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The cell cycle DB: a systems biology approach to cell cycle analysis.

Alfieri R, Merelli I, Mosca E, Milanesi L - Nucleic Acids Res. (2007)

Bottom Line: The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes.The database, which is accessible at the web site http://www.itb.cnr.it/cellcycle, has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly.The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models.

View Article: PubMed Central - PubMed

Affiliation: Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, Segrate, Milano, Italy. roberta.alfieri@itb.cnr.it

ABSTRACT
The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database, which is accessible at the web site http://www.itb.cnr.it/cellcycle, has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly. The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models.

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Model of Bai et al 2003 [15]. Examples of two objects shown by the user friendly interfaces in the “models section” of the Cell Cycle Database: (A) the ordinary differential equations as they appear on the web interface; (B) plot of time courses of three state variables of the model.
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Figure 2: Model of Bai et al 2003 [15]. Examples of two objects shown by the user friendly interfaces in the “models section” of the Cell Cycle Database: (A) the ordinary differential equations as they appear on the web interface; (B) plot of time courses of three state variables of the model.

Mentions: In the SBML data structure section, users can explore the SBML components of the selected model including its mathematical expressions. Mathematical formulas within the SBML models are expressed using the Mathematical Markup Language (MathML or MML) (12). To view the expressions on the web, our resource relies on a XHTML + MathML page. This technology allows the generation of high-quality documents in which mathematical expressions are treated as text in a HTML web page: it is possible to use the browser functions to find strings inside mathematical expressions and to change their size, operations that are usually not possible using images to represents formulas (Figure 2a).Figure 2.


The cell cycle DB: a systems biology approach to cell cycle analysis.

Alfieri R, Merelli I, Mosca E, Milanesi L - Nucleic Acids Res. (2007)

Model of Bai et al 2003 [15]. Examples of two objects shown by the user friendly interfaces in the “models section” of the Cell Cycle Database: (A) the ordinary differential equations as they appear on the web interface; (B) plot of time courses of three state variables of the model.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238882&req=5

Figure 2: Model of Bai et al 2003 [15]. Examples of two objects shown by the user friendly interfaces in the “models section” of the Cell Cycle Database: (A) the ordinary differential equations as they appear on the web interface; (B) plot of time courses of three state variables of the model.
Mentions: In the SBML data structure section, users can explore the SBML components of the selected model including its mathematical expressions. Mathematical formulas within the SBML models are expressed using the Mathematical Markup Language (MathML or MML) (12). To view the expressions on the web, our resource relies on a XHTML + MathML page. This technology allows the generation of high-quality documents in which mathematical expressions are treated as text in a HTML web page: it is possible to use the browser functions to find strings inside mathematical expressions and to change their size, operations that are usually not possible using images to represents formulas (Figure 2a).Figure 2.

Bottom Line: The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes.The database, which is accessible at the web site http://www.itb.cnr.it/cellcycle, has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly.The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models.

View Article: PubMed Central - PubMed

Affiliation: Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, via F.lli Cervi 93, Segrate, Milano, Italy. roberta.alfieri@itb.cnr.it

ABSTRACT
The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database, which is accessible at the web site http://www.itb.cnr.it/cellcycle, has been developed in a systems biology context, since it also stores the cell cycle mathematical models published in the recent years, with the possibility to simulate them directly. The aim of our resource is to give an exhaustive view of the cell cycle process starting from its building-blocks, genes and proteins, toward the pathway they create, represented by the models.

Show MeSH