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FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, FANTOM consortiumForrest A, Kasukawa T, Kawaji H - Database (Oxford) (2016)

Bottom Line: To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR).SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan.

No MeSH data available.


Related in: MedlinePlus

Measurements of page-timing. x-axis shows FANTOM5 categories and the y-axis is the different timing in seconds. Memcached ON and OFF, for the six categories: n = 87, n = 1003, n = 3011, n = 52, n = 16 and n = 10 . The box denotes the median. The bars on each column show the 25 and 75 percentiles. Latency time changed drastically between cache-on and cache-off. No change in the loading and parsing time and rendering time for all categories.
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baw105-F4: Measurements of page-timing. x-axis shows FANTOM5 categories and the y-axis is the different timing in seconds. Memcached ON and OFF, for the six categories: n = 87, n = 1003, n = 3011, n = 52, n = 16 and n = 10 . The box denotes the median. The bars on each column show the 25 and 75 percentiles. Latency time changed drastically between cache-on and cache-off. No change in the loading and parsing time and rendering time for all categories.

Mentions: We assessed the performance of SSTAR on the server side and the client side depending on each category of data. Performance varied depending on the page category, with typical durations of less than one second for gene pages and nearly five seconds for sample pages (Figure 4) without memory caching. Use of a memory cache improved the server processing time more than tenfold (i.e. 0.1 s for all page categories; see Figure 4. The durations required on the client side also differ depending on page categories (Figure 4). Detailed results of the performance evaluation are included in the Supplementary Data.Figure 4.


FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, FANTOM consortiumForrest A, Kasukawa T, Kawaji H - Database (Oxford) (2016)

Measurements of page-timing. x-axis shows FANTOM5 categories and the y-axis is the different timing in seconds. Memcached ON and OFF, for the six categories: n = 87, n = 1003, n = 3011, n = 52, n = 16 and n = 10 . The box denotes the median. The bars on each column show the 25 and 75 percentiles. Latency time changed drastically between cache-on and cache-off. No change in the loading and parsing time and rendering time for all categories.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940433&req=5

baw105-F4: Measurements of page-timing. x-axis shows FANTOM5 categories and the y-axis is the different timing in seconds. Memcached ON and OFF, for the six categories: n = 87, n = 1003, n = 3011, n = 52, n = 16 and n = 10 . The box denotes the median. The bars on each column show the 25 and 75 percentiles. Latency time changed drastically between cache-on and cache-off. No change in the loading and parsing time and rendering time for all categories.
Mentions: We assessed the performance of SSTAR on the server side and the client side depending on each category of data. Performance varied depending on the page category, with typical durations of less than one second for gene pages and nearly five seconds for sample pages (Figure 4) without memory caching. Use of a memory cache improved the server processing time more than tenfold (i.e. 0.1 s for all page categories; see Figure 4. The durations required on the client side also differ depending on page categories (Figure 4). Detailed results of the performance evaluation are included in the Supplementary Data.Figure 4.

Bottom Line: To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR).SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan.

No MeSH data available.


Related in: MedlinePlus