Evidence map›Paper›PMID 31638901›Full record

ArticleBMC bioinformatics2019

PlantSimLab - a modeling and simulation web tool for plant biologists.

S Ha, E Dimitrova, S Hoops, D Altarawy, M Ansariola, D Deb, J Glazebrook, R Hillmer, H Shahin, F Katagiri and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

15 authors.

S HaDepartment of Computer and Information Sciences, Virginia Military Institute, Lexington, VA, USA.
E DimitrovaSchool of Mathematical and Statistical Sciences, Clemson University, Clemson, SC, USA.
S HoopsBiocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.
D AltarawyVirginia Tech, Blacksburg, VA, USA.
M AnsariolaCelgene, San Francisco, CA, USA.
D DebDepartment of Natural Sciences, Mercy College, Dobbs Ferry, NY, USA.
J GlazebrookCollege of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
R HillmerMendel Biological Solutions, San Franciso, CA, USA.
H ShahinVirginia Tech, Blacksburg, VA, USA.
F KatagiriCollege of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
J McDowellDepartment of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.
M MegrawDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
J SetubalBiochemistry Department, University of Sao Paolo, Sao Paolo, Brazil.
B M TylerCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA.
R LaubenbacherCenter for Quantitative Medicine, School of Medicine, University of Connecticut, Hartford, USA. laubenbacher@uchc.edu.ORCID http://orcid.org/0000-0002-9143-9451

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundAt the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling. One of the biggest challenges to making this integration a reality is that many life scientists do not possess the mathematical expertise needed to build and manipulate mathematical models well enough to use them as tools for hypothesis generation. Available modeling software packages often assume some modeling expertise. There is a need for software tools that are easy to use and intuitive for experimentalists.

resultsThis paper introduces PlantSimLab, a web-based application developed to allow plant biologists to construct dynamic mathematical models of molecular networks, interrogate them in a manner similar to what is done in the laboratory, and use them as a tool for biological hypothesis generation. It is designed to be used by experimentalists, without direct assistance from mathematical modelers.

conclusionsMathematical modeling techniques are a useful tool for analyzing complex biological systems, and there is a need for accessible, efficient analysis tools within the biological community. PlantSimLab enables users to build, validate, and use intuitive qualitative dynamic computer models, with a graphical user interface that does not require mathematical modeling expertise. It makes analysis of complex models accessible to a larger community, as it is platform-independent and does not require extensive mathematical expertise.

Indexed as

Computer SimulationModels, BiologicalPlantsSoftwareInternetSystems BiologyUser-Computer InterfaceBiological networkDynamic network modelMathematical modelModeling softwarePlant biology

Identifiers

PMID31638901
PMCPMC6805577

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

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.