My thoughts
I’m not sure exactly what will go on this blog but I think I wanted some place to put my bioinformatics thoughts…
Posts by Collection (grid view)
personal
Welcome to Jekyll!
You’ll find this post in your _posts directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different wa...
old posts
I’ll see if I can continue my blog here. For previous entries, please see my blogspot at http://bioinformaticsthoughts.blogspot.com.
Site has been updated
Hey all, I updated the website to have a nicer interface. I also imported all my blogspot posts. Hopefully this will be a better online home for a long time.
Story about Ginger
Ginger passed away early this morning. Samantha had a good obituary for her
The war from Christmas
Today while I was raking leaves, my neighbor asked me if I was going to take my kids to the Pink Pig. This is a roller coaster that they set up at the mall a...
Finding liberty bells on vacation
I visited my brother in Philadelphia in February earlier this year and stopped by the Liberty Bell.
Golden Girls Murder Mystery
Samantha took me on a date yesterday to see the Golden Girls Murder Mystery.
Home Ownership
My wife and I have been furloughed from our jobs since October 1 and we aren’t sure when we’re going to be able to work. I want to be absolutely clear about ...
Yearbook template
My wife volunteers on the school yearbook committee. Her job is to solicit pictures, organize them, and help with the yearbook layout. She and the other volu...
portfolio
Annapotater Permalink
A quick SNP annotator for microbial variant analysis.
CG-Pipeline Permalink
Command-line pipeline for genome assembly, prediction, and annotation.
dists2trees Permalink
A generic pipeline for converting pairwise distance matrices into phylogenetic trees.
Kalamari Permalink
A curated database of completed genome assemblies with taxonomy IDs for metagenomic classification.
LYVE-SET Permalink
High-quality SNP-based phylogenetics for infectious disease outbreak investigations.
Bio::Minimizer Permalink
Perl module for computing minimizers from biological sequences.
MLST-CLI Permalink
Command-line tools for building and manipulating whole-genome MLST allele databases.
MLST Hash Template Example Permalink
A worked example of building a genomic epidemiology database using the MLST hash template.
bio-sketch-perl Permalink
Pure Perl implementation of min-hash sketching for genomic sequence comparison.
SneakerNet Permalink
QA/QC pipeline for MiSeq, HiSeq, Ion Torrent, and assembly-only sequencing runs.
Suffix::Trie Permalink
Pure Perl suffix trie for efficient sequence substring searches.
Awesome Bioinformatics Education Permalink
A curated list of courses, tutorials, and learning resources for bioinformatics.
Awesome Bioinformatics Jobs Permalink
A curated list of resources for bioinformatics job seekers.
Fundamentals of Bioinformatics Permalink
Course materials and exercises covering foundational bioinformatics concepts.
Doggo Chat Permalink
A chat-based game featuring dog characters.
Elemental Masters Permalink
A strategy game featuring elemental-based gameplay, built with AI assistance.
File::Find::Fast Permalink
A faster drop-in replacement for Perl’s built-in File::Find module.
Yearbook Template Permalink
A Jekyll template for generating a yearbook-style website from structured data.
recipes
Moist flapjack with condensed milk
This recipe makes enough flapjack for two hungry children for several weeks of school lunches.
Chocolate Mousse
This recipe is from our friends the Poggios. We first ate it at their house and when they came to dinner we insisted they brought chocolate mousse with them.
A no-effort white loaf using a Kenwood Chef
This is how I make an easy and quick white loaf using my kitchen mixer. It’s trouble-free and reliable and a great time-saver.
Healthy Butter Chickpeas
This tastes so much like butter chicken.