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First, I'd like to express my appreciation for the docetl library. It has been incredibly useful not only as a tool but also as a learning resource for understanding common patterns in LLM-powered dat…
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I have tested e2efold on a set of 361 PDB chains, where secondary structures for RNAs shorter than 600 nucleotides are predicted by ``e2efold_productive/e2efold_productive_short.py``, while those lon…
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Sorry for the delays!
[scores.zip](https://github.com/kad-ecoli/rna3db/files/5469708/scores.zip)
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Hi,
I'm running modkit pileup (v0.2.4) as follows:
```
modkit pileup -t 8 --filter-threshold 0.9 {$bam} {$out_bed} --ref /ref/hg38.fa --preset traditional
```
Basecalling has been done usi…
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I am using version 2.4.0 of Arriba and I stumbled across this error:
```
...
[2024-08-24T15:53:20] Reading chimeric alignments from '~/bams/sample1_trimmed.star.hg38.Chimeric.bam' (total=138010)
…
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Hello everybody!! I ran the following command
(base) [ntilikj@login1 clean_data]$ #!/bin/bash
(base) [ntilikj@login1 clean_data]$
(base) [ntilikj@login1 clean_data]$ #
(base) [ntilikj@login1 clean…
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I think from a database perspective we want a world of fully user-defined hardware/platform. We can trust users as much :-).
Today we do not allow for easy addition of additional fields.
It is n…
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There are a lot of finite map and finite set implementations out there and I think it would be good to discuss what the shape of these types should be in stdlib2. Off the top of my head there are impl…
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```
> ./intersections
# Triangle Mesh Intersection Detection
|VA| 2002
|FA| 4000
|VB| 6669
|FB| 13334
| Method | Time in seconds |
|:------------|----------------:…
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Hello.
Some databases (for example [Valkey](https://valkey.io)) are using Lua as a user exposed scripting language.
Lua interpreter has to be properly sandboxed for that (one should not probably all…