PMID: 10068694Mar 9, 1999

E-CELL: software environment for whole-cell simulation

Bioinformatics
M TomitaC A Hutchison

Abstract

Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implici...Continue Reading

References

Feb 27, 2001·Mass Spectrometry Reviews·J Godovac-Zimmermann, L R Brown
May 29, 2000·Bulletin of Mathematical Biology·P SmolenJ H Byrne
Nov 13, 2009·Acta Biotheoretica·Jacques Demongeot
Aug 1, 2013·Acta Biotheoretica·Anne Jeannin-GirardonVincent Rodin
Apr 1, 2008·Journal of Biological Physics·Jordi FerrerDaniel López
Aug 19, 2007·Cell Biochemistry and Biophysics·Philip LeDuc, Russell Schwartz
Oct 5, 2007·Journal of Biosciences·Prashant KhodadeNagasuma Chandra
May 13, 2005·Bio Systems·Ken Webb, Tony White
Dec 4, 2003·Computational Biology and Chemistry·Elizabeth L Weitzke, Peter J Ortoleva
Apr 16, 2005·Current Opinion in Biotechnology·Kirsi-Marja Oksman-Caldentey, Kazuki Saito
Nov 19, 2003·Neural Networks : the Official Journal of the International Neural Network Society·Shinichi KikuchiM Tomita
Aug 11, 2004·Progress in Biophysics and Molecular Biology·Colin G JohnsonWilliam J Gullick
Jul 1, 2005·Progress in Biophysics and Molecular Biology·Nobuaki SaraiAkinori Noma
Jan 19, 2008·Theory in Biosciences = Theorie in Den Biowissenschaften·F Castiglione, S Succi
Jun 1, 2005·Trends in Biotechnology·Sang Yup LeeTae Yong Kim
Oct 25, 2003·Journal of Theoretical Biology·Nathan D PriceBernhard O Palsson
Dec 12, 2002·Progress in Biophysics and Molecular Biology·Upinder S Bhalla
May 18, 2001·Trends in Biotechnology·M Tomita
Oct 6, 2001·Trends in Biotechnology·L M Loew, J C Schaff
Apr 8, 2003·Trends in Biotechnology·Nathan D PriceBernhard O Palsson
Jan 17, 2002·Journal of Biotechnology·Wolfgang Wiechert
Nov 5, 2002·Trends in Genetics : TIG·Douglas B Kell
Mar 30, 2002·Advanced Drug Delivery Reviews·George M Grass, Patrick J Sinko
Jun 19, 2002·Bio Systems·Katarzyna Bogunia-Kubik, Masanori Sugisaka
Mar 29, 2001·Journal of Pharmacological and Toxicological Methods·S EkinsJ H Wikel
Dec 18, 2003·Drug Discovery Today·Eric Werner
Feb 13, 2001·Current Opinion in Chemical Biology·M Pellegrini
Feb 13, 2001·Current Opinion in Chemical Biology·S J Fey, P M Larsen
Jul 10, 2002·Biomolecular Engineering·Arne BuchholzRalf Takors
Sep 1, 2002·Journal of Biological Physics·S V SabauS Ihara
Nov 13, 2008·Cytotechnology·F R SidoliS P Asprey
Feb 5, 2000·Nature Biotechnology·G A Evans
Nov 5, 2013·Nature Methods·Jayodita C SanghviMarkus Covert
Sep 18, 2008·Nature Reviews. Molecular Cell Biology·Guy Karlebach, Ron Shamir
Jun 30, 2009·Molecular BioSystems·Javier CarreraAlfonso Jaramillo
May 10, 2002·Environmental Microbiology·Jeremy S EdwardsBernhard O Palsson
Nov 13, 2012·Journal of Biomolecular Structure & Dynamics·Y SobolevskyE N Trifonov
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hidde de Jong
Sep 26, 2003·Omics : a Journal of Integrative Biology·Jochen FörsterJens Nielsen
Oct 30, 2003·Omics : a Journal of Integrative Biology·Nicholas A AllenJason W Zwolak
Sep 23, 2008·Briefings in Bioinformatics·Dong-Yup LeeIftekhar A Karimi
Jan 20, 2009·Briefings in Bioinformatics·Jürgen Pahle
Sep 11, 2004·Bioinformatics·Antti PettinenMarja-Leena Linne

Related Concepts

Metabolic Process, Cellular
In Silico
Biochemical Pathway
Complex (molecular entity)
Protoplasm
Transcription, Genetic
Computer Graphics
Plasma Protein Binding Capacity
Gene Expression
Computer Programs and Programming

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Synapse Loss as Therapeutic Target in MS

As we age, the number of synapses present in the human brain starts to decline, but in neurodegenerative diseases this occurs at an accelerated rate. In MS, it has been shown that there is a reduction in synaptic density, which presents a potential target for treatment. Here is the latest research on synapse loss as a therapeutic target in MS.

Artificial Intelligence in Cardiac Imaging

Artificial intelligence (ai) techniques are increasingly applied to cardiovascular (cv) medicine in cardiac imaging analysis. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

Social Learning

Social learning involves learning new behaviors through observation, imitation and modeling. Follow this feed to stay up to date on the latest research.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Single Cell Chromatin Profiling

Techniques like ATAC-seq and CUT&Tag have the potential to allow single cell profiling of chromatin accessibility, histones, and TFs. This will provide novel insight into cellular heterogeneity and cell states. Discover the latest research on single cell chromatin profiling here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.