Verify installation
Some of these tests run very quick. Their main goal is to validate the behavior of some important classes and functions (in the spirit of unit tests).
Other tests are more focused on the execution of protocols and complete workflows. They usually take more time to execute, and require some input data (which should be downloaded automatically on demand).
In the following sections you will find a brief explanation about the more important tests, and their input data. All of them must be executed from the command line using the specified commands.
Table of Contents
Small tests
Basic tests
Plugins |
Core, Xmipp, Relion |
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Spider MDA Workflow
Plugins |
Spider |
Command |
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Input |
Fake dataset of Worm Hemoglobin with 76 images |
Time |
~50 sec |
EMX import
Plugins |
emxlib |
Command |
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Input |
The different data sets used in http://i2pc.cnb.csic.es/emx |
Time |
~10 sec |
CTF Discrepancy
Plugins |
Xmipp, Cistem |
Command |
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Input |
CTF obtained from micrograph of PcV (http://dx.doi.org/doi:10.1073/pnas.1404330111) |
Time |
~10 sec |
Medium tests
Xmipp Workflow
Plugins |
Xmipp |
Command |
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Input |
Same data as in Xmipp Workflow. A refined volume generated with Frealign is obtained |
Time |
~300 sec |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Mixed Workflow 3D Reconstruction
Plugins |
Xmipp, EMAN |
Command |
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Input |
Same data as in Xmipp Workflow. A refined volume generated with Frealign is obtained |
Time |
~150 sec |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Mixed Workflow Initial Volume
Plugins |
Xmipp, EMAN |
Command |
|
Input |
Same data as in Xmipp Workflow. An initial volume generated with EMAN is obtained |
Time |
~200 sec |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Large Tests
[WARNING] The following tests must be run on computers with enough processing power.
Mixed Workflow Relion 2D classification
Plugins |
Xmipp, Cistem, EMAN, Relion |
Command |
|
Input |
Dataset with 20 micrographs of the Ribosome. |
Time |
~3*h* sec |
CPU |
16 CPUs. Xeon(R) E5540 2.53 GHz, 64 GB RAM |
Random Conical Tilt reconstruction
Plugins |
Xmipp |
Command |
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Input |
Dataset with 6 pairs of untilted-tilted micrographs. |
Time |
~15 min |
CPU |
4 CPUs. Intel(R) Core(TM) i7-2640M CPU @ 2.80GHz, 8 GB RAM |
Procotol Tests
Import different type of objects
Plugins |
Scipion |
Import micrographs |
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Import particles |
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Import volumes |
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Input |
From different datasets |
Time |
~15 min |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Processing micrographs
Plugins |
Xmipp |
preprocess |
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ctf estimation |
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Extract Particles |
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Software |
Cistem |
ctf estimation |
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Input |
Dataset xmipp tutorial |
Time |
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CPU |
i7-2640M 2.8GHz, 8GB RAM |
Preprocessing 2D
Software |
Xmipp |
Create Mask 2D |
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Apply Mask 2D |
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Filter Particles |
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Software |
Relion |
Preprocess Particles |
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Input |
From different datasets |
Time |
~400 sec |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Particles alignment and classification
Software |
Xmipp |
ML2D |
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CL2D |
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CL2D Align |
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Apply Alignment |
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Rotational Spectra |
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Kerdensom |
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Software |
Relion |
Classify 2D |
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Input |
Mda dataset |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Preprocessing 3D
Software |
Xmipp |
Create Mask 3D |
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Apply Mask 3D |
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Filter Volumes |
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Preprocess Volumes |
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Input |
Same data as in Xmipp Workflow. |
Time |
~400 sec |
CPU |
i7-2640M 2.8GHz, 8GB RAM |
Initial volume
tests |
Significant |
Software |
Xmipp |
Reconstruct significant |
|
Input |
Groel data |
Time |
~27 min |
CPU |
4 CPUs on Asimov |
Classify 3D
tests |
Classify 3D |
Software |
Relion |
Relion Classify 3D |
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Input |
MDA data |
Time |
~200 sec |
CPU |
i7-2640M 2.8GHz, 8GB RAM |