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sdwfrost / gist:6c448e50c261d60cf18aeb57824a0793
Created May 17, 2017 11:52 — forked from karpathy/gist:587454dc0146a6ae21fc
An efficient, batched LSTM.
"""
This is a batched LSTM forward and backward pass
"""
import numpy as np
import code
class LSTM:
@staticmethod
def init(input_size, hidden_size, fancy_forget_bias_init = 3):
@sdwfrost
sdwfrost / color-turtles.js
Created April 24, 2017 07:54
Tweaking turtles.js example from asx
// Import the lib/ mmodules via relative paths
const Color = AS.Color
const ColorMap = AS.ColorMap
// import Color from '../../src/Color.js'
// import DataSet from '../../src/DataSet.js'
// import Mouse from '../../src/Mouse.js'
const Model = AS.Model
const util = AS.util
const modules = {Color, ColorMap, Model, util }
@sdwfrost
sdwfrost / ebov_tmrca.ipynb
Created February 17, 2017 10:51
TMRCA analysis of BEAST EBOV trees from Dudas et al.
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@sdwfrost
sdwfrost / neighbor-joining-experiments.ipynb
Created January 20, 2017 13:32 — forked from gregcaporaso/neighbor-joining-experiments.ipynb
initial experiments with implementing neighbor joining for scikit-bio
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@sdwfrost
sdwfrost / git_create_orphan.sh
Created November 28, 2016 10:13 — forked from seanbuscay/git_create_orphan.sh
Create an orphan branch in a repo.
cd repository
git checkout --orphan orphan_name
git rm -rf .
rm '.gitignore'
echo "#Title of Readme" > README.md
git add README.md
git commit -a -m "Initial Commit"
git push origin orphan_name
@sdwfrost
sdwfrost / mingw-w64-3.10-osx10.9.sh
Created November 26, 2016 13:49 — forked from Drakulix/mingw-w64-3.10-osx10.9.sh
Script to install a Mingw-w64 Cross-Compiler Suite on Mac OS X 10.9
#!/bin/sh
# dependencies
echo "Installing dependencies via Homebrew (http://brew.sh)"
ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
brew update
brew install gcc48
@sdwfrost
sdwfrost / pi_qemu.sh
Created November 24, 2016 12:34 — forked from JasonGhent/pi_qemu.sh
OSX raspberry pi emulation via QEMU. v2 attempt @ https://gist.github.com/JasonGhent/922f38f57c8cb77b10f3
# pulled from http://xecdesign.com/qemu-emulating-raspberry-pi-the-easy-way/
# expanded via http://superuser.com/questions/690060/how-to-enable-network-with-a-raspberry-pi-emulated-on-qemu
# tested with 2015-02-16-raspbian-wheezy.zip on OSX Mavericks
# OSX terminal
brew install qemu
# kernel-qemu is a linux kernel compiled with ARM1176 support.
# learn more here: http://xecdesign.com/compiling-a-kernel/
curl -OL http://xecdesign.com/downloads/linux-qemu/kernel-qemu
curl -o raspbian_latest.zip -L http://downloads.raspberrypi.org/raspbian_latest
@sdwfrost
sdwfrost / SRR765688.fasta
Last active October 23, 2016 06:33
Test files for vdjtools/ChangeO
>SRR765688.30659 HQP9GKT01B1E02 length=380|SEQORIENT=F,RC,F|MID=MID54|CPRIMER=IgG-PCR|VPRIMER=LR3|DUPCOUNT=3
NNNNNNNNNNNNNNNNNNNNACGAAGCCTGGGGCCTCAGTGAAGATTTCCTGCAAGGCTT
CTGGATACATTTTCACTAAATATTCAATGAGTTGGGTGCGACAGGCCCCTGGACAAGGGC
TTGAGTGGATGGGATACATCAACACCATCACTGGTAACCCAACTTACGCCCAGGCCTTCA
CAGGACGGTTTGTCTTTTCCTTGGACACCTCTATCAGCACGGCATATCTGCAGATCAGCA
GCCTAAAGACTGACGACACTGGCATGTATTATTGTTCGACCCTCCAACCGCGTATTGCAG
CACCTGAATTCTGGGGCCAGGGAGCCCTGGTCGCCGTCTCCTCGGCCTCCAC
>SRR765688.38189 HQP9GKT01B1F8D length=357|SEQORIENT=F,F,F|MID=MID53|CPRIMER=IgG-PCR|VPRIMER=LR1|DUPCOUNT=2
NNNNNNNNNNNNNNNNNNNCTGTGACATCTCCGGGGAGAGTATCTCTAACACCAATGTTG
GCTGGACCTGGATCAGGCAGTCCCCATCGAGAGGTCTTGAGTGGCTGGGAAGGACATTCT
@sdwfrost
sdwfrost / forms.html
Created September 20, 2016 05:18 — forked from gnunicorn/forms.html
Jinja2 WTForms macros for twitter bootstrap
{%- macro form_field_label(field) -%}
<label for="{{ field.id }}">{{ field.label.text }}
{%- if field.flags.required -%}
<abbr title="Diese Feld muss angegeben werden">*</abbr>
{%- endif %}</label>
{% endmacro %}
{%- macro form_field_description(field) -%}
{% if field.description %}
<span class="descr">{{ field.description }}</span>
@sdwfrost
sdwfrost / mktest.Rmd
Created August 18, 2016 15:16
MKn model in diversitree with deSolve and custom initial conditions
---
title: "mkn test"
author: "Simon D.W. Frost"
date: "18 August 2016"
output: html_document
---
```{r}
library(ape)
library(diversitree)