James B. Hanks

The Best of the Best: My Favorite Links

Essentials


I expect that most people who would be interested in these sites already know about them, but if you do not, do yourself a favor and check them out.
All Sites - Stack Exchange Stack Exchange is bar none the greatest knowledge-sharing platform created to date.
Home - PubMed - NCBI Search all published biomedical literature back to 1966, as well as selections from earlier years.
Colossal | Art, design, and visual culture. One of the best art sites on the internet, a constant source of content that goes viral for good reason.
My Modern Met – The Big City That Celebrates Creative Ideas Another fantastic site for discovering new art.
Kaggle The granddaddy of data science websites.
Adobe Color Adobe tool to find well-matching colors.

NYC


Interesting things in and around NYC.
Open House New York An annual event where achitecturally notable private spaces around NYC open for public tours.
Waterbody Advisories - DEP I like to swim in the Hudson River. It's probably never all that safe, but I pay attention to water quality advisories so as to avoid exposing myself to excess risk.
Culture Pass NYC: How to Get and Use it for 47 NYC Attractions Requires some planning ahead, but if you have a New York/Brooklyn/Queens Public Library card, you can use culturepass.nyc to sign up and get passes for events around the city.
Riverkeeper - Protecting the Hudson River & NYC's Drinking Water Supply Local organization that conducts its own water quality monitoring and lobbies for a cleaner river.
List of museums and cultural institutions in New York City - Wikipedia Even if you are a born and bred New Yorker, I bet there is stuff here you've never heard of.
An alternative view of New York Long-running blog about City history hiding in plain sight.
NYC Housing Court Knowing the basic rules around NYC housing is essential for life in NYC, if you live here and have not been to this site, do it now.

Amazing Art


Select artists whose work made a particular impression on me.
Eiko Ojala Illustration Gorgeous illustrations with a remakable sense of depth.
Diana Sudyka Fantastic and colorful illustrations.
Albane Simon – The Surreal Collagist Surreal collages
Tiffany Bozic Deeply psychedelic wildlife-themed paintings.
Catalina Toro Art NYC based painter and illustrator. Her series of glow-in-the dark paintings is especially beautiful.
Strange Gods: Art of Valin Mattheis Filled with skeletons and sorcery, this work seems almost alive.
Olga Klimova Visionary artist of lush, layered, fantastically detailed paintings.
The Art of Anna-Maria Jung Illustrator and maker of comics and shirts with playful fantasy/sci-fi themes.

Software


Some of my favorite free software.
Zotero: Your personal research assistant I use this every day and have found it indispensible for organizing scientific papers. I have tried severl PDF organization solutions, and have found Zotero to be the best, especially when my library got very large. It must, however, be used with a good PDF reader with annotation capabilities to be maximally useful.
Drawboard PDF My favorite PDF annotation tool.
Qoppa PDF studio Commercial software, but the only decent option for annotating PDFs on Linux that I am aware of.
Rstudio Integrated development environment makes the open-source statistics package R a pleasure to use.
Pycharm My favorite IDE for Python.
Trilium Notes Build your personal knowledge base on a self-hosted server. The syntax highlighting makes it perfect for storing code snippets.
Paule Bourke: Geometry, Surfaces, Curves, Polyhedra A treasure trove of geometry demonstrations, the most famouse of which is probably
Supershape Program for making natural looking 3d shapes

Tutorials and Explainers


Tutorials and explainers that I found particularly useful.
The UNIX School: awk - 10 examples to group data in a CSV or text file If you've ever been frustrated by tedious work manipulating Excel spreadsheets and dealing with clunky macros, consider converting to a plain text format and doing your modifications with Awk (and its cousin, Sed). It is difficult at first, but can save you enormous amounts of time if you deal with a lot of spreadsheets that need cleaning.
Running Windows 10 on Linux using KVM with VGA Passthrough I might not have my current computer setup were it not for this post, or at least it would have taken me a lot longer without it.
ArchWiki Even if you do not use Arch, this is a great resource for general Linux how-to and troubleshooting.
Main Linux problems on the desktop, or why Linux sucks I love Linux and use it every day for 90% of my computing, but there are definitely some things about it that are less than wonderful, and this is a good list of them. It is for many of the reasons listed here that I feel the need to use a Windows machine alongside Linux.

Datasets, data exploration tools, and reference tables


My background and main interest is bioinformatics, so this list is heavily skewed towards that. However, bioinformatics has led me to a broader interest in data science, so this list includes resources related to a variety of topics.
Gene Expression Omnibus (GEO) - NCBI NCBI repository of gene expression data.
ENCODE RNA Dashboard (hg19) Transcriptome data from the ENCODE project.
World Bank Open Data Data from the World Bank.
The GDELT Project A constantly updated resource for the monitoring of global media.
OpenCelliD Database of Cell Towers & Geolocation Database of cell towers & geolocation. Requires registration.
NIMS Materials Database (MatNavi) Multiple databases of properties of different materials and chemical compounds. Requires registration and somewhat confusing to navigate.
Engineering ToolBox Extremely comprehensive collection of physics and engineering related equations.
Virtual Metabolic Human Explore the known human metabolome with interactive maps.
GTEx Portal GTEx is a massive project to gather RNA-seq data from different human tissues, as well as computing expression quantitative trait loci (eQTLs).
EMBL-EBI Home: Expression Atlas < EMBL-EBI Gene expression data and atlas' for a number of species
Ensembl genome browser Explore and compare the genomes of many species.
1000 Genomes The 1000 Genomes Project, the most complete sequencing of the human genome to date.
Online Ancient Genome Repository Ancient DNA (which actually includes DNA that is just a few years old) is a fascinating topic that will only grow in coming years.
OMIM: Online Mendelian Inheritance in Man An Online Catalog of Human Genes and Genetic Disorders
GWAS Catalog The NHGRI-EBI Catalog of published genome-wide association studies
NYC OpenData Open Data is free public data published by New York City agencies and other partners.

DIY, homemaking and homesteading


These are a mix of how-to's that I found useful and sites that generally have good information or interesting ideas.
Walden Labs: Solutions for Self-Reliance Solutions for self-reliance: DIY food, water, energy, and shelter.
Hackaday: Fresh Hacks Every Day Constant source of cool DIY ideas.
The Bucket Farm: How To: Building a cheapskate DWC system I build a very similar hydroponic system to grow herbs in my apartment and it worked very well.
Making Worm Tea - Delivering Essential Micro-nutrients Instructions for making "worm casting tea" for promoting healthy microbiota in a hydroponic garden. I found it quite effective in staving off root rot.
Storage Stairs for a Bunk or Loft Bed | Ana White I used this to build stairs to the loft bed that I built.
The Sagulator – WoodBin Calculator for estimating how much load boards of different length, thickness, and material will withstand weight. Useful for designing shelves, desks, and tables.
Swing up fixed frame screen (altenative to pull down) I went with a very similar design for my home theater.
How to Start Woodworking in a Basement or Apartment Advice for DIY-ers with limited space.

History: primary sources, archives, data exploration tools


I have a fascination with ancient manuscripts and I love reading the words of people involved in historical events. If you do too, you will like these links.
CIA FOIA: Freedom of Information Act Electronic Reading Room Search declassified documents from the CIA. Make sure to use the advanced search.
Wikileaks: Full-text search I have very mixed feelings about Wikileaks and whether it is a good thing for the world. But once documents are (for better or for worse) out in public, I have no compunctions about reading them. It is important to keep in mind that these document dumps are rarely if ever made without desire for a specific political effect, and that forged documents mixed in with real ones are a possibility.
US Department of State Office of the Historian Historical documents from the US Department of State.
US Navy historical photos collection Photo collections at the online archives of the US Navy.
Lynching acts of white supremacy interactive map "Discover in four pages the heroism of Monroe and Florence Work, who in 1920 showed us that quietly behind the scenes, you can make a whole nation hear you"
OldNYC: Mapping Historical Photographs of New York City Find old photographs of NYC by location.
BBC: WW2 People's War BBC project to record and archive people's stories and photographs from Britain in WWII.
OPenn primary digital resources: curated collections Collections of primary source documents and manuscript fragments from ancient up through modern times.
Digitised Manuscripts at the British Library Digitized archives going back into Anglo-Saxon times.
DMMapp: Digitized Medieval Manuscripts app Links to medieval manuscripts in the digital archives of numerous institutions.
The Electronic Text Corpus of Sumerian Literature Archive of Sumerian writings with translation.

Information, Literature and Media Sources


Online archives of published media.
Royalty-Free Stock Video and Music Library | Pond5 Large collection of royalty-free (but not free!) video footage.
NYPL Digital Collections The digital collections of the New York Public Library, including archives of photography, art, and orignal manuscripts. Unfortunately, you must pay for high-resolution images. Another annoying thing is that to view the images larger than thumbnail, it makes you download them instead of showing them in the browser.
Internet History Sourcebooks from Fordham University English translations of medieval literature from Europe and the Middle East.
The British Library on Flickr Flickr account for the British Library containing many themed collections.
OZ magazine from the Historical & Cultural Collections at University of Wollongong PDF archives of a counter-culture/arts magazine that existed from 1967-1973
UFDC: Baldwin Library of Historical Children's Literature Vintage children's books.
Books with Full-Text Online from MetPublications at The Metropolitan Museum of Art Online version of many publications from the Metropolitan Museum's press.
WikiArt.org - Visual Art Encyclopedia If you want to see the good quality images of the work of any past artist, this is a good place to start.
NASA Image and Video Library NASA's image archive.

Blogs


Blogs with conistently interesting content that I like to keep up with.
Failed Architecture - Architecture and the Real World Blog about architeture and society.
Maps Mania Blog highlighting interesting and unique maps.
Archaeology in Europe News News about the latest discoveries and ideas in the archaeology of Europe.
Quanta Magazine – Illuminating Science | Quanta Magazine Examinations current scientific theories and controversies written in clear and accessible style.
Phys.org The latest and most exciting new scientific findings.
NIH Director's Blog Blog from the office of the Director of the NIH on current topics in biomedical research.
Lawfare Top-quality analysis of issues related to national security law.
War on the Rocks In-depth analysis of military affairs.
RNA-Seq Blog Current news on the latest methods in RNA-seq and other -omics research.

Podcasts


What would my life be without podcasts? Most of these are history podcasts, but some are about current affairs. I have spent dozens of hours listening to each of these podcasts.
Current Hardcore History Available for Free The granddaddy of history podcasts.
WDFpodcast.com The most thorough coverage of Western history available in podcast form.
The History of Rome: Archives One of the finest history podcast series ever made.
Revolutions Mike Duncan of History of Rome covers the major revolutions of the Western world. Every bit as excellent as History of Rome.
The History of England David Crowther's amazing podcast on English history. The lively narration and dry wit make it extra-enjoyable to listen to.
The Lawfare Podcast The best national security law podcast around. I find it an essential resource for cutting through the media hype and getting a grasp on what is actually going on.
HOME | theredlinepodcast An excellent global affairs podcast featuring expert guests.
The Eastern Border podcast – The Other Side of the Cold War Excellent podcast on Soviet and post-Soviet history.
War on the Rocks Podcast Military affairs discussed in detail, but accessible to the layman.
Our Fake History – Historical Myths Relished and Ruined! Always informative and entertaining.
The History of English Podcast: The Spoken History of a Global Language Absolutely fascinating exploration of the English language back to proto-Indo-European roots.
Literature & History A deep dive into the great works of the Western literary canon, starting in ancient times. At the time time of writing this page, it is just getting into late antiquity.
The History in the Bible Podcast A scholarly look at the Bible(s), both their content and the origins of the texts.

Art websites and blogs


My favorite sites to discover new art.
Juxtapoz Magazine An excellent magazine of contemporary art.
Hi-Fructose Magazine Another excellent magazine for contempoarary art.
Metal on Metal Although no longer updated, the archives of this blog are a great place to explore and discover art with dark and/or gory themes.
Monster Brains A blog of monster/creature art. Also no longer updated.
Giornale Nuovo Another defunct blog. now only available via Archive.
Open Culture An ever-growing collection of open-source media.
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