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Prepare ColabFoldDB #29

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NZ99 opened this issue Aug 25, 2023 · 6 comments
Open

Prepare ColabFoldDB #29

NZ99 opened this issue Aug 25, 2023 · 6 comments
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@jamaliki

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@NZ99
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NZ99 commented Aug 25, 2023

Download and prepare ColabFoldDB on the cluster.

ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. They are the backend of our ColabFold MMseqs2 searches.

https://colabfold.mmseqs.com/
@NZ99 NZ99 self-assigned this Aug 25, 2023
@NZ99 NZ99 converted this from a draft issue Aug 25, 2023
@NZ99 NZ99 removed their assignment Aug 25, 2023
@jamaliki
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/take

@Geraldene
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happy to take this on

@NZ99
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NZ99 commented Sep 7, 2023

cc @jamaliki @Geraldene let me know if any help is needed, I can start pulling it on the cluster in the meantime

@Geraldene
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thanks @NZ99 is cluster access available to everyone? sorry I might have missed a few messages

@pascalnotin pascalnotin moved this from Todo to In Progress in project-lm-scaling Sep 21, 2023
@NZ99
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NZ99 commented Oct 12, 2023

Sorry @Geraldene, had not seen this. Cluster access is restricted to significant contributors unfortunately. In any case ColabFoldDB is now available on our openbioml bucket, let me know if anyone wants to collaborate re: any processing that needs to be done, happy to help.

@Geraldene
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Happy to help with the processing @NZ99 :)

@jamaliki jamaliki mentioned this issue Nov 28, 2023
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@Geraldene @jamaliki @NZ99