Evidence map›Paper›PMID 31749833›Full record

ArticleFrontiers in genetics2019

XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images.

Kaito Ii, Kota Mashimo, Mitsunori Ozeki, Takahiro G Yamada, Noriko Hiroi, Akira Funahashi

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in genetics, 2019. 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. Review
  2. Tools for computational analysis of moving boundary problems in cellular mechanobiology.Wiley interdisciplinary reviews. Systems biology and medicine · 2020
    Review
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

6 authors.

Kaito IiSystems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
Kota MashimoSystems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
Mitsunori OzekiSystems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
Takahiro G YamadaSystems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
Noriko HiroiSystems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.
Akira FunahashiSystems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Yokohama, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

XitoSBML is a software tool designed to create an SBML (Systems Biology Markup Language) Level 3 Version 1 document from microscopic cellular images. It is implemented as an ImageJ plug-in and is designed to create spatial models that reflect the three-dimensional cellular geometry. With XitoSBML, users can perform spatial model simulations based on realistic cellular geometry by using SBML-supported software tools, including simulators such as Virtual Cell and Spatial Simulator. XitoSBML is open-source and is available at https://github.com/spatialsimulator/XitoSBML/. XitoSBML is confirmed to run on most 32/64-bit operating systems: Windows, MacOS, and Linux.

Indexed as

ImageJimage processingspatial modelingspatial model simulationsystems biology markup language

Identifiers

PMID31749833
PMCPMC6842926

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.