ArticleIEEE transactions on visualization and computer graphics2018
Instant Construction and Visualization of Crowded Biological Environments.
Article in IEEE transactions on visualization and computer graphics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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.
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.
Who cites it
20 citing papers in PubMed, 47 citations in OpenAlex.
- Cryo-electron tomography of Nipah virus structural protein complexes in virus-like particles.bioRxiv : the preprint server for biology · 2026Article
- Molecular architecture of Influenza A virions.bioRxiv : the preprint server for biology · 2026Article
- Electrophysical cardiac remodeling at the molecular level: Insights into ryanodine receptor activation and calcium-induced calcium release from a stochastic explicit-particle model.Biophysical journal · 2024Article
- Mesoscale explorer: Visual exploration of large-scale molecular models.Protein science : a publication of the Protein Society · 2024Article
- Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models.bioRxiv : the preprint server for biology · 2024Article
- Integrative modeling of JCVI-Syn3A nucleoids with a modular approach.Current research in structural biology · 2024Article
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- Integrative structural modelling and visualisation of a cellular organelle.QRB discovery · 2022Article
- Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API.Journal of chemical information and modeling · 2021Article
- Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.Journal of molecular biology · 2021Article
- Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models.IEEE transactions on visualization and computer graphics · 2021Article
- Grand Challenges in Bioinformatics Data Visualization.Frontiers in bioinformatics · 2021Article
- Art and Science of the Cellular Mesoscale.Trends in biochemical sciences · 2020Review
- Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation.MolVa : Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020 · 2020Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Securing the future of research computing in the biosciences.PLoS computational biology · 2019Article
- Integrative Modeling and Visualization of Exosomes.The Journal of biocommunication · 2019Article
- Perspectives on Structural Molecular Biology Visualization: From Past to Present.Journal of molecular biology · 2018Review
- Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell.Journal of integrative bioinformatics · 2018Article
- Lattice Models of Bacterial Nucleoids.The journal of physical chemistry. B · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
Abstract
We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.