For all currently installed software packages call:
module avail conda env list
For archived versions call:
module load cssb/archive module avail
To search for a specific package call:
module avail -l 2>&1 | grep packagename
The following software is available with CSSB specific notes.
| Package | Version | Environment | Note |
|---|---|---|---|
| cisTEM | 1.0.0-beta | module load cistem | Official binary installation |
| crYOLO | 1.7.6 | module load cryolo | Deep-learning GPU-based particle picking |
| cryoSPARC | 3.0.1 | web interface | Single particle cryoEM data analysis |
| localrec | 1.2.1 | conda activate localrec-1.2 | Localized reconstruction (git version) |
| ProTomo | 2.4.3 | module load protomo | Software for electron tomography and 3D image processing. |
| Relion3 | 3.0.8 | module load relion/3.0-gcc8-gpu | Generic CPU and GPU version (GNU compiler, OpenMPI, CUDA 9.1, single-precision GPU support) |
| Relion3 | 3.0.8 | module load relion/3.0-icc2020-altcpu | Optimized CPU version for using threads (Intel compiler, OpenMPI, AVX2 CPU-accelerated vectorisation, Intel MKL) |
| Relion3 | 3.1.1 | module load relion/3.1-gcc8-gpu | Generic CPU and GPU version (GNU compiler, OpenMPI, CUDA 10.1, single-precision GPU support) |
| Relion3 | 3.1.1 | module load relion/3.1-icc2020-altcpu | Optimized CPU version for using threads (Intel compiler, OpenMPI, AVX2 CPU-accelerated vectorisation, Intel MKL) |
| Scipion | 3.0.6 | module load scipion/3.0 | Full installation with tested SPA plugins |
| SPHIRE | 1.3 | module load sphire/1.3-mpi | Official binary installation with special OpenMPI 3.x for the maxwell cluster |
The following software is maybe of interest for special use cases or data conversion.
Functionality tests have been performed but the packages will be updated on request only.
Some CSSB/DESY specific configuration settings, submission scripts and pre-trained models are at:
/beegfs/cssb/software/etc/em/$software/$version
For usage examples and help ask Wolfgang Lugmayr.
| Package | Version | Environment | Note |
|---|---|---|---|
| 3DFSC | 3.0 | conda activate 3dfsc-3.0 | Anisotropy GPU version (call: run3DFSC.sh -h) |
| Amira | 2019.4 | module load amira/2019.4 | 2D-5D visualization and analysis software |
| APPLEpicker | git | conda activate applepicker-git | A particle picker for single-particle CryoEM (call: applepicker.py -h) |
| git | module load bashem | CryoEM data conversion and other tools | |
| CCP-EM | 1.4.1 | special login on Analysis PC | Collaborative Computational Project for electron cryo-microscopy software packages |
| CCTBX | git | module load cctbx/git | Computational Crystallography Toolbox |
| Cinderella | 0.7 | conda activate cinderella-0.7 | GPU-based automatic 2D class selection |
| COOT | 0.8.9.2-pre | module load coot/0.8.9.2-pre | 0.9 pre-release with new CryoEM Basics and Tutorial. |
| cryoDRGN | 0.3 | conda activate cryodrgn-0.3 | A a neural network based algorithm for heterogeneous cryo-EM reconstruction. |
| deepEMhancer | 0.13 | conda activate deepemhancer-0.13 | Post-processing of cryo-EM maps |
| EMAN2 | 2.31-final | module load eman2/2.31 | Scientific image processing suite |
| EM2EM | 2016-10-26 | alias | Data conversion tool (call: em2em) |
| emClarity | 1.5.0.2 | module load emclarity | Tomography tools based on Matlab |
| EMRinger | git | conda activate emringer-git | Side-chain-directed model and map validation for 3D CryoEM (publication version, now use CCTBX or Scipion2 version) |
| EPU_group_AFIS | git | conda activate base | Group micrographs for Relion 3.1 based on EPU beamshift values (call: EPU_group_AFIS.py -h) |
| FDRthresholding | git | conda activate fdrcontrol-git | False discovery rate control of CryoEM maps (call: FDRcontrol.py -h) |
| Focus | 1.1.0 | module load focus/git | (Incoming-) CryoEM processing pipeline |
| JANNI | 0.1.3 | conda activate janni-0.1 | GPU-based denoising of micrographs (e.g. for easier hand-picking of particles) |
| LocScale | 0.2 | conda activate locscale-0.2 | A reference-based local amplitude scaling tool using prior model information |
| MicAssess | git | conda activate cryoassess-git | GPU-based micrograph (K2) and 2D classes assessment |
| MicrographCleaner | 0.32 | conda activate cleanmics-0.3 | Deep learning software to segmentate micrographs into good regions and bad regions (call: cleanMics -h) |
| Nextflow | 19.10 | default $PATH | Data-driven computational pipelines. Use the singularity version. |
| Phoelix | 1.4 | special $PATH | Image processing of helical macromolecular complexes |
| PowerFit | git | conda activate powerfit-git | Automatically fit high-resolution atomic structures in cryo-EM densities |
| PyEM | git | conda activate pyem-git | CryoEM command-line tools (e.g. cryoSPARC data conversion) |
| PyRelion | 1.0.1 | module load pyrelion | Various PyRelion-based scripts |
| PySeg | 1.0 | conda activate pyseg-1.0 | Template-free detection and classification of membrane-bound complexes in cryoET |
| relion-yolo-it | 0.3.0.1 | conda activate cryolo-rit30 | relion_it with crYOLO support |
| SIDESPLITTER | 1.0 | included in relion 3.1 module | Mitigating local over-fitting in SPA |
| SPRING | 0.86-1644 | module show spring | A single-particle based helical reconstruction package |
| SuRVoS | 1.1.3 | conda activate survos-1.1 | Software for segmentation of tomograms |
| THUNDER | 1.4.14 | module load thunder | A particle-filter framework for robust cryoEM 3D reconstruction |
| Topaz | 0.2.4 | conda activate topaz-0.2 | Deep-learning GPU-based particle picking, can be used within the cryoSPARC GUI. |
| TranSPHIRE | 1.4 | conda activate transphire-1.4 | CryoEM incoming processing pipeline |
| Unet-Segmentation | git | conda activate caffe-unet | Deep Learning for cell counting, detection, and morphometry |