Evidence map›Paper›PMID 26069879›Full record

ArticleJournal of big data

DCMS: A data analytics and management system for molecular simulation.

Anand Kumar, Vladimir Grupcev, Meryem Berrada, Joseph C Fogarty, Yi-Cheng Tu, Xingquan Zhu, Sagar A Pandit, Yuni Xia

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of big data. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Anand KumarDepartment of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
Vladimir GrupcevDepartment of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
Meryem BerradaDepartment of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
Joseph C FogartyDepartment of Physics, University of South Florida, 4202 E. Fowler Ave., PHY114, Tampa, 33620 Florida USA.
Yi-Cheng TuDepartment of Computer Science and Engineering, University of South Florida, 4202 E. Fowler Ave., ENB118, Tampa, 33620 Florida USA.
Xingquan ZhuDepartment of Electrical Engineering and Computer Science, Florida Atlantic University, 777 Glades Road, EE308, Boca Raton, 33431 Florida USA.
Sagar A PanditDepartment of Physics, University of South Florida, 4202 E. Fowler Ave., PHY114, Tampa, 33620 Florida USA.
Yuni XiaDepartment of Computer Science, Indiana University - Purdue University Indianapolis, 723 W. Michigan St, SL280E, Indianapolis, 46202 Indiana USA.

Funding

Database-centric data analysis of molecular simulationsR01GM086707 · NIGMS · UNIVERSITY OF SOUTH FLORIDA · PI TU, YICHENG · 2010 to 2014
$863k
NIGMS NIH HHS R01 GM086707
6 · The paper itself

Abstract

Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface (

Indexed as

Data compressionMolecular dynamicsMolecular simulationScientific databaseSpatiotemporal database

Identifiers

PMID26069879
PMCPMC4456345

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.