File:Fig3 Calabria BMCBioinformatics2015 16-Suppl9.jpg

Figure 3: adLIMS workflow. The circular schema represents the adLIMS workflow from sample input to NGS pool generation. In the first step, a user with the SampleManager role fills the "Cell" and "Sample" forms that contain data about tissue source, lineage, cell type, cell marker, project, subject, DNA metadata. The two subplots related to this step highlight examples of real input data, in which on the back is visible a sample DNA list in the context of the adLIMS window layout whereas on the foreground is opened a sample image of a DNA quantification from an input data, stored as attachment in adLIMS. In the second step a user with the WetManager role processes samples along the LAM-PCR protocol setting-up the required Linear, 1° and 2° Exponential PCR amplification. Here the two subplots represent a sample window layout on the back and a picture of an agarose gel electrophoresis of LAM-PCR products in foreground. In the third step a subset of PCR samples are pooled together through the NGS Pool Setup and the sample window layout allows visualizing all required fields of the forms. The final step is the NGS sequencing and sample sheet acquisition, in which is possible to upload raw data quality reports such as the per-base sequence quality visible on the windowed subplot.

Calabria, Andrea; Spinozzi, Giulio; Benedicenti, Fabrizio; Tenderini, Erika; Montini, Eugenio (2015). "adLIMS: A customized open source software that allows bridging clinical and basic molecular research studies". BMC Bioinformatics 16 (Suppl 9): S5. doi:10.1186/1471-2105-16-S9-S5. ISSN 1471-2105. http://www.biomedcentral.com/1471-2105/16/S9/S5. 

2015

Calabria, Andrea; Spinozzi, Giulio; Benedicenti, Fabrizio; Tenderini, Erika; Montini, Eugenio

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