Software and data format standards for management of microscopy image data. Joint project between international private and public research
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This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?
- Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
- Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.
We use the intermine API and the IDR API
The notebook can be launched ...
This notebook demonstrates how to retrieve metadata associated to the paper A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection and available in IDR at idr0094-ellinger-sarscov2. Over 300 compounds were used in this investigation. This notebook allows the user to calculate the half maximal inhibitory concentration (IC50) for ...