Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

E-CELL: software environment for whole-cell simulation.

M Tomita1, K Hashimoto, K Takahashi

  • 1Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, Japan.mt@sfc.keio.ac.jp

Bioinformatics (Oxford, England)
|March 9, 1999
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Design and methods of the REMOVAL-HD study: a tRial Evaluating Mid cut-Off Value membrane clearance of Albumin and Light chains in HaemoDialysis patients.

BMC nephrology·2018
Same author

The relationship between high-sensitivity CRP and polyclonal free light chains as markers of inflammation in chronic disease.

International journal of laboratory hematology·2013
Same author

Kinetic modelling of haemodialysis removal of myoglobin in rhabdomyolysis patients.

Computer methods and programs in biomedicine·2013
Same author

Evaluation of Parkinson disease and Alzheimer disease with the use of neuromelanin MR imaging and (123)I-metaiodobenzylguanidine scintigraphy.

AJNR. American journal of neuroradiology·2013
Same author

Monoclonal gammopathy of undetermined significance: an update for nephrologists.

Advances in chronic kidney disease·2012
Same author

Characterization of brain D(2) dopamine receptors.

Neurochemistry international·2010
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

A new software environment, E-CELL, enables integrative cell modeling and in silico experiments. This tool simulates cellular processes using gene sets, advancing our understanding of dynamic cell behavior and genome engineering.

Area of Science:

  • Computational Biology
  • Systems Biology
  • Molecular Systems Biology

Background:

  • Genome sequencing generates vast molecular data, enabling cell behavior simulation.
  • Previous models focused on isolated pathways, lacking integration of gene regulation, metabolism, and signaling.
  • Developing integrative cell models is crucial for predicting dynamic cellular processes.

Purpose of the Study:

  • To develop a software environment for building integrative cell models based on gene sets.
  • To enable in silico experiments for studying cellular molecular processes.
  • To establish methods for incorporating gene regulation, metabolism, and signaling into cell models.

Main Methods:

  • Developed the E-CELL modeling and simulation environment.

Related Experiment Videos

  • Users define cellular components and interactions as reaction rules.
  • Simulates cell behavior by numerically integrating differential equations.
  • Constructed a hypothetical cell model with 127 genes from Mycoplasma genitalium.

    • Main Results:

    • E-CELL allows definition of protein functions, interactions, and gene expression regulation.
    • The system simulates dynamic changes in cellular compound concentrations.
    • A minimal cell model demonstrated transcription, translation, energy production, and phospholipid synthesis.
    • The model utilized genes from Mycoplasma genitalium, the organism with the smallest known genome.

    Conclusions:

    • E-CELL provides a platform for integrative cell modeling and simulation.
    • The developed software facilitates in silico experimentation for biological research.
    • Future applications include advancements in genome engineering and synthetic biology.
    • The E-CELL system is available upon request, with model details online.