topaz 0.2.5.20231120-foss-2023a-CUDA-12.1.1
A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep de- noising models.Accessing topaz 0.2.5.20231120-foss-2023a-CUDA-12.1.1
To load the module for topaz 0.2.5.20231120-foss-2023a-CUDA-12.1.1 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):
📋
module load bear-apps/2023a
module load topaz/0.2.5.20231120-foss-2023a-CUDA-12.1.1
BEAR Apps Version
Architectures
EL8-icelake (GPUs: NVIDIA A100, NVIDIA A30)
The listed architectures consist of two parts: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
More Information
For more information visit the topaz website.
Dependencies
This version of topaz has a direct dependency on: CUDA/12.1.1 foss/2023a Python/3.11.3-GCCcore-12.3.0 PyTorch-bundle/2.1.2-foss-2023a-CUDA-12.1.1 scikit-image/0.22.0-foss-2023a scikit-learn/1.3.1-gfbf-2023a SciPy-bundle/2023.07-gfbf-2023a
Required By
This version of topaz is a direct dependent of: RELION/5.0.0-foss-2023a-CUDA-12.1.1
Other Versions
These versions of topaz are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.
| Version | BEAR Apps Version |
|---|---|
| 0.2.5-foss-2021a-CUDA-11.3.1 | 2021a |
| 0.2.5-foss-2021a | 2021a |
| 0.2.4-foss-2020b-PyTorch-1.7.1 | 2020b |
Last modified on 3rd March 2025