5895cd29b0c68e5f0c2e8f13456632606ce80667
SBGrid-Wiki.md
| ... | ... | @@ -13,6 +13,8 @@ SBGrid is a global consortium of research labs in academia and industry using st |
| 13 | 13 | This site provides information on how to install, use, and get help with your SBGrid software installation. Here you can also find information about SBGrid services. Please let us know if you have questions. |
| 14 | 14 | |
| 15 | 15 | ### Recent Wiki Posts |
| 16 | +- [2022.03.12 - Installation Manager version 2.6.14](client_downloads) |
|
| 17 | +- [2022.03.11 - Alphafold 2.2.0 usage examples](examples/alphafold2) |
|
| 16 | 18 | - [2021.11.10 - Alphafold 2.1.2 usage examples](examples/alphafold2) |
| 17 | 19 | - [2022.01.03 - Installation Manager version 2.6.5](client_downloads) |
| 18 | 20 | - [2021.12.06 - Installation Manager version 2.6.3](client_downloads) |
client_downloads.md
| ... | ... | @@ -5,8 +5,8 @@ The SBGrid Installation is the primary |
| 5 | 5 | |
| 6 | 6 | - [SBGrid Installation Manager - Downloads](#sbgrid-installation-manager---downloads) |
| 7 | 7 | - [Requirements](#requirements) |
| 8 | - - [SBGrid Installation Manager for MacOS and Linux, v2.6.5](#sbgrid-installation-manager-for-macos-and-linux-v265) |
|
| 9 | - - [SBGrid Command-line Installation Manager for MacOS and Linux, v2.6.5](#sbgrid-command-line-installation-manager-for-macos-and-linux-v265) |
|
| 8 | + - [SBGrid Installation Manager for MacOS and Linux, v2.6.14](#sbgrid-installation-manager-for-macos-and-linux-v2614) |
|
| 9 | + - [SBGrid Command-line Installation Manager for MacOS and Linux, v2.6.14](#sbgrid-command-line-installation-manager-for-macos-and-linux-v2614) |
|
| 10 | 10 | |
| 11 | 11 | <!-- /TOC --> |
| 12 | 12 | |
| ... | ... | @@ -22,24 +22,24 @@ filesystem. The GUI Installation Manager will create this automatically. See |
| 22 | 22 | The SBGrid installation manager requires an account. Set up an account by |
| 23 | 23 | registering here : [SBGrid registration](https://sbgrid.org/registration/register/) |
| 24 | 24 | |
| 25 | -### SBGrid Installation Manager for MacOS and Linux, v2.6.5 |
|
| 25 | +### SBGrid Installation Manager for MacOS and Linux, v2.6.14 |
|
| 26 | 26 | |
| 27 | -- [Linux : SBGrid-installation-manager-2.6.5.AppImage ](https://sbgrid.org/downloads/2.6.5/SBGrid-installation-manager-2.6.5.AppImage) |
|
| 27 | +- [Linux : SBGrid-installation-manager-2.6.14.AppImage ](https://sbgrid.org/downloads/2.6.14/SBGrid-installation-manager-2.6.14.AppImage) |
|
| 28 | 28 | |
| 29 | -- [macOS : SBGrid-installation-manager-2.6.5.dmg ](https://sbgrid.org/downloads/2.6.5/SBGrid-installation-manager-2.6.5.dmg) |
|
| 29 | +- [macOS : SBGrid-installation-manager-2.6.14.dmg ](https://sbgrid.org/downloads/2.6.14/SBGrid-installation-manager-2.6.14.dmg) |
|
| 30 | 30 | |
| 31 | 31 | See [this page](client_usage) for usage info. |
| 32 | 32 | |
| 33 | -### SBGrid Command-line Installation Manager for MacOS and Linux, v2.6.5 |
|
| 33 | +### SBGrid Command-line Installation Manager for MacOS and Linux, v2.6.14 |
|
| 34 | 34 | |
| 35 | -- [Linux : sbgrid-cli_2.6.5-linux.tar.gz ](https://sbgrid.org/downloads/2.6.5/sbgrid-cli_2.6.5-linux.tar.gz) |
|
| 35 | +- [Linux : sbgrid-cli_2.6.14-linux.tar.gz ](https://sbgrid.org/downloads/2.6.14/sbgrid-cli_2.6.14-linux.tar.gz) |
|
| 36 | 36 | |
| 37 | -- [macOS : sbgrid-cli_2.6.5-macos.tar.gz ](https://sbgrid.org/downloads/2.6.5/sbgrid-cli_2.6.5-macos.tar.gz) |
|
| 37 | +- [macOS : sbgrid-cli_2.6.14-macos.tar.gz ](https://sbgrid.org/downloads/2.6.14/sbgrid-cli_2.6.14-macos.tar.gz) |
|
| 38 | 38 | |
| 39 | 39 | You can download this tar.gz file from the command line with this command in the Terminal: |
| 40 | 40 | |
| 41 | 41 | ``` |
| 42 | -curl -k -LO https://sbgrid.org/downloads/2.6.5/sbgrid-cli_2.6.5-macos.tar.gz |
|
| 42 | +curl -k -LO https://sbgrid.org/downloads/2.6.14/sbgrid-cli_2.6.14-macos.tar.gz |
|
| 43 | 43 | ``` |
| 44 | 44 | |
| 45 | 45 | This will prevent the need to [remove the com.apple.quarantine attribute.](https://sbgrid.org//wiki/macos#download-the-installation-manager-sbgrid-cli) |
examples/alphafold2.md
| ... | ... | @@ -109,6 +109,18 @@ It is possible to run alphafold through a web portal. See |
| 109 | 109 | https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb . |
| 110 | 110 | |
| 111 | 111 | ### Changes in latest versions |
| 112 | +**2.2.0** |
|
| 113 | + |
|
| 114 | +- Added new AlphaFold-Multimer models with greatly reduced numbers of clashes on average and slightly increased accuracy. |
|
| 115 | +- Removed unused bias argument in GlobalAttention |
|
| 116 | +- Removed prokaryotic MSA pairing algorithm as it didn’t improve accuracy on average. |
|
| 117 | +- Added the ability to run with multiple seeds per model to match the AlphaFold-Multimer paper. |
|
| 118 | +- Fixed degraded performance when using num_recycle=0 with models trained with recycling due to incorrect skipping of layers |
|
| 119 | +- Added split_rng=False (current default) to sharded_map to support new Haiku release. |
|
| 120 | +- Removed unused code in amber_minimize.py. |
|
| 121 | + |
|
| 122 | +New model parameters are required. Those can be found here : [https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar](https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar) |
|
| 123 | + |
|
| 112 | 124 | **2.1.2** |
| 113 | 125 | Version 2.1.2 adds a few new features that must be explictly defined on the command line. |
| 114 | 126 | See the examples below for and example and `run_alphafold.py --help` for more info. |