Programming in Bioinformatics
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Rescooped by Nathan Watson-Haigh from cereal bioinformatics
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Unix Paste for FASTQ and FASTA files - Gluten for Punishment

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Nathan Watson-Haigh's curator insight, February 10, 2015 6:28 PM

My blog post about the use of Unix "paste" in helping to process FASTQ and FASTA files

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Travis CI: The Build Environment

Travis CI: The Build Environment | Programming in Bioinformatics | Scoop.it
Nathan Watson-Haigh's insight:

Useful stuff for Travis-CI, especially the environmental variables which get set by Travis.

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Git Workflows

Git Workflows | Programming in Bioinformatics | Scoop.it
Nathan Watson-Haigh's insight:

An excellent book with both context and details on useful git workflows. I'll try to keep this at my fingertips.

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LLiseil's comment, March 20, 2015 1:14 PM
awsome reference
LLiseil's curator insight, March 20, 2015 1:17 PM

If you your git memos feela bit short or scatered, look at « Git Workflows » by Yan Pritzker.

Rescooped by Nathan Watson-Haigh from Viruses and Bioinformatics from Virology.uvic.ca
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A New Online Computational Biology Curriculum

A New Online Computational Biology Curriculum | Programming in Bioinformatics | Scoop.it

A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary and career advice.


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Permanently remove files and folders from a git repository

Permanently remove files and folders from a git repository | Programming in Bioinformatics | Scoop.it

Also goodLearn how to permanently remove files and folders from a git repository that you have added by mistake.

Nathan Watson-Haigh's insight:

Also good when moving some files/directories, together with their history, to a new repository.

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Rescooped by Nathan Watson-Haigh from Bioinformatics Software: Sequence Analysis
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RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA | RNA-Seq Blog

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA | RNA-Seq Blog | Programming in Bioinformatics | Scoop.it
The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences.

Via Mel Melendrez-Vallard
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Rescooped by Nathan Watson-Haigh from Bioinformatics Software: Sequence Analysis
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Hadoop for Bioinformatics: Building a Scalable Variant Store

Talk at Mount Sinai School of Medicine. Introduction to the Hadoop ecosystem, problems in bioinformatics data analytics, and a specific use case of building...

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Rescooped by Nathan Watson-Haigh from Bioinformatics, Comparative Genomics and Molecular Evolution
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Computational Biology Primers in Nature Biotechnology


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Arjen ten Have's curator insight, April 14, 2014 2:28 PM

Nice collection of links to primers!!

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suan/vim-instant-markdown

suan/vim-instant-markdown | Programming in Bioinformatics | Scoop.it
vim-instant-markdown - Instant Markdown previews from VIm!
Nathan Watson-Haigh's insight:

A pretty nice tool for vim users who edit markdown files. When you open a markdown file in vim, you get a browser window with the markdown rendered as HTML. As you edit the file in vim, the browser updates in real-time so you can see the formatting straight away! nice :)

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Rescooped by Nathan Watson-Haigh from Viruses and Bioinformatics from Virology.uvic.ca
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Decoding long nanopore sequencing reads of natural DNA : Nature Biotechnology :

Decoding long nanopore sequencing reads of natural DNA : Nature Biotechnology : | Programming in Bioinformatics | Scoop.it
Laszlo et al. demonstrate sequence alignment, and proof-of-concept organism identification, genome assembly and polymorphism detection from nanopore analysis of natural DNA.

Via Chris Upton + helpers
Nathan Watson-Haigh's insight:

Nice use of a de Bruijn sequence to enable the meauserment of all possible 4bp (the number they determined as contributing to the the unique current levels) combinations as they pass through the pore. That's B(4,4) = 256 http://www.hakank.org/comb/debruijn.cgi?k=4&n=4&submit=Ok

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Git Cheatsheet • NDP Software

Interactive Git Cheatsheet, categorizing commands based on what they affect.
Nathan Watson-Haigh's insight:

This is awsome!

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LLiseil's curator insight, March 20, 2015 1:18 PM

Un pense-bête Git visuel, interactif et en français.

Rescooped by Nathan Watson-Haigh from Bioinformatics Software: Sequence Analysis
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CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce

CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce | Programming in Bioinformatics | Scoop.it
by Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, Wen-Lian Hsu, Yu-Chun Wang, D. T.

Via Mel Melendrez-Vallard
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Rescooped by Nathan Watson-Haigh from Bioinformatics
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A novel approach to represent and compare RNA secondary structures

A novel approach to represent and compare RNA secondary structures | Programming in Bioinformatics | Scoop.it

Via Wei Shen
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Rescooped by Nathan Watson-Haigh from Bioinformatics Software: Sequence Analysis
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Getting Genetics Done: Using Volcano Plots in R to Visualize Microarray and RNA-seq Results

Getting Genetics Done: Using Volcano Plots in R to Visualize Microarray and RNA-seq Results | Programming in Bioinformatics | Scoop.it

Via Mel Melendrez-Vallard
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Ubuntu / Debian Linux Server Install Keychain SSH Key Manager For OpenSSH

Ubuntu / Debian Linux Server Install Keychain SSH Key Manager For OpenSSH | Programming in Bioinformatics | Scoop.it
Explains how to install and configure keychain manager for ssh-agent under Debian or Ubuntu Linux server running in cloud or dedicated server.
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Rescooped by Nathan Watson-Haigh from Bioinformatics Software: Sequence Analysis
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What is the extent of gender bias in bioinformatics? Please help me find out. - SEQanswers

What is the extent of gender bias in bioinformatics? Please help me find out. Bioinformatics (What is the extent of gender bias in bioinformatics? Please help me find out.

Via Mel Melendrez-Vallard
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Rescooped by Nathan Watson-Haigh from Viruses and Bioinformatics from Virology.uvic.ca
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Bioinformatician's Pocket Reference !!

Bioinformatician's Pocket Reference !! | Programming in Bioinformatics | Scoop.it
  It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special cir...

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Unit Testing in R

Unit Testing in R | Programming in Bioinformatics | Scoop.it
Nathan Watson-Haigh's insight:

I found this to be an excellent summary of unit testing in R and it was easy to follow in terms of adding unit tests to a package I already have.

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How to SSH to a VirtualBox Ubuntu guest externally through a Windows host?

How to SSH to a VirtualBox Ubuntu guest externally through a Windows host? | Programming in Bioinformatics | Scoop.it
I have a Ubuntu VM running on my Windows 7 machine. How do I set it up so that I can access an the webserver externally through ssh?

I found steps (in Setup SSH access between VirtualBox Host...
Nathan Watson-Haigh's insight:

I wanted to SSH into my guest Ubuntu VM once I had VPN'd into my corporate network from overseas. My first/normal network adapter was bridged, so I added a second adapter, set it to NAT and then setup port forwarding. Now I can connect SSH directly to my VM using the host's IP address and port 3022.

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