Teams: Cimorgh IT solutions
Organizations: cimorgh IT
Hi! I'm Russell.
I'm a microbiologist who uses graph theory and machine learning to study the relationships that bacteria and archaea form with their host organisms, and lately giant viruses and their hosts. Or, I'm a computer scientist who builds software that uses concepts from evolution to extract knowledge about ecology from large datasets. Or, I'm a data scientist who uses Python to explore biological systems. Or, I'm a physicist that went rouge and defected to the squishy side of science. ...
Teams: EOSC-Life WP3 OC Team, cross RI project, EOSC-Life WP3, Euro-BioImaging
Organizations: EOSC-Life, Euro-BioImaging
Biomedical Engineer working on preclinical image dataset repository and cross researching RIs
I am a Ph.D. student in Gong lab. I am interested in cancer genomics, including the mining of genetic risk determinants in cancer, functional prediction of genetic variants, tumor-associated molecular epidemiology, large-scale data integration, analysis, and mining, as well as the construction of bioinformatical data platforms.
Teams: Not specified
Organizations: Not specified
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Teams: Bioinformatics Innovation Lab
Organizations: Pondicherry University
https://orcid.org/0000-0003-4854-8238
Ph.D. Student at Department of Bioinformatics, Pondicherry University
Bioinformatician in Stockholm, Sweden. Lead for nf-core and MultiQC projects.
Teams: IBISBA Workflows
Organizations: Unspecified
IDR is based on OMERO and thus all what we show in this notebook can be easily adjusted for use against another OMERO server, e.g. your institutional OMERO server instance.
The main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools.
The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August ...
Learning objectives
- Read data to analyse from an object store.
- Analyse data in parallel using Dask.
- Show how to use public resources to train neural network.
- Load labels associated to the original data
- Compare results with ground truth.
The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August 2019: https://doi.org/10.1371/journal.pbio.3000388, considered several image ...
Type: Unrecognized workflow type
Creators: Jean-Marie Burel, Petr Walczysko
Submitter: Jean-Marie Burel
Learning Objectives
- How to access genomic resource via its Python API
- How to access image resource via its Python API
- Relate image data to genomic data
Diabetes related genes expressed in pancreas
This notebook looks at the question Which diabetes related genes are expressed in the pancreas? Tissue and disease can be modified.
Steps:
- Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the ...
The image is referenced in the paper "NesSys: a novel method for accurate nuclear segmentation in 3D" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388 and can be viewed online in the Image Data Resource.
This original image was converted into the Zarr format. The analysis results produced by the authors of the paper were converted into labels and linked to the Zarr file which was placed into a public ...
Type: Unrecognized workflow type
Creators: Jean-Marie Burel, Petr Walczysko
Submitter: Jean-Marie Burel
BatchConvert 
A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.
The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.
The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...
