Calculate extended gamma-ray source halo using crbeam simulation

Crop Wild Relatives distribution modeling workflow using the ModGP; a prototype Digital Twin from BioDT.

Workflow to perform nuclei cell counting on High Content Screening (HCS) Data and upload result into OMERO

In this workflow, cell images are first uploaded to both Galaxy and OMERO using the “OMERO Image Import” tool. Concurrently, image processing is performed. After thresholding and binarization, key features of nuclei, such as area, label number, and perimeter, are computed from the processed images and saved as a CSV file. The result file is then attached to each image stored in OMERO using ...

General workflow to upload data into OMERO using Galaxy

A dataset for testing can be found at: https://zenodo.org/records/14205500

Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.

Point-based Individual Tree Delineation from 3D LiDAR Point Cloud Data.

This module implements a lightweight and easy-to-use Point-based method for individual tree delineation from 3D point cloud data using pure C/C++.

The source code files are included in folder [TreeSeparation], which consists of a project generated from Visual Studio 2015. The CLASS for tree separation is named "FoxTree" and can be found in the respect FoxTree.h and FoxTree.cpp files.

Inupt

The ...

The workflow starts with selecting EH38E2924876 as the search term. Genomic position of provided unique regulatory element identifier was retrieved from CFDE Linked Data Hub[1]. A list of variants in the region of the regulatory element was retrieved from CFDE Linked Data Hub[1]. Variant/variant set associated allele specific epigenomic signatures were retrieved from CFDE LDH[5] based on Roadmap and ENTEx data[6], [4]. GTEx eQTL and sQTL evidence for the given variant(s) were retrieved from CFDE ...

A file containing GEO Aging Signatures was first uploaded. The file containing GEO Aging Signatures was loaded as a gene signature. A file containing GTEx Aging Signatures was first uploaded. The file containing GTEx Aging Signatures was loaded as a gene signature. Significant genes were extracted from the GEO Aging Signatures. Significant genes were extracted from the GTEx Aging Signatures. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[1]. Resolved ...

A file was first uploaded. The file was parsed as a gene count matrix. Significantly over-expressed genes when compared to tissue expression in GTEx[1] were identified. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of IMP3 were visualized. Drugs which down-regulate the expression of IMP3 were identified from the RNA-seq-like LINCS L1000 Chemical Perturbagens[3]. Genes which down-regulate the expression of IMP3 were identified from the RNA-seq-like LINCS L1000 ...

The workflow starts with selecting RPE as the search term. For the given gene ID (SYMBOL), StringDB PPI was extracted using their API[1]. For the Given StringDB PPI, the list of nodes (Gene Set) is generated. For the Given StringDB PPI, the list of nodes (GeneSet) is generated. Reversers and mimickers from over 1 million signatures were identified using SigCom LINCS[2]. The gene set was submitted to Enrichr[4]. The gene set was then searched in the Metabolomics Workbench[5] to identify relevant ...