ArticleBMC systems biology2012
The Cell Collective: toward an open and collaborative approach to systems biology.
Article in BMC systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers, 2 of them syntheses that pooled 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.
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
130 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A meta-analysis of Boolean network models reveals design principles of gene regulatory networks.Science advances · 2024Pooled it
- Recent applications of quantitative systems pharmacology and machine learning models across diseases.Journal of pharmacokinetics and pharmacodynamics · 2022Pooled it
- TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.bioRxiv : the preprint server for biology · 2026Article
- Web-based collaborative model development in interdisciplinary consortia: Design principles and practical guidance.PLoS biology · 2026Article
- ECMSim: A high-performance interactive web application for real-time spatiotemporal simulation of cardiac ECM signaling and diffusion.Matrix biology plus · 2026Article
- Succession-diagram-based Markov chains reveal the attractor landscape of asynchronous Boolean networks.NPJ systems biology and applications · 2026Article
- Unveiling toxicological adverse outcomes: toward construction and simulation of large-scale networks.Toxicological sciences : an official journal of the Society of Toxicology · 2026Review
- MetaScreener: a robust dual-mode framework for directional prioritization of actionable signatures through multi-dataset and multi-approach integration.Journal of translational medicine · 2026Article
- Dynamics of attractor transitions in Boolean networks under noise.Chaos (Woodbury, N.Y.) · 2026Article
- Canalization as a stabilizing principle of gene regulatory networks: a discrete dynamical systems perspective.NPJ systems biology and applications · 2026Review
- From mechanistic models to artificial intelligence: exploring the potential of digital twins in geriatric oncology.Frontiers in artificial intelligence · 2026Article
- A comprehensive mechanistic multicellular model of the human immune system spanning 11 diseases.Frontiers in immunology · 2026Article
- BioLogical: a universal analysis framework for biosystem logical dynamics.Computational and structural biotechnology journal · 2026Article
- Path-based quantification of activation and repression in Boolean models using BooLEVARD.NPJ systems biology and applications · 2025Article
- CANA v1.0.0: efficient quantification of canalization in automata networks.Bioinformatics (Oxford, England) · 2025Article
- Upper bound for the stability of Boolean networks.Physical review. E · 2025Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Article
- Automated model refinement using perturbation-observation pairs.NPJ systems biology and applications · 2025Article
- An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?Journal of mathematical biology · 2025Article
70 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
backgroundDespite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic study of biochemical pathways requires computer modeling. Due to the complexity of cells, it is not feasible for one person or group to model the cell in its entirety.
resultsThe Cell Collective is a platform that allows the world-wide scientific community to create these models collectively. Its interface enables users to build and use models without specifying any mathematical equations or computer code - addressing one of the major hurdles with computational research. In addition, this platform allows scientists to simulate and analyze the models in real-time on the web, including the ability to simulate loss/gain of function and test what-if scenarios in real time.
conclusionsThe Cell Collective is a web-based platform that enables laboratory scientists from across the globe to collaboratively build large-scale models of various biological processes, and simulate/analyze them in real time. In this manuscript, we show examples of its application to a large-scale model of signal transduction.
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.