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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

Retrieving information. Screen-grab of the data associated with an experiment. The collection of experiments can be queried and the data and metadata retrieved. In this example, the entry for “time course D. C. infection for RNA seq” has been edited since its original creation in ICeE. Clicking on the pull-down menu at the top right gives access to previous versions. In this specific example, RNA samples were prepared from worms infected with the fungus Drechmeria coniospora for subsequent RNaseq analysis (S. Omi, unpublished results). In addition to the report on the RNA quality (the pdf file at the bottom of the list), the raw data for qRT-PCR tests on selected genes (the xls file at the top) and a graphical summary (the xlsx file) conducted to characterize the samples, are included.
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f0005: Retrieving information. Screen-grab of the data associated with an experiment. The collection of experiments can be queried and the data and metadata retrieved. In this example, the entry for “time course D. C. infection for RNA seq” has been edited since its original creation in ICeE. Clicking on the pull-down menu at the top right gives access to previous versions. In this specific example, RNA samples were prepared from worms infected with the fungus Drechmeria coniospora for subsequent RNaseq analysis (S. Omi, unpublished results). In addition to the report on the RNA quality (the pdf file at the bottom of the list), the raw data for qRT-PCR tests on selected genes (the xls file at the top) and a graphical summary (the xlsx file) conducted to characterize the samples, are included.

Mentions: Since researchers may perform the same type of experiment repeatedly, an existing experimental protocol can be duplicated as a template for a new experiment, simply by clicking “Insert similar” (Fig. 5), alleviating the need to re-enter all the experimental details. In this way, data entry becomes increasingly simple and rapid as more types of experimental protocols are included. Further, once an experiment has been entered into ICeE, users can return to the corresponding entry in the database and add additional files at any time. Thus, for example, having initially entered the raw data, a user can subsequently upload any number of files of data analysis; an initial raw text or CSV data file from the Biosort can be complemented with graphical representations or statistical analyses generated in software such as Open Office™, or using dedicated tools.5 Comments can be added to the stored experiment to explain the contents of the different files.Figure 5.


ICeE an interface for C. elegans experiments.

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

Retrieving information. Screen-grab of the data associated with an experiment. The collection of experiments can be queried and the data and metadata retrieved. In this example, the entry for “time course D. C. infection for RNA seq” has been edited since its original creation in ICeE. Clicking on the pull-down menu at the top right gives access to previous versions. In this specific example, RNA samples were prepared from worms infected with the fungus Drechmeria coniospora for subsequent RNaseq analysis (S. Omi, unpublished results). In addition to the report on the RNA quality (the pdf file at the bottom of the list), the raw data for qRT-PCR tests on selected genes (the xls file at the top) and a graphical summary (the xlsx file) conducted to characterize the samples, are included.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0005: Retrieving information. Screen-grab of the data associated with an experiment. The collection of experiments can be queried and the data and metadata retrieved. In this example, the entry for “time course D. C. infection for RNA seq” has been edited since its original creation in ICeE. Clicking on the pull-down menu at the top right gives access to previous versions. In this specific example, RNA samples were prepared from worms infected with the fungus Drechmeria coniospora for subsequent RNaseq analysis (S. Omi, unpublished results). In addition to the report on the RNA quality (the pdf file at the bottom of the list), the raw data for qRT-PCR tests on selected genes (the xls file at the top) and a graphical summary (the xlsx file) conducted to characterize the samples, are included.
Mentions: Since researchers may perform the same type of experiment repeatedly, an existing experimental protocol can be duplicated as a template for a new experiment, simply by clicking “Insert similar” (Fig. 5), alleviating the need to re-enter all the experimental details. In this way, data entry becomes increasingly simple and rapid as more types of experimental protocols are included. Further, once an experiment has been entered into ICeE, users can return to the corresponding entry in the database and add additional files at any time. Thus, for example, having initially entered the raw data, a user can subsequently upload any number of files of data analysis; an initial raw text or CSV data file from the Biosort can be complemented with graphical representations or statistical analyses generated in software such as Open Office™, or using dedicated tools.5 Comments can be added to the stored experiment to explain the contents of the different files.Figure 5.

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