Tweet
Wardrobe Web-based Experiment Management System
Hi,
Almost a year ago I have started to develop a system to simplify a growing routine work with NGS data. The lab (to which I belong) works on epigenetics and all connected experiments RNA-Seq (single/pair, spikeins, dUTP) DNA-Seq (single/pair, ChIP, Transcription binding sites). There are a lot of biological parameters like histone modifications (H3K4Me3,H3K4me1,H3K27ac, H2AZ, etc.), fragmentation (Sonication, MNase, etc.), etc., as well as technical for an each experiment.
At some point I have realized, that I did not make new analysis. I only did the same work over and over again (even with prepared pipelines). Thats why I designed a web interface, which does not scare professors or technicians, because adding a record is simple as in Excel. Then for combinations of parameters I programmed a corresponded pipeline which runs automatically in the background. All output is represented as charts and tables in the interface. I don't need to send it by email or bring a flash or something like that anymore. Preliminary analysis is fully automated mapping (bowtie/tophat), QC, quantification (enriched islands, RPKMs), island distribution, all data is deposited as a track to a local UCSC genome browser for the best visualization and annotation. And it is worked, they indirectly did whole routine work.
In addition to that I have added a project designer and now biologists with no extensive experience in informatics can run DESeq, MANorm, AVTD and so on.
I think, that the System is somehow different from existed Galaxy, Illumina basespace, Genespring server.
Almost a year ago I have started to develop a system to simplify a growing routine work with NGS data. The lab (to which I belong) works on epigenetics and all connected experiments RNA-Seq (single/pair, spikeins, dUTP) DNA-Seq (single/pair, ChIP, Transcription binding sites). There are a lot of biological parameters like histone modifications (H3K4Me3,H3K4me1,H3K27ac, H2AZ, etc.), fragmentation (Sonication, MNase, etc.), etc., as well as technical for an each experiment.
At some point I have realized, that I did not make new analysis. I only did the same work over and over again (even with prepared pipelines). Thats why I designed a web interface, which does not scare professors or technicians, because adding a record is simple as in Excel. Then for combinations of parameters I programmed a corresponded pipeline which runs automatically in the background. All output is represented as charts and tables in the interface. I don't need to send it by email or bring a flash or something like that anymore. Preliminary analysis is fully automated mapping (bowtie/tophat), QC, quantification (enriched islands, RPKMs), island distribution, all data is deposited as a track to a local UCSC genome browser for the best visualization and annotation. And it is worked, they indirectly did whole routine work.
In addition to that I have added a project designer and now biologists with no extensive experience in informatics can run DESeq, MANorm, AVTD and so on.
I think, that the System is somehow different from existed Galaxy, Illumina basespace, Genespring server.
Comment