ArticleFrontiers in physiology2018
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.
Article in Frontiers in physiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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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.
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Who cites it
37 citing papers in PubMed.
- Ten quick tips for causal analysis of biomedical omics data.PLoS computational biology · 2026Article
- Succession-diagram-based Markov chains reveal the attractor landscape of asynchronous Boolean networks.NPJ systems biology and applications · 2026Article
- Mesenchymal to epithelial transition (MET) in cancer progression: insights from logical modeling.Scientific reports · 2026Article
- Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.NPJ systems biology and applications · 2026Article
- Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming.NPJ systems biology and applications · 2025Article
- Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial.Interface focus · 2025Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Automated model refinement using perturbation-observation pairs.NPJ systems biology and applications · 2025Article
- Refining Boolean models with the partial most permissive scheme.Bioinformatics (Oxford, England) · 2025Article
- GTAT-GRN: a graph topology-aware attention method with multi-source feature fusion for gene regulatory network inference.Frontiers in genetics · 2025Article
- Predictive modelling of acute Promyelocytic leukaemia resistance to retinoic acid therapy.Briefings in bioinformatics · 2024Article
- scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics.PLoS computational biology · 2024Article
- MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps.Journal of integrative bioinformatics · 2024Article
- SimService: a lightweight library for building simulation services in Python.Bioinformatics (Oxford, England) · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- From time-series transcriptomics to gene regulatory networks: A review on inference methods.PLoS computational biology · 2023Review
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- Reducing Boolean networks with backward equivalence.BMC bioinformatics · 2023Article
- Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts.Computational and structural biotechnology journal · 2023Article
- Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualization of the results. The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to the software tools GINsim, BioLQM, Pint, MaBoSS, and Cell Collective, for the modeling and analysis of Boolean and multi-valued networks. More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses.
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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.