Page tree

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.

PackageVersionEnvironmentNote
cisTEM1.0.0-betamodule load cistemOfficial binary installation
crYOLO1.7.0module load cryoloDeep-learning GPU-based particle picking
cryoSPARC2.15.0web interfaceSingle particle cryoEM data analysis
localrec1.2.1conda activate localrec-1.2Localized reconstruction (git version)
ProTomo2.4.3module load protomo

Software for electron tomography and 3D image processing.

Relion33.0.8module load relion/3.0-gcc8-gpuGeneric CPU and GPU version (GNU compiler, OpenMPI, CUDA 9.1, single-precision GPU support)
Relion33.0.8module load relion/3.0-icc2020-altcpuOptimized CPU version for using threads (Intel compiler, OpenMPI, AVX2 CPU-accelerated vectorisation, Intel MKL)
Relion33.1-betamodule load relion//3.1-beta-gcc8-gpuGeneric CPU and GPU version (GNU compiler, OpenMPI, CUDA 10.1, single-precision GPU support)
Relion33.1-betamodule load relion/3.1-beta-icc2020-altcpuOptimized CPU version for using threads (Intel compiler, OpenMPI, AVX2 CPU-accelerated vectorisation, Intel MKL)
Scipion22.0module load scipion/2.0Full installation with all available plugins
SPHIRE1.3module load sphire/1.3-mpiOfficial 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.

PackageVersionEnvironmentNote
3DFSC3.0conda activate 3dfsc-3.0Anisotropy GPU version (call: run3DFSC.sh -h)
Amira2019.4module load amira/2019.4

2D-5D visualization and analysis software

APPLEpickergitconda activate applepicker-gitA particle picker for single-particle CryoEM (call: applepicker.py -h)

bashEM

gitmodule load bashemCryoEM data conversion and other tools
CCTBXgitmodule load cctbx/gitComputational Crystallography Toolbox
Cinderella0.6conda activate cinderella-0.6GPU-based automatic 2D class selection
COOT0.8.9.2-premodule load coot/0.8.9.2-pre0.9 pre-release with new CryoEM Basics and Tutorial.
EMAN22.31module show eman2/2.31-gitSscientific image processing suite
EM2EM2016-10-26aliasData conversion tool (call: em2em)
emClarity1.5.0.2module load emclarityTomography tools based on Matlab
EMRingergitconda activate emringer-gitSide-chain-directed model and map validation for 3D CryoEM (publication version, now use CCTBX or Scipion2 version)
FDRthresholdinggitconda activate fdrcontrol-git

False discovery rate control of CryoEM maps (call: FDRcontrol.py -h)

Focus1.1.0module load focus/git(Incoming-) CryoEM processing pipeline
JANNI0.1.3conda activate janni-0.1GPU-based denoising of micrographs (e.g. for easier hand-picking of particles)
LocScale0.2conda activate locscale-0.2A reference-based local amplitude scaling tool using prior model information
MicAssessgitconda activate cryoassess-gitGPU-based micrograph (K2) and 2D classes assessment
MicrographCleaner0.32conda activate cleanmics-0.3Deep learning software to segmentate micrographs into good regions and bad regions (call: cleanMics -h)
Nextflow19.10default $PATHData-driven computational pipelines. Use the singularity version.
Phoelix1.4special $PATHImage processing of helical macromolecular complexes
PowerFitgitconda activate powerfit-gitAutomatically fit high-resolution atomic structures in cryo-EM densities
PyEMgitconda activate pyem-gitCryoEM command-line tools (e.g. cryoSPARC data conversion)
PyRelion1.0.1module load pyrelion

Various PyRelion-based scripts

PySeg1.0conda activate pyseg-1.0

Template-free detection and classification of membrane-bound complexes in cryoET

SIDESPLITTER1.0included in relion 3.1 module

Mitigating local over-fitting in SPA

SPRING0.86-1644module show springA single-particle based helical reconstruction package
SuRVoS1.1.3conda activate survos-1.1Software for segmentation of tomograms
THUNDER1.4.14module load thunder

A particle-filter framework for robust cryoEM 3D reconstruction

Topaz0.2.3conda activate topaz-0.2Deep-learning GPU-based particle picking, external: web gui version
TranSPHIRE1.4conda activate transphire-1.4CryoEM incoming processing pipeline
Unet-Segmentationgitconda activate caffe-unet

Deep Learning for cell counting, detection, and morphometry

  • No labels