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universvm / thesis-eisvogel
Created December 2, 2022 12:45
An adaptation of https://github.com/Wandmalfarbe/pandoc-latex-template but for academic thesis with minor changes to the layout
%%
% Copyright (c) 2017 - 2021, Pascal Wagler;
% Copyright (c) 2014 - 2021, John MacFarlane
%
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions
% are met:
%
@universvm
universvm / book tracker with dataview note
Created August 25, 2022 08:13
book tracker with dataview note
### [Books MOC](../0.%20MOC/Books%20MOC.md)
# Social Engineering : The Art of Human Hacking
**Author**:: Chris Hadnagy
**Date**:: 2022-01-01
**Tags**:: #psychology/socialengineering #psychology
**Grade**:: 9/10
**Links**::
## Gathering Information
@universvm
universvm / dataview template
Created August 25, 2022 08:08
dataview template
### Basics
```dataview
table tags as "Tags"
from "2. Notes"
WHERE contains(tags, "optimisation")
SORT file.name ASC
```
### VAE
```dataview
https://kpwulab.com/2020/01/04/pymol-cartoon-mode/
.markdown-source-view.mod-cm6 .cm-scroller, .markdown-source-view, .cm-s-obsidian, .cm-s-obsidian span.cm-formatting-task{
margin-top: 40px !important;
}
.workspace-leaf.mod-active .view-header {
background: linear-gradient(
120deg
, var(--color-view-header-gradient-2) 0.5%, var(--color-view-header-gradient-2) 0.5%);
}
@universvm
universvm / monomers
Created July 28, 2021 12:55
monomers AF2
3e3vA, 5dicA, 1dvoA, 3cxbA, 3rf0A, 2ra1A, 1a41A, 3giaA, 3dadA, 2of3A, 4y5jA, 4ozwA, 1uzkA, 3klkA, 1g3pA, 2dyiA, 3zbdA, 3kyfA, 1o7iA, 1x8qA, 4i1kA, 2bhuA, 3q1nA, 1jovA, 2v3iA, 4efpA, 4le7A, 3kstA, 3o4pA, 2w18A, 1l0sA, 2j8kA, 1hxrA, 3maoA, 4a6qA, 5b1rA, 3oajA, 4m4dA, 6baqA, 3e8tA, 2v3gA, 5c12A, 3kluA, 3gohA, 3dkrA, 2imhA, 1hq0A, 1ds1A, 3zh4A, 3swgA, 5bufA, 3hvmA, 1h70A, 4fs7A, 3e4gA, 4fcgA, 4wp6A, 4ecoA, 3essA,
@universvm
universvm / monomers_af2.txt
Created July 26, 2021 14:00
Sequence Recovery Benchmark Monomers
4le7A
4ozwA
3e8tA
3zh4A
1o7iA
6baqA
3q1nA
1x8qA
3klkA
5b1rA
@universvm
universvm / convert_to_json.py
Last active July 26, 2021 14:01
Convert TIMED-style benchmark predictions to json file
# Written by Rokas Petrenas (https://github.com/rokaske199)
from benchmark import get_cath
from pathlib import Path
import json
PATH_TO_PDB=Path('/scratch/datasets/pdb/')
cath_location = "cath-domain-description-file.txt"
cath_df = get_cath.read_data(cath_location)
#select only monomers
new_df=get_cath.filter_with_user_list(cath_df,"/home/s1706179/project/sequence-recovery-benchmark/monomers_af2.txt")
@universvm
universvm / wandb
Created May 10, 2021 10:47
Start Wandb
docker run --rm -d -v /opt/wandb:/vol -p 9988:8080 --name wandb-local wandb/local
@universvm
universvm / wikipapers.txt
Created January 16, 2021 11:04
Full list of Biology-related papers obtained manually from Wikipedia
Acta Biológica Colombiana
Alces
American Journal of Physical Anthropology
The American Naturalist
Annual Review of Physiology
BioEssays
Biologia
The Biological Bulletin
Biological Communications
Biological Reviews