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mmView: a web-based viewer of the mmCIF format.

Cech P, Svozil D - BMC Res Notes (2011)

Bottom Line: While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited.The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form.The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technick√° 5, CZ-166 28 Prague, Czech Republic. daniel.svozil@vscht.cz.

ABSTRACT

Background: Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited.

Findings: In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol.

Conclusions: The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user's computer, and as a publicly available web server.

No MeSH data available.


mmView software architecture. The mmView web application uses Model-Template-View (MTV) software architecture. The MTV architecture provides a way to separate the web interface (template layer) from the domain logic (model and view layers) making it easier to implement and modify each of these components independently. The View layer receives the request from the user's browser, invokes a desired functional operation and returns the template (i.e. the graphical data representation) as a response to the browser.
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Figure 2: mmView software architecture. The mmView web application uses Model-Template-View (MTV) software architecture. The MTV architecture provides a way to separate the web interface (template layer) from the domain logic (model and view layers) making it easier to implement and modify each of these components independently. The View layer receives the request from the user's browser, invokes a desired functional operation and returns the template (i.e. the graphical data representation) as a response to the browser.

Mentions: The mmView application is implemented as a dynamic web system using open source scripting language Python [17,18]. Python, which popularity is steadily rising among the bioinformatics community [19], is a modern object-oriented programming language that is easy to learn, easy to read, multiplatform and offers a wealth of available ready to use modules, as well as a strong support for integration with other languages and tools. To ease the development of the mmView system, a Python-based web framework Django [20,21] was utilized. Django is a high-level web framework based on a model-template-view (MTV) software architectural pattern (Figure 2), which represents a flavor of widely accepted model-view-controller (MVC) architecture. The MVC architecture provides a way to separate the user interface from the domain-specific representation of the data (e.g. data stored in the relational database), and from the domain logic (i.e. from functional algorithms that handle information exchange between a database and a user interface). The separation of the application in the three layers makes it easier to implement and modify each component independently. The Django's architecture assures portability to the user's preferred operating system (Linux, MS Windows, Mac OS X), web server (Apache) and database server (SQLite, MySQL, PostgreSQL). The core of the Django's MTV architecture consists of three layers. The Model layer defines underlying data storage mechanism, and provides easy access to the available data. The View defines which data will be presented to the user (including also the inner programmatic processing of the data), and the Template layer is responsible for the displaying of this data.


mmView: a web-based viewer of the mmCIF format.

Cech P, Svozil D - BMC Res Notes (2011)

mmView software architecture. The mmView web application uses Model-Template-View (MTV) software architecture. The MTV architecture provides a way to separate the web interface (template layer) from the domain logic (model and view layers) making it easier to implement and modify each of these components independently. The View layer receives the request from the user's browser, invokes a desired functional operation and returns the template (i.e. the graphical data representation) as a response to the browser.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3094370&req=5

Figure 2: mmView software architecture. The mmView web application uses Model-Template-View (MTV) software architecture. The MTV architecture provides a way to separate the web interface (template layer) from the domain logic (model and view layers) making it easier to implement and modify each of these components independently. The View layer receives the request from the user's browser, invokes a desired functional operation and returns the template (i.e. the graphical data representation) as a response to the browser.
Mentions: The mmView application is implemented as a dynamic web system using open source scripting language Python [17,18]. Python, which popularity is steadily rising among the bioinformatics community [19], is a modern object-oriented programming language that is easy to learn, easy to read, multiplatform and offers a wealth of available ready to use modules, as well as a strong support for integration with other languages and tools. To ease the development of the mmView system, a Python-based web framework Django [20,21] was utilized. Django is a high-level web framework based on a model-template-view (MTV) software architectural pattern (Figure 2), which represents a flavor of widely accepted model-view-controller (MVC) architecture. The MVC architecture provides a way to separate the user interface from the domain-specific representation of the data (e.g. data stored in the relational database), and from the domain logic (i.e. from functional algorithms that handle information exchange between a database and a user interface). The separation of the application in the three layers makes it easier to implement and modify each component independently. The Django's architecture assures portability to the user's preferred operating system (Linux, MS Windows, Mac OS X), web server (Apache) and database server (SQLite, MySQL, PostgreSQL). The core of the Django's MTV architecture consists of three layers. The Model layer defines underlying data storage mechanism, and provides easy access to the available data. The View defines which data will be presented to the user (including also the inner programmatic processing of the data), and the Template layer is responsible for the displaying of this data.

Bottom Line: While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited.The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form.The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technick√° 5, CZ-166 28 Prague, Czech Republic. daniel.svozil@vscht.cz.

ABSTRACT

Background: Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited.

Findings: In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol.

Conclusions: The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user's computer, and as a publicly available web server.

No MeSH data available.