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| It is critical that all participants in the tutorials have all required software installed and tested before they leave for the workshop. This is why we are giving you instructions 2 weeks in advance. We are happy to assist people via email in advance of the workshop. At the workshop itself, if you try and install the software during the session, you will almost certainly not keep up with the tutorials. While there will be network access at the site, with 180 people sharing a WiFi connection, you will have limited available bandwidth for downloads, etc. Please come prepared, so we can all have a good experience! | '''''It is critical that you install and test all required software before arriving at the workshop.''''' |
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| '''''We may add some additional data files here before the workshop. While these will be optional, we'd encourage you to check back on this page a day or two before the workshop to see if there are any last minute additions.''''' There are a number of tools you will need to take part in all of the tutorials, and it could easily take you a day to get everything set up and working, so please don't wait until the last minute. We are happy to assist people via email in advance of the workshop. You will not be able to complete installation on-site! Please come prepared, so we can all have a good experience! |
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| * EMAN/SPARX 2.12 (or snapshot version released after Oct. 16, 2015) - Required for all Day 1 and some Day 2 tutorials * [[https://www.cgl.ucsf.edu/chimera/download.html|Chimera]] 1.10 or newer - For 3-D visualization of maps/models * For Segmentation and Modeling at Medium Resolutions on Day 4 * [[https://www.cgl.ucsf.edu/chimera/download.html#daily|Chimera Daily Build]] Oct. 17 or later (Segger v1.9.2) |
* [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_133|EMAN/SPARX 2.12]] (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version. * [[http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install|Relion 1.4]] (optional, day 2-3) - The Relion session will largely be a demo. Linux users may opt to install so they can explore with the demo. * [[http://www.open-mpi.org/|OpenMPI]] and [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_121|PyDusa]] (day 2-3) SPARX tutorial may also largely be a demo, but this is required if you wish to run any major SPARX tasks. * [[https://www.cgl.ucsf.edu/chimera/download.html#daily|Chimera Daily Build]] Oct. 17 or later - For PDB viewing and Segger tutorial (day 4, specific version required) * [[https://github.com/GorgonCryoEM/Gorgon/releases/tag/workshop-2015|Gorgon]] - Gorgon Tutorial (day 4) Please install the appropriate binary AND Data-Sets.zip * [[http://www.phenix-online.org/download/|Phenix]] - (end of day 4) real-space refinement of models You will also need all of the demonstration data, which we will use when going through the tutorials: * [[attachment:Bgal.zip]] * [[attachment:ribosome.zip]] |
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| * Gorgon ... * [[http://www.phenix-online.org/download/|Phenix]] - Used on day 4 to refine models * [[http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install|Relion 1.4]] (optional) - The Relion session will largely be a demo, if you wish to have it installed to experiment during the workshop you may * [[http://www.open-mpi.org/|OpenMPI]] and [[http://ncmi.bcm.edu/ncmi/software/counter_222/software_121|PyDusa]] (special version) - This will only be required for some optional SPARX demos |
* [[attachment:sparx_sorting.tgz]] * Data-Sets.zip from [[https://github.com/GorgonCryoEM/Gorgon/releases/tag/workshop-2015|Gorgon site]] ''While you are also welcome to bring your own data to play with, we strongly encourage you to download the official tutorial data as well.'' There is nothing to configure after downloading these files, simply unpack them into a convenient folder on your hard drive. ---- === Additional information about installation === These are not additional downloads, but rather are links which may assist in installing some of the required packages above. * Please insure that you meet the specific version requirements above for each software package. Tutorials will be tested only on these specific versions. * There are detailed instructions on installing the EMAN/SPARX 2.12 binaries [[http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall|in the Wiki]] * Most SPARX tasks require MPI to run correctly, and are normally used on clusters. It is possible to install MPI on a single laptop/desktop as well, and requires minimal work or configuration to do so, you will simply be limited to the number of CPUs available on your laptop. Much of the SPARX presentation will be 'demo style' rather than a formal tutorial anyway, so you will not miss too much if you don't get MPI configured. Instructions are available [[http://blake.bcm.edu/emanwiki/EMAN2/Parallel/Mpi|here]]. * Due to the required computation for most Relion refinements, Sjors plans to run a demo-style session rather than a tutorial. However, if you install Relion, you may be able to experiment with it a bit during the session. * Chimera and Phenix have some restrictions on commercial use. If you work for a commercial entity, and your IT group will not install these packages, you will still be able to directly participate in most of the workshop. Phenix will only be used at the very end of day 4 to learn about real-space refinement. Chimera will be used on day 4 for a segmentation tutorial. It is also a useful utility to have available, but should otherwise not be strictly required. * Warning - there may be some minor issues with EMAN/SPARX 2.12 on MacOS ElCapitan. If you have not upgraded, you may consider delaying until after the workshop. |
NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling
Oct 30 - Nov 2, 2015
It is critical that you install and test all required software before arriving at the workshop.
We may add some additional data files here before the workshop. While these will be optional, we'd encourage you to check back on this page a day or two before the workshop to see if there are any last minute additions.
There are a number of tools you will need to take part in all of the tutorials, and it could easily take you a day to get everything set up and working, so please don't wait until the last minute. We are happy to assist people via email in advance of the workshop. You will not be able to complete installation on-site! Please come prepared, so we can all have a good experience!
Please insure that you have the following software packages installed:
EMAN/SPARX 2.12 (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version.
Relion 1.4 (optional, day 2-3) - The Relion session will largely be a demo. Linux users may opt to install so they can explore with the demo.
OpenMPI and PyDusa (day 2-3) SPARX tutorial may also largely be a demo, but this is required if you wish to run any major SPARX tasks.
Chimera Daily Build Oct. 17 or later - For PDB viewing and Segger tutorial (day 4, specific version required)
Gorgon - Gorgon Tutorial (day 4) Please install the appropriate binary AND Data-Sets.zip
Phenix - (end of day 4) real-space refinement of models
You will also need all of the demonstration data, which we will use when going through the tutorials:
Data-Sets.zip from Gorgon site
While you are also welcome to bring your own data to play with, we strongly encourage you to download the official tutorial data as well. There is nothing to configure after downloading these files, simply unpack them into a convenient folder on your hard drive.
Additional information about installation
These are not additional downloads, but rather are links which may assist in installing some of the required packages above.
- Please insure that you meet the specific version requirements above for each software package. Tutorials will be tested only on these specific versions.
There are detailed instructions on installing the EMAN/SPARX 2.12 binaries in the Wiki
Most SPARX tasks require MPI to run correctly, and are normally used on clusters. It is possible to install MPI on a single laptop/desktop as well, and requires minimal work or configuration to do so, you will simply be limited to the number of CPUs available on your laptop. Much of the SPARX presentation will be 'demo style' rather than a formal tutorial anyway, so you will not miss too much if you don't get MPI configured. Instructions are available here.
- Due to the required computation for most Relion refinements, Sjors plans to run a demo-style session rather than a tutorial. However, if you install Relion, you may be able to experiment with it a bit during the session.
- Chimera and Phenix have some restrictions on commercial use. If you work for a commercial entity, and your IT group will not install these packages, you will still be able to directly participate in most of the workshop. Phenix will only be used at the very end of day 4 to learn about real-space refinement. Chimera will be used on day 4 for a segmentation tutorial. It is also a useful utility to have available, but should otherwise not be strictly required.
Warning - there may be some minor issues with EMAN/SPARX 2.12 on MacOS ElCapitan. If you have not upgraded, you may consider delaying until after the workshop.