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vishnubob / histone_mod_table.md
Created May 12, 2025 16:26
Histone Modification Cheat Sheet

Histone Modification Cheatsheet

Key Histone Marks and Their Functions

Histone modifications play crucial roles in regulating chromatin structure and gene expression. This cheatsheet provides a quick reference for the most common and well-characterized histone marks.

Histone Mark Associated With Function/Location Writers Erasers
H3K4me3 Active promoters Found near transcription start sites (TSS) of actively transcribed genes. Creates a sharp, localized peak at the 5' end of genes. Provides docking sites for chromatin remodeling complexes. SET1A/B, MLL1-4 KDM5A-D (JARID1A-D)
H3K27ac Active enhancers and promoters Distinguishes active enhancers/promoters from poised ones. Often co-occurs with H3K4me1 at active enhancers. Mutually exclusive with repressive H3K27me3. CBP, p300 HDAC1, HDAC2, SIRT1
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vishnubob / awe_res_sen.md
Created February 27, 2025 19:03
Awesome Residential Sensor Data Tracking

Awesome Residential Sensor Data Tracking

A curated list of sensor-based data tracking categories suitable for deployment at your domicile. This list includes relevant sensors, available public data repositories, DIY vs. commercial options, and applications for each category.

Contents

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vishnubob / model-organisms-list.md
Created October 11, 2019 15:39
List of Model Organisms

Viruses

  • Phage lambda
  • Phi X 174
  • SV40
  • T4 phage
  • Tobacco mosaic virus
  • Herpes simplex virus

Prokaryotes

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vishnubob / python-run.vimrc
Last active September 24, 2022 01:32
Add this to your .vimrc to execute python in a new window. If your program produces no output, no windows is created.
nnoremap <silent> <leader><space> :call SaveAndExecutePython()<CR>
vnoremap <silent> <leader><space> :<C-u>call SaveAndExecutePython()<CR>
" https://stackoverflow.com/questions/18948491/running-python-code-in-vim
function! SaveAndExecutePython()
" SOURCE [reusable window]: https://github.com/fatih/vim-go/blob/master/autoload/go/ui.vim
" save and reload current file
silent execute "update | edit"
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vishnubob / simple-autoencode.py
Created March 31, 2018 20:44
Simple Autoencoder with useful PIL based image tiler
# MXNet Autoencoder
# based on example from SherlockLiao
# https://github.com/SherlockLiao/mxnet-gluon-tutorial/blob/master/08-AutoEncoder/simple_autoencoder.py
import operator
import bisect
import os
import numpy as np
import mxnet as mx
from mxnet import gluon
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vishnubob / lesson_1.md
Last active November 15, 2017 22:32
Tables and Scales: Do'h-Ray-Meh

Tables and Scales: Do'h-Ray-Meh

Digital Music systems such as MIDI use integers to represent different notes. This method of representation is known an enumeration. For this exercise, we will write a program to build a hash table that translates note values to numerical values, and an array to translate numerical values back to note values. In order to accomplish this, we will need to know two pieces of information, and let our program enumerate our two lookup tables.

  1. What are the two pieces of information our program needs to enumerate the tables?
  2. Why use a hash table for note lookups, and an array for numerical lookups?

For now, we will ignore sharps and flats, and just utilize the "white keys" of a piano when building our table. A full octave is represented by eight notes: C D E F G A B C. When specifying note values, we will use scientific pitch notation.

  1. How many full octaves can we enumerate with an 8-bit unsigned integer? h
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vishnubob / randoseq.py
Last active January 15, 2016 22:45
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
import random
def random_sequence_generator(length):
return str.join('', [random.choice('AGTC') for x in range(length)])
def gc_good(sequence, ideal=.5, spread=.05):
val = (sequence.count('G') + sequence.count('C')) / float(len(sequence))
return (ideal - spread) < val < (ideal + spread)
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vishnubob / pdf_leech.py
Created August 25, 2015 20:13
#!/usr/bin/env python
# -*- coding: latin-1 -*-
import google
import requests
import magic
def get_pdf(url, title):
print url
pdf = requests.get(url)
with magic.Magic() as m:
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vishnubob / bac_pw.txt
Created August 21, 2015 23:05
ghall@littletit:[~/code/chainsaw/python] python vt_passwd.py -p /dev/ttyUSB2
Sun Jul 4 20:28:38 2010
____ _ ____ ______ _____ ____ ____
| _ \ / \ / ___/ ___\ \ / / _ \| _ \| _ \ _ _
| |_) / _ \ \___ \___ \\ \ /\ / / | | | |_) | | | | (_|_)
| __/ ___ \ ___) |__) |\ V V /| |_| | _ <| |_| | _ _
|_| /_/ \_\____/____/ \_/\_/ \___/|_| \_\____/ (_|_)
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vishnubob / shapeoko_grbl_settings.txt
Created January 4, 2015 15:42
Shapeoko GRBL Settings
$0=40.020 (x, step/mm)
$1=40.020 (y, step/mm)
$2=320.000 (z, step/mm)
$3=30 (step pulse, usec)
$4=500.000 (default feed, mm/min)
$5=500.000 (default seek, mm/min)
$6=224 (step port invert mask, int:11100000)
$7=255 (step idle delay, msec)
$8=25.000 (acceleration, mm/sec^2)
$9=0.050 (junction deviation, mm)