infrastructure and capabilities for enhancing and complementing clinical and
epidemiological research. The challenges as well as the opportunities for cyber-infrastructure for enhancing Indo-US collaborations in clinical and epidemiological research will also be discussed. In
biomedical research, epidemiological, clinical, social, behavioral and laboratory data need to be integrated. Sometimes, although databases are available, special data mining tools and approaches need
to be employed to extract meaningful data. There is a rapid change in focus from provider oriented medical informatics focusing on clinical medicine to consumer health informatics focusing on public
health. Modern thinking is to utilize informatics tools to make the environment more enabling for prevention and self-help rather than assisted care or disease management by experts. Biomedical
informatics has wide applications in understanding molecular and cellular processes. Imaging informatics is very useful in studying tissues and organs. Although clinical informatics deals with
understanding various dimensions of disease in individuals; public health informatics helps to understand diseases and health of the populations or the community. Critical areas of focus in biomedical
informatics are managing computational resources, efficient data management and establishing and sustaining collaborative environments. Evolution of computational resources should be concurrent with
growing landscape of biomedical research. There are major issues related to data management including challenges due to varied nature of data and variation in data collection, entry, archiving,
transmittal, and storage methods. Efficiency of data management and sophisticated statistical analysis is essentially dependent on bioinformatics infrastructure, capacity and human resources. More and
more biomedical research that is being recently undertaken is collaborative at the national and the global levels and it is essential to leverage intramural and extramural funding opportunities and
conducting high impact research that could have policy implications. Bioinformatics tools could play a significant role in facilitating this process. Future needs in biomedical informatics will be to create
ability to handle large data sets, minimize turnaround time of complex laboratory assays, fast track data management and intricate data quality management mechanisms that will help in rapid translation
of bench research to bedside application.

National Library of Medecine Resources for Researchers
10.10 - 10.30 Hemant Shah, M.D. , Senior Research Medical Informatician at the Henry Ford Health System

Abstract: The National Library of Medicine (NLM) of the USA is an organization that develops valuable technology and content to empower biomedical investigators in their research and to facilitate
adoption of the research findings into clinical practice and products. The resources and services offered by NLM are many and can be freely accessed by nearly everyone in the world. This presentation
will outline the demonstration (see Demo program) of several well known and some lesser known offerings of NLM. The resources covered will include, MedLine/PubMed, ClinicalTrials.gov, WebMIRS,
NLM Gateway, Entrez, MESH, RxNorm etc. An overview of these resources will be followed by demo of the features of these tools to exploit them for your purposes. We will also address how your
institution can integrate some of these with your own software systems or develop completely new tools using them.

10.30 11.00 Morning Tea



Bioinformatics
11.00 - 11.05 Session Chair: Prof. Indira Ghosh, Jawaharlal Nehru University (JNU), Delhi

Operonic structure of key metabolic pathways in cyanobacteria
11.05 - 11.25 Prof Pramod P. Wangikar,Department of Chemical Engineering, Indian Institute of Technology Bombay
Abstract: Genes involved in a common metabolic pathway are often organized in the form of an operon, which are transcribed into a single poly-cistronic mRNA. Analysis of the operonic structure of a
genome can be a useful tool in obtaining pathway level annotation for hypothetical genes. In this work we have used a comparative genomics based approach for the prediction of cyanobacterial operons
using intergenic distance and gene neighborhood conservation as features. The predicted operons were then mapped to KEGG metabolic pathways to identify operons whose genes map to a common
metabolic pathway. We identified a total of 39 pathways in cyanobacteria which correspond to at least one operon. These included operons unique to cyanobacteria such as those involved in
photosynthesis. We detected a significant rearrangement in the operonic structure of genes in metabolic pathways across different cyanobacteria. To exemplify, the phycobilisome five-gene operon in
photosynthesis pathway of Synechocystis sp. PCC 6803 was found to be rearranged and extended in the form of a ten-gene operon containing new phycocyanobilin lyase subunits and additional
phycobilisome linker proteins in Anabaena species. Further, a total of 317 genes were annotated at the pathway level using our analysis. The results provide a vast resource for biologists working on
cyanobacteria for further experimental validation

Cyber-infrastructures for Genetic Design Automation
11.25 - 11.45
Dr. Jean Peccoud, School of Biomedical Engineering and Sciences, Virginia Tech
Abstract: DNA is rapidly becoming a new engineering substrate as fabrication processes are being developed to assemble designer DNA molecules as large as a bacterial genomes. Genetic Design
Automation (GDA) is an emerging field focused on the development of tools to streamline the design, fabrication, and test of synthetic genetic systems. GDA represents an opportunity to use and develop
cyber-infrastructures to foster collaborations between teams of biologists, engineers, and computer scientists involved in the development of large synthetic genetic systems. We lead the development of
GenoCAD, GenoCAM, GenoAPE, and GenoTHREAT, an integrated suite of GDA tools that illustrate this trend

Selection of data features for machine learning in the prediction of genome-wide protein:protein interactions
11.45 - 12.05
Dr. Shekhar C. Mande, Centre for DNA Fingerprinting and Diagnostics, Hyderabad
Abstract: Complex cellular functions are the outcomes of interactions among biomolecules, one such class of interactions is between proteins. Availability of genome sequences and small scale protein
interactions facilitate prediction of genome-wide protein:protein interactions employing machine learning algorithms. Number of data features have been used for the prediction of genome-wide
protein:protein interactions such as similarity of phylogenetic profiles, distance of genes on the genome, frequency of co-occurrence in the operons, correlation in gene expression and gene order
conservation. Considering Escherichia coli and Mycobacterium tuberculosis as examples, we demonstrate the ability of these features to distinguish between protein pairs that are known to interact and
those that are not likely to interact. Utilizing the predictive capability of such method, we derive protein functional networks for both the organisms, the analysis of which helps us understand the organisms
better.

12.05 - 12.25 Systems Biology, Global Analysis, and Biomarker Target Identification
Professor Mathew J. Palakal, School of Informatics/Department of Computer & Information Science, Indiana University-Purdue University Indianapolis, Indiana, USA
Abstract: Biological processes are more complicated than the knowledge of individual genes, proteins, or pathways. Systems biology approaches facilitate global understanding of a biological
phenomenon and bibliomics can play an important role in Systems Biology along with the other “omics” data. During the last decade, data published in biomedical literature has grown exponentially. Since
experimental data is often incomplete, biomedical literature data can be effectively used to augment the shortcomings experimental data that would help to discover the missing nodes and connections in
the networks and pathways. In this talk we highlight the significance of global analysis for making local hypothesis on disease and drug target discoveries.

12.25 - 13.30 Lunch



Nanotechnology and High Energy and Computational Physics
13.30 - 13.55 Session Chair: Dr P.S.Dhekne, Bhabha Atomic Research Centre(BARC) Mumbai

Computational Nanoelectronics: Current Status & Trends
13.35 - 13.55
Professor V. Ramgopal Rao, Electrical Engineering Department, IIT Bombay

Abstract: In the last few years, Nanoelectronics has emerged as a multi-disciplinary science paving way for development of new technologies and applications. With the slowing down of CMOS scaling
owing to the huge cost, power and variability constraints, researchers are focussing more on the “More than Moore” technologies, allowing for the integration of heterogeneous technologies on a CMOS
platform. The key idea is to achieve a functional diversification on the chip by empowering the CMOS technologies with a variety of “sense & interact” functions. In this talk, we will look at the convergence
of Bio-Nano-Information technologies and how it helps development of new applications and platforms addressing the societal needs. The scaling of CMOS technologies has also impacted the device
behaviour significantly, necessitating a development of advanced simulation tools for understanding of such nano-scale device phenomena. The ever increasing levels of component densities on the chip
coupled with their functional diversity further adds to the computational challenges in the nano-scale regime. In this talk we will also look at the growth of Nanoelectronics activities in India over the past
few years with a specific focus on the current level of infrastructure and the opportunities for growth.

Atomistic Modeling and Simulation Tools for Nanoelectronics and their Deployment on nanoHUB.org
13.55 - 14.15
Michael McLennan, Senior Research Scientist, the Rosen Center for Advanced Computing, Purdue University

Abstract: At the nanometer scale the concepts of device and material meet and a new device is a new material and vice versa. While atomistic device representations are novel to device physicists, the
semiconductor materials modeling community usually treats infinitely periodic structures. NEMO 1-D originally developed at Texas Instruments first demonstrated the need to resolve resonant tunneling
diodes at an atomistic level to obtain quantitative agreements with experiments. NEMO 3-D enables 52 million atom electronic structure simulations of quantum dots, quantum wells, nanowires, and
impurities with relevant device dimensions. The new OMEN code enables quantum transport in atomistically resolved systems.

This presentation will briefly review motivations of the need to model nanoelectronic devices at the atomistic level and overview some critical elements in the NEMO1-D, NEMO 3-D, and OMEN
developments. NEMO 1-D capabilities are discussed in the quantitative and predictive simulations of resonant tunneling diodes. NEMO 3-D capabilities are discussed for InAs quantum dots embedded in
an InGaAs strain reducing layer on top of a GaAs substrate. OMEN capabilities are demonstrated with quantum transport simulations of band-to-band-tunneling transistors will be shown using the next
generation OMEN tool. Both NEMO 3-D and OMEN perform very well on parallel machines and demonstrated efficient usage of up to 8,192 and 222,720 processors, respectively.

Ultimately these simulation tools will have the most impact if they can leave the hands of computational scientists and be put into the hands of experimentalists and educators. nanoHUB.org provides a
platform for such tool deployment and we will highlight our achievements and plans on tool deployment of OMEN and NEMO3D on the nanoHUB.

LHC-CMS Tier-2 Facility at the Tata Institute for Fundemental Research (TIFR)
14.15 - 14.35
Professor Atul Gurtu, TIFR LHC Tier 2 Facility, Mumbai (India)
Abstract: The field of experimental high energy physics has always needed the highest end computing facilities for successful and efficient processing of large data sets to extract the science as quickly
as possible. The use of large state-of-the-art mainframes in the 1960’s to 80’s, was followed by PC farms till recently. As soon as the LHC was approved in the mid-1990’s it was clear to the experimental
community that an order of magnitude increase in computing resources would be needed for successful extraction of physics from the vast amount of data expected to be spewed out by the four major
experiments. World-wide distributed computing resources utilizing GRID technology was identified as the only way to successfully tackle this computing challenge. The development of necessary
middleware and setting up of high speed connectivity between countries was driven by the necessity of LHC science. India has participated significantly in the LHC program, contributing towards the
accelerator, towards GRID related software effort in collaboration with CERN, and is also part of two physics collaborations CMS and ALICE. Tier-2 computing centers for India-CMS and India-ALICE are
operating at TIFR, Mumbai and VECC/SINP, Kolkata, respectively. This talk will cover the setting up of the TIFR Tier-2 center and its present status.



14.35 -14.55 Computing and Networking Needs for Lattice Field Theory
Professor Steven Gottlieb, Indiana University
Abstract: Lattice field theory provides a nonperturbative approach to study quantum field theory. It has had a number of successes in predicting experimental results. However, it requires very
significant computational resources, and future, higher precision calculations will have even greater requirements.

There have been long standing and excellent contacts between Indian and American physicists working in this field. We will consider future opportunies for joint work and how improved networking might
help.

15.00 - 15.30 Afternoon Tea

15:30 - 16.30 Panel Session and Discussion - Where to from here?
A panel led by four scientists, two from India and two from the US, and taking into account the contributions made during the workshop, and drawing on audience participation will debate
and deliberate on ways to significantly enhance Indo-US network enabled collaboration. In doing so the panel and audience will try to Identify key issues, challenges, obstacles, and
opportunities needed for the development of action plans, and identify next steps snf future deliverables. The output of this session will form the basis for the second part of the US-India
Workshop, tentatively planned for October 2011 in Washington, DC

16.30 - 16.40 Summing up of workshop-Jim Williams & N. Mohan Ram DG, ERNET India
16.40 - 16.45 Closing Remarks - Dipak Singh, Director ERNET
16.45 - 16.50 Vote of Thanks-(Praveen Misra, Additional Director, ERNET)


Us india workshop workshop program v 7.1

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