ArticleNucleic acids research2023
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.Biology · 2026Article
- Transfer learning with pre-trained language models for protein expression level prediction inSynthetic and systems biotechnology · 2026Article
- NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks.Bioinformatics (Oxford, England) · 2026Article
- Enzyme-constrained genome-scale modeling resolves growth-production trade-offs in fermentative biohydrogen production.Environmental science and ecotechnology · 2026Article
- Article
- GBA Solver: a user-friendly web server for growth balance analysis.Bioinformatics (Oxford, England) · 2025Article
- HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learning.Bioinformatics (Oxford, England) · 2025Article
- MTD: A cloud-based omics database and interactive platform forSynthetic and systems biotechnology · 2025Article
- Systems metabolic engineering ofSynthetic and systems biotechnology · 2025Article
- Advances and trends for astaxanthin synthesis in Phaffia rhodozyma.Microbial cell factories · 2025Review
- Reprogramming yeast metabolism for customized starch-rich micro-grain through low-carbon microbial manufacturing.Nature communications · 2025Article
- Exploring Biomass Precursor Synthesis as a Determinant in Microbial Adaptation to Unadapted Carbon Sources with AdaptUC.Research (Washington, D.C.) · 2025Article
- Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Deciphering and designing microbial communities by genome-scale metabolic modelling.Computational and structural biotechnology journal · 2024Review
- Integrating Experimental and Computational Analyses of Yeast Protein Profiles for Optimizing the Production of High-Quality Microbial Proteins.Applied biochemistry and biotechnology · 2024Article
- ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models.Synthetic and systems biotechnology · 2024Article
- CPhaMAS: The first pharmacokinetic analysis cloud platform developed by China.Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2024Article
- State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs.Microorganisms · 2023Review
- Reconstruction and metabolic profiling of the genome-scale metabolic network model ofSynthetic and systems biotechnology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Flux balance analysis (FBA) is an important method for calculating optimal pathways to produce industrially important chemicals in genome-scale metabolic models (GEMs). However, for biologists, the requirement of coding skills poses a significant obstacle to using FBA for pathway analysis and engineering target identification. Additionally, a time-consuming manual drawing process is often needed to illustrate the mass flow in an FBA-calculated pathway, making it challenging to detect errors or discover interesting metabolic features. To solve this problem, we developed CAVE, a cloud-based platform for the integrated calculation, visualization, examination and correction of metabolic pathways. CAVE can analyze and visualize pathways for over 100 published GEMs or user-uploaded GEMs, allowing for quicker examination and identification of special metabolic features in a particular GEM. Additionally, CAVE offers model modification functions, such as gene/reaction removal or addition, making it easy for users to correct errors found in pathway analysis and obtain more reliable pathways. With a focus on the design and analysis of optimal pathways for biochemicals, CAVE complements existing visualization tools based on manually drawn global maps and can be applied to a broader range of organisms for rational metabolic engineering. CAVE is available at https://cave.biodesign.ac.cn/.
Indexed as
Identifiers
What Socratic 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 Socratic graph.