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Spencer Bliven sbliven

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sbliven / forester-1.038.pom
Created December 2, 2015 13:52
POM file for forester 1.038 based on the 1.005 POM. The URLs seem to be out-of-date here
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.biojava.thirdparty</groupId>
<artifactId>forester</artifactId>
<packaging>jar</packaging>
<name>Forester</name>
<description>Applications and software libraries for evolutionary biology and comparative genomics research</description>
<url>https://code.google.com/p/forester/</url>
<version>1.038</version>
@sbliven
sbliven / ngltest.html
Created May 30, 2016 16:03
NGL test of spheres and labels
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
</head>
<body>
<script src="https://rawgit.com/arose/ngl/master/js/build/ngl.embedded.min.js"></script>
<script>
@sbliven
sbliven / 404ForCaseSensitiveURLs.js
Last active March 16, 2024 09:32 — forked from AmrEldib/404ForCaseSensitiveURLs.js
Jekyll 404 page on GitHub Pages to fix case sensitive URLs
var allposts = [];
function redirectToCorrectPage() {
console.log("Unable to find page. Trying other URL cases.");
{% for post in site.pages %}
allposts.push("{{ post.url }}");
{% endfor %}
var url = window.location.pathname;
// strip trailing /
if (url.slice(-1) === "/") {
url = url.slice(0, -1);
@sbliven
sbliven / GenericsHell.java
Created November 15, 2016 10:31
Reduction of biojava/biojava#354 into a form suitable for asking at http://stackoverflow.com/questions/40598972/java-two-level-parameterized-type-inference
package demo;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Set;
public class GenericsHell {
@sbliven
sbliven / cif2pdb.py
Created April 26, 2017 19:27
Convert mmCIF files to PDB format using biopython
#!/usr/bin/env python
"""
Script to convert mmCIF files to PDB format.
usage: python cif2pdb.py ciffile [pdbfile]
Requires python BioPython (`pip install biopython`). It should work with recent version of python 2 or 3.
@author Spencer Bliven <spencer.bliven@gmail.com>
"""
@sbliven
sbliven / guido_structures.html
Last active May 18, 2017 14:20
Demo of many NGL instances on one page
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<script
src="https://code.jquery.com/jquery-3.2.1.min.js"
integrity="sha256-hwg4gsxgFZhOsEEamdOYGBf13FyQuiTwlAQgxVSNgt4="
@sbliven
sbliven / JupyterGenomeDiagram.ipynb
Created June 29, 2017 13:35
Demo of displaying GenomeDiagram objects in Jupyter
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@sbliven
sbliven / JupyterGenomeDiagram.ipynb
Last active August 22, 2017 13:13
Example of BioPython #1329 (broken version)
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@sbliven
sbliven / JupyterGenomeDiagram.ipynb
Created August 22, 2017 13:09
Example of BioPython #1329 (fixed version)
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@sbliven
sbliven / interfaces
Created October 10, 2017 15:55
ZHAW Raspberry Pi network settings.
# /etc/network/interfaces
# interfaces(5) file used by ifup(8) and ifdown(8)
# Please note that this file is written to be used with dhcpcd
# For static IP, consult /etc/dhcpcd.conf and 'man dhcpcd.conf'
# Include files from /etc/network/interfaces.d:
source-directory /etc/network/interfaces.d
auto lo