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@ehazlett
ehazlett / pub_med.py
Created July 25, 2011 16:27
Search PubMed with BioPython
#!/usr/bin/env python
# numpy and biopython are required -- pip install numpy biopython
from Bio import Entrez
from Bio import Medline
MAX_COUNT = 10
TERM = 'Tuberculosis'
print('Getting {0} publications containing {1}...'.format(MAX_COUNT, TERM))
@jaseemabid
jaseemabid / git tutorials.md
Last active March 24, 2024 00:07 — forked from netroy/git tutorials.md
Awesome git tutorials I am finding here and there
@bonzanini
bonzanini / search_biopython.py
Last active May 19, 2024 08:45
Searching PubMed with Biopython
# This code uses Biopython to retrieve lists of articles from pubmed
# you need to install Biopython first.
# If you use Anaconda:
# conda install biopython
# If you use pip/venv:
# pip install biopython
# Full discussion:
@xarem
xarem / README.md
Last active May 4, 2020 04:11
Upload files from context menu in OS X
  • Step 1, create Service in Automator:

Step 1

  • Step 2, set Service for files:

Step 2

  • Step 3: insert bash script (see below)
  • Step 4, save:
@gtallen1187
gtallen1187 / scar_tissue.md
Created November 1, 2015 23:53
talk given by John Ousterhout about sustaining relationships

"Scar Tissues Make Relationships Wear Out"

04/26/2103. From a lecture by Professor John Ousterhout at Stanford, class CS142.

This is my most touchy-feely thought for the weekend. Here’s the basic idea: It’s really hard to build relationships that last for a long time. If you haven’t discovered this, you will discover this sooner or later. And it's hard both for personal relationships and for business relationships. And to me, it's pretty amazing that two people can stay married for 25 years without killing each other.

[Laughter]

> But honestly, most professional relationships don't last anywhere near that long. The best bands always seem to break up after 2 or 3 years. And business partnerships fall apart, and there's all these problems in these relationships that just don't last. So, why is that? Well, in my view, it’s relationships don't fail because there some single catastrophic event to destroy them, although often there is a single catastrophic event around the the end of the relation

@tomsing1
tomsing1 / luigi_first_steps.md
Last active June 19, 2024 21:52
First steps with the Luigi workflow manager

First steps with the Luigi workflow manager

As an introduction into Luigi, I am following this tutorial with some modifications, e.g. installation using conda.

The problems and solutions described in the examples below have led to the development of sciluigi,

@samesense
samesense / run-phenoxome.md
Last active October 15, 2019 13:51
Run docker phenoxome

Data download; put data in /absolute/local/data/, called YOUR_DIR below

  • Make a directory to hold data (/absolute/local/data/).
  • Make these folders under your data dir: phenoxome_data/
  • Put data in {YOUR_DIR}/phenoxome_data/
    • human_g1k_v37.fasta
    • HGMD.vcf.gz and HGMD.vcf.gz.tbi (rename HGMD file in vcfanno toml file)
    • gnomad.exomes.r2.0.1.sites.vcf.gz and gnomad.exomes.r2.0.1.sites.vcf.gz.tbi

Start the phenoxome container with a mount to your local data.