NDLI: Scalable online comparative genomics of mononucleosomes: a BigJob

Please wait, while we are loading the content...

New atomic resolution insights into dynamic protein-carbohydrate interactions enabled by high-performance computing

Integration of science gateways: a case study with CyberGIS and OpenTopography

The XSEDE ticket system: from concept to implementation

Providing a supported online course on parallel computing

Low entropy data mapping for sparse iterative linear solvers

Scalable spectral transforms at petascale

Hadoop deployment and performance on Gordon data intensive supercomputer

INSTANCES: incorporating computational scientific thinking advances into education & science courses

Large-scale land use optimization by enhancing a scalable parallel genetic algorithm library

'Spring through the gateway': deploying genomic workflows with XSEDE

Using XDMoD to facilitate XSEDE operations, planning and analysis

The condo of condos

Multiscale characterization of macromolecular dynamics: application to photoacitve yellow protein

A neuroscience gateway: software and implementation

Optimizing utilization across XSEDE platforms

Getting started with high performance computing for humanities, arts, and social science

Attacking HIV, tuberculosis and histoplasmosis with XSEDE resources

A sustainable national gateway for biological computation

Preliminary experiences with the uintah framework on Intel Xeon Phi and stampede

Development of undergraduate programs in computational science: panel

Biomedical CyberInfrastructure challenges

FluMapper: an interactive CyberGIS environment for massive location-based social media data analysis

OSC OnDemand: a web platform integrating access to HPC systems, web and VNC applications

US-SOMO cluster methods: year one perspective

Low-temperature isomers of the water hexamer as predicted by q-TIP4P/F and TTM3-F potentials

Experiences in building a next-generation sequencing analysis service using galaxy, globus online and Amazon web service

Comprehensive job level resource usage measurement and analysis for XSEDE HPC systems

1000 words: advanced visualization for the humanities

An investigation of the effects of error correcting code on GPU-accelerated molecular dynamics simulations

SeedMe preview: your results from disk to device

Developing a high-volume batch submission system for earthquake engineering

HPC university: getting information about computational science professional and educational resources and opportunities for engagement

Alleviating the scaling problem of cosmological hydrodynamic simulations with HECA

MuMMI: multiple metrics modeling infrastructure for exploring performance and power modeling

Adaptive latency-aware parallel resource mapping: task graph scheduling onto heterogeneous network topology

Opposites attract: computational and quantitative outreach through artistic expressions

XSEDE-enabled high-throughput lesion activity assessment

Scalasca support for MPI+OpenMP parallel applications on large-scale HPC systems based on Intel Xeon Phi

CILogon: a federated X.509 certification authority for cyberinfrastructure logon

Scaling a code in the human dimension

The influence of an applied heat flux on the violence of reaction of an explosive device

Exploiting MapReduce and data compression for data-intensive applications

A Maya use case: adaptable scientific workflows with ADIOS for general relativistic astrophysics

The Oklahoma cyberinfrastructure initiative

Referee consensus: a platform technology for nonlinear optimization

Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures

NCAR storage accounting and analysis possibilities

The institute for cyber-enabled research: regional organization to promote computation in science

National Center for Genome Analysis support leverages XSEDE to support life science research

Embedding CIPRES science gateway capabilities in phylogenetics software environments

Enhancing the performance of scientific workflow execution in e-science environments by harnessing the standards based parameter sweep model

A tale of three outreach programs: strategic collaboration across XSEDE outreach services

Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networks

iData: a community geospatial data sharing environment to support data-driven science

In-situ visualization for global hybrid simulations

Training, education, and outreach: raising the bar

Using Lucene to index and search the digitized 1940 US census

Ab initio elasticity workflow in the VLab science gateway

A high-level framework for parallelizing legacy applications for multiple platforms

Human centered game design for bioinformatics and cyberinfrastructure learning

Enabling dark energy survey science analysis with simulations on XSEDE resources

Providing resource information to users of a national computing center

Using Gordon to accelerate LHC science

Making campus bridging work for researchers: a case study with mlRho

SocialMapExplorer: visualizing social networks of massively multiplayer online games in temporal-geographic space

High performance computing workflow for protein functional annotation

Exploring Twitter networks in parallel computing environments

The parallel system for integrating impact models and sectors (pSIMS)

Supercomputer assisted generation of machine learning agents for the calibration of building energy models

Scalable online comparative genomics of mononucleosomes: a BigJob

Fast construction of nanosecond level snapshots of financial markets

Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects

A framework for flexible and scalable replica-exchange on production distributed CI

Enabling large-scale next-generation sequence assembly with Blacklight

Scalable online comparative genomics of mononucleosomes: a BigJob

Content Provider	ACM Digital Library
Author	El Khamra, Yaakoub Mantha, Pradeep Kumar Smith, Jack A. Romanus, Melissa Jha, Shantenu Bishop, Thomas C.
Abstract	Our goal is to develop workflows for simulating arbitrary collections of mononucleosomes in atomic detail as an on demand analysis tool for online comparative genomics. The limiting factor is resource availability. The aim of this paper is to document and share our experiences in providing a general-purpose, easy-to-use and extensible solution for such computations. At the core it involves supporting the execution of high-throughput workloads of high-performance biomolecular simulations on one or more XSEDE machines. Although conceptually simple, it is still a difficult practical problem to solve, especially in a flexible, robust, scalable manner. Specifically, we employ BigJob-- an interoperable Pilot-Job. The bulk of this paper is about our experience in executing a very large number of ensembles including the associated non-trivial data management problem. Our experience suggests that although a nascent and fledgling technology, BigJob provides a flexible and scalable Pilot-Job to support workloads that were hitherto not easy.
Starting Page	1
Ending Page	8
Page Count	8
File Format	PDF
ISBN	9781450321709
DOI	10.1145/2484762.2484819
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2013-07-22
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Chromatin Nucleosome positioning Md Comparative genomics Computational workflow Bigjob Hpc Large scale Distributed computing Namd Saga
Content Type	Text
Resource Type	Article

Central Library (ISO-9001:2015 Certified)
Indian Institute of Technology Kharagpur
Kharagpur, West Bengal, India | PIN - 721302

See location in the Map
03222 282435
Mail: support@ndl.gov.in

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in