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ICeE an interface for C. elegans experiments.

Montañana F, Julien RA, Vaglio P, Matthews LR, Tichit L, Ewbank JJ - Worm (2014)

Bottom Line: An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems.We describe a simple electronic database designed to allow easy storage and retrieval of Biosort data for C. elegans, but that has a wide potential application for organizing electronic files and data sets.ICeE is an Open Source application.

View Article: PubMed Central - PubMed

Affiliation: Centre d'Immunologie de Marseille-Luminy; UM2 Aix-Marseille Université ; Marseille, France ; INSERM U1104 ; Marseille, France ; CNRS UMR7280 ; Marseille, France.

ABSTRACT
An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems. While providing a powerful tool for generating quantitative data, the utility of the Biosort is currently limited by the absence of resources for data management. We describe a simple electronic database designed to allow easy storage and retrieval of Biosort data for C. elegans, but that has a wide potential application for organizing electronic files and data sets. ICeE is an Open Source application. The code and accompanying documentation are freely available via the web at http://www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html.

No MeSH data available.


Related in: MedlinePlus

Initial data entry in ICeE. Screen-grabs of data entry for an imaginary experiment. Having specified a name for the experiment and defining its nature (A), users are prompted to list the strains used, by entering either the strain genotype (B) or strain name (C). In both cases, pull-down lists of strains containing the typed text appear. Once a strain is chosen, its name and details of its genotype appear. (D) For strains that are at the CGC, clicking on the “Strain Report” button links to the relevant strain report page at Wormbase (E).
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f0001: Initial data entry in ICeE. Screen-grabs of data entry for an imaginary experiment. Having specified a name for the experiment and defining its nature (A), users are prompted to list the strains used, by entering either the strain genotype (B) or strain name (C). In both cases, pull-down lists of strains containing the typed text appear. Once a strain is chosen, its name and details of its genotype appear. (D) For strains that are at the CGC, clicking on the “Strain Report” button links to the relevant strain report page at Wormbase (E).

Mentions: We constructed a web-based application, ICeE, using PHP and Javascript, coupled to an associated MySQL database. While ICeE is designed to be compatible with the most commonly used web browsers, the use of Firefox™ is recommended. ICeE permits users to specify a series of pre-defined parameters to provide a complete description of an experiment, inspired by the MIAME guidelines (www.mged.org), and to associate these experimental criteria with a set of data. First, there are general identifiers, such as the date and the experimenter's name. Then, there is the rubric “protocol,” which can contain free-text, or be linked to one or more separate files. Under the section, “Conditions,” the experimenter adds precise details of the experimental conditions. Since it is designed for C. elegans, the application comes pre-loaded with a list of the nematode strains available from the Caenorhabditis Genetics Center (http://www.cbs.umn.edu/CGC). ICeE offers the possibility of updating this list and of importing a custom list of strains from a tab-delimited text file. Many laboratories use proprietary software, such as Filemaker™ to record their strain collections. Most allow data export in a tab-delimited format and so are easily compatible with ICeE. Strains can be picked from a pull-down menu; the first few characters of a strain's name or genotype will be auto-completed to give the user a more and more refined list of the corresponding strains. As individual users may frequently use the same nematode strains, these can be added simply to an easily accessible list of “favorites.” The database entries for strains from the CGC are directly linked to Wormbase; users can access the corresponding Wormbase strain report page with a click (Fig. 1).Figure 1.


ICeE an interface for C. elegans experiments.

Montañana F, Julien RA, Vaglio P, Matthews LR, Tichit L, Ewbank JJ - Worm (2014)

Initial data entry in ICeE. Screen-grabs of data entry for an imaginary experiment. Having specified a name for the experiment and defining its nature (A), users are prompted to list the strains used, by entering either the strain genotype (B) or strain name (C). In both cases, pull-down lists of strains containing the typed text appear. Once a strain is chosen, its name and details of its genotype appear. (D) For strains that are at the CGC, clicking on the “Strain Report” button links to the relevant strain report page at Wormbase (E).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588384&req=5

f0001: Initial data entry in ICeE. Screen-grabs of data entry for an imaginary experiment. Having specified a name for the experiment and defining its nature (A), users are prompted to list the strains used, by entering either the strain genotype (B) or strain name (C). In both cases, pull-down lists of strains containing the typed text appear. Once a strain is chosen, its name and details of its genotype appear. (D) For strains that are at the CGC, clicking on the “Strain Report” button links to the relevant strain report page at Wormbase (E).
Mentions: We constructed a web-based application, ICeE, using PHP and Javascript, coupled to an associated MySQL database. While ICeE is designed to be compatible with the most commonly used web browsers, the use of Firefox™ is recommended. ICeE permits users to specify a series of pre-defined parameters to provide a complete description of an experiment, inspired by the MIAME guidelines (www.mged.org), and to associate these experimental criteria with a set of data. First, there are general identifiers, such as the date and the experimenter's name. Then, there is the rubric “protocol,” which can contain free-text, or be linked to one or more separate files. Under the section, “Conditions,” the experimenter adds precise details of the experimental conditions. Since it is designed for C. elegans, the application comes pre-loaded with a list of the nematode strains available from the Caenorhabditis Genetics Center (http://www.cbs.umn.edu/CGC). ICeE offers the possibility of updating this list and of importing a custom list of strains from a tab-delimited text file. Many laboratories use proprietary software, such as Filemaker™ to record their strain collections. Most allow data export in a tab-delimited format and so are easily compatible with ICeE. Strains can be picked from a pull-down menu; the first few characters of a strain's name or genotype will be auto-completed to give the user a more and more refined list of the corresponding strains. As individual users may frequently use the same nematode strains, these can be added simply to an easily accessible list of “favorites.” The database entries for strains from the CGC are directly linked to Wormbase; users can access the corresponding Wormbase strain report page with a click (Fig. 1).Figure 1.

Bottom Line: An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems.We describe a simple electronic database designed to allow easy storage and retrieval of Biosort data for C. elegans, but that has a wide potential application for organizing electronic files and data sets.ICeE is an Open Source application.

View Article: PubMed Central - PubMed

Affiliation: Centre d'Immunologie de Marseille-Luminy; UM2 Aix-Marseille Université ; Marseille, France ; INSERM U1104 ; Marseille, France ; CNRS UMR7280 ; Marseille, France.

ABSTRACT
An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems. While providing a powerful tool for generating quantitative data, the utility of the Biosort is currently limited by the absence of resources for data management. We describe a simple electronic database designed to allow easy storage and retrieval of Biosort data for C. elegans, but that has a wide potential application for organizing electronic files and data sets. ICeE is an Open Source application. The code and accompanying documentation are freely available via the web at http://www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html.

No MeSH data available.


Related in: MedlinePlus