Cool Links

Some links I've collected!

Educational things.

• Dr. David Malloch's Mycology Web Pages

  A brilliant resource for microbiology students. Dr. Malloch's book on moulds is especially great, and his mould identification keys are very useful.

• Zotero

  Not really a 'cool link', but I just really like Zotero. Its a great open source citation manager/tool. I have no idea how people do research without it. It also has great $\LaTeX$ integration.

• Sci-Hub Mirrors: [1] [2] [3]

  A shadow library which provides free access to scholarly journal articles. It was created by Alexandra Elbakyan. If you don't have a university library to access research papers and books from, or your university does not subscribe to the journal you need to get a paper from, its invaluable. One of my favourite channels Medlife Crisis made a great video talking about the issue of academic publishers paywalling researchers' articles and interviewed Elbakyan.

• Library Genesis Mirrors: [1]

  A shadow library which provides access to academic papers, and books.

• Roche's Biochemical Pathways Posters (PDF)

  DOI: 10.5281/zenodo.4446230

  Roche made two biochemical pathway posters, a Metabolic Pathway poster and a Cellular and Molecular Processes poster. After some looking, I found a PDF version on the Zenodo database under its DOI.

• The RESB Protein Data Bank

  A database of protein structures. They have a great 3D protein structure viewer if you don't have the software to view protein structures on your computer. Here's the human coagulation factor VIII (PDB DOI: 10.2210/pdb6MF2/pdb).

• colorbrewer2

  An open source tool to make good colour schemes for data visualisations.

• Data to Viz

  A catalogue of various data visualisations and how to make them in R.

• The R Graph Gallery

  Another R graph catalogue.

• Crossref

  A database of academic journal articles, books, datasets, etc. If you have a DOI, PMID, title, or a citation, you can use this database to find the article from that data. Its useful to look for journal articles from a bibliography where a DOI isn't linked.

• Overleaf

  A web LaTeX editor. Sort of like google docs but for LaTeX documents. It's a great place to start out with LaTeX as a beginner because you don't have to go through the process of installing a TeX distribution on your system and they also have great tutorials that i used a lot as i was learning how to use it (and still do), especially because TeX documentation tends to be dense and confusing. They have a feature where multiple people can collaborate on one tex document, but i haven't been in a group where anyone else knows LaTeX and/or wanted to use it for a project (despite my pleas, i just hate working on larger documents on word especially with figures because formatting is a nightmare).

• Unofficial $\LaTeX2e$ Reference Manual

  An Unofficial manual for $\LaTeX2e$. Great for looking up macros or specifics on how to use $\LaTeX$.

• Comprehensive list of $\LaTeX$ symbols

  A comprehensive list of $\LaTeX$ symbols. If you don't know how to type a symbol, chances are you'll find it here with the macro and/or package you need listed here.

• Zotero CSL Style Repository

  A repository of bibliography and citation styles in CSL format. Chances are someone has already made a CSL specification for the style you're looking for. If thy haven't, you can find a similar one and edit it to your needs.

• Visual CSL Editor

  An great CSL editor for editing bibliography styles in a CSL format.

• Nocebo effects with antidepressant clinical drug trial placebos

  DOI: 10.1016/j.genhosppsych.2007.01.010

  A case report on a patient experiencing very strong nocebo effects when taking a large dose of a placebo during a suicide attempt. he was participating in a clinical trial of an antidepressant, and attempted suicide using the placebo he was assigned. As he believed it was the active drug, he attempted to overdose on the placebo to commit suicide and experienced very strong negative symptoms. After being told that the drug he took was actually a placebo the symptoms quickly abated. This case report was featured in Medlife Crisis' video on placebo. I found it really interesting so I decided to link the case report here.

• botany4u.neocities.org

  A cool neocities botany page.

• The Nib — Repeat After Me

  A great comic on the replication crisis we're facing in science right now.

• Retraction Watch

  A blog keeping track of retracted papers and hijacked journals.

• Word$\TeX$ — A WYSIPCTWOTCG Typesetting Tool

  Made by Tom Wildenhain. A fun video and MS Word template that aims to emulate $\LaTeX$. See also his PowerPoint Turing machine.

• Histology @ Yale

  A great Histology resource.

• Babe wake up, new antibiotic mechanism just dropped [web archive]

  The antibiotic (called Zosurabalpin) works by inhibiting lipopolysaccharide transport proteins in the membrane of gram-negative bacteria. Gram-negative bacteria have lipopolysaccharide (LPS) complexes embedded on their outer membrane. When LPSs are made in the cell, specific transport proteins move them to the outside of the cell from the cell cytoplasm. Inhibiting these proteins will be very damaging to gram-negative bacteria. This class of antibiotics targets these proteins in Acinetobacter. What's very exciting about this is it targets Carbapenem-resistant Acinetobacter baumannii (dubbed CRAB), a World Health Organisation Priority 1 pathogen for which new antibiotics are urgently needed.

  Read the articles:

  Pahil, K. S., Gilman, M. S. A., Baidin, V., Clairfeuille, T., Mattei, P., Bieniossek, C., Dey, F., Muri, D., Baettig, R., Lobritz, M., Bradley, K., Kruse, A. C., & Kahne, D. (2024). A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature, 625(7995), 572–577. https://doi.org/10.1038/s41586-023-06799-7

  Zampaloni, C., Mattei, P., Bleicher, K., Winther, L., Thäte, C., Bucher, C., Adam, J.-M., Alanine, A., Amrein, K. E., Baidin, V., Bieniossek, C., Bissantz, C., Boess, F., Cantrill, C., Clairfeuille, T., Dey, F., Di Giorgio, P., du Castel, P., Dylus, D., … Bradley, K. A. (2024). A novel antibiotic class targeting the lipopolysaccharide transporter. Nature, 625(7995), 566–571. https://doi.org/10.1038/s41586-023-06873-0

• The Conversation

  A media site which only publishes articles written by academics and researchers. Great, accessible articles on health, the environment, and science, along with some research reports by academics talking about something they published. They also publish articles on other topics like art and culture, books, economy, politics, etc. Good read on the morning commute, i can just check my rss feed and look for an article that catches my interest (also thank you for offering a different feed for each topic).

• Donald E. Knuth's Home Page

  The home page of Donald E. Knuth, known for The Art of Computer Programming [wiki] and for creating $\TeX$ and METAFONT.

• $\KaTeX$

  A very fast open source javascript library which displays mathematics. Uses $\LaTeX$ notation and aims to emulate $\LaTeX$ math typesetting. I prefer it over MathJax.

  Example (some hs homework): Let $a>0$ be any positive integer. Prove $E(a+X) = a + E(X)$.

  Proof. Let $\displaystyle E(X) = \sum_{i=1}^n \frac{x_i}{n}$. $$\begin{align*} E(a + X) &= \sum_{i=1}^n \frac{a_i+x_i}{n}\\ &= \sum_{i=1}^n \frac{a_i}{n} + \sum_{i=1}^n \frac{x_i}{n}\\ &= \frac{na}{n} + \sum_{i=1}^n \frac{x_i}{n}\\ &= a + E(X) \end{align*}$$

  $\square$
• Homebrew

  A package manager for mac. I got sucked in to using macs from high school, where we all had to get macs, so I ended up sticking with it. After starting to use a package manager I never went back. The convenience and simplicity is just great.

• Scoop

  On windows I use scoop as my package manager.

• gitignore.io

  A tool which generates a gitignore file ready for you to use depending on your OS, programming language, environment, etc.

• Catppuccin Theme

  The colour theme I use. It's the one I use on this site! It comes in light and dark flavours you can switch between, and has a large ecosystem of themes for different programs so you can theme a lot of things you use regularly if you're into that.

• Iosevka font [github]

  The font I use. It's the one I use on this site! It's open source and very customisable! You can pick and choose between different options and individual styles for glyphs on their website, and it will generate a config that you can use to compile your own custom font. It's easier than it sounds. Although chances are they already have a ready-made compiled version for you to download that meets your preferences though.

• Regexr

  Tool to help visualise regex expressions.

• grep.app

  Search open source git repos.

• Ruffle

  An open source flash emulator for the web

• Project Euler

  A growing collection of math/programming problems

• QOI

  A very efficient image format. I learned about it from this video by Reducible.

• The Fuck

  Corrects spelling error in your previous console command by suggesting what you meant to write. Just invoke the fuck command after you misspelled.

• Pygments

  A python syntax highlighter. The one I use on this website! It takes my code, spits out some HTML, and I just need to include the stylesheet, and that's it. I use the catppuccin colour scheme, so I used the catppuccin python library which provides a pygments style. If i want a new style, or even just to switch over to a dark theme, i can just swap out the stylesheet! Here is a little example:

  #include <stdio.h>
  
  int main()
  {
      printf("Hello, World!\n");
  
      return 0;
  }
  

• RenderCV

  Make a cv from a yaml file. I spent way too long trying to make a nice cv directly in a LaTeX doc using a .cls file i got off someone's website a few years ago so when it came time to update it i kept putting it off. So i looked around and found this project and it was exactly what i was looking for. I can describe my cv in a yaml file (including basic markdown syntax and LaTeX macros) so i still get to use version control and keep it in a neat little folder. Plus, from the documentation it seems like i can extend the LaTeX template it uses and add in my own fields, so i can add some missing features like multi-column bullet lists that i could make in LaTeX alone. But right now i'm quite happy with the normal theme. They also seem to have an overleaf-esque web app but i haven't tried it because they have a nice cli.

• Thorazine

  An advertisement for Chlorpromazine (Thorazine), an ℞ only antipsychotic medication. It functions primarily by antagonising D2 dopamine receptors, causing decreased neural activity. It was the first antipsychotic medicine sold on the market. The advertisement linked here is particularly cool.

• Brain Fag Syndrome

  Literally me.

• United States v. Article Consisting of 50,000 Cardboard Boxes More or Less, Each Containing One Pair of Clacker Balls

  A famous and funny case name in US court.

• Dicksonia antarctica

  A native Australian fern with a very amusing name.

• Boops boops

  A species of seabream with a funny scientific name.

• Dog's Bollocks

  A colon and an em dash: :—. Just has a funny name.

• London Necropolis Railway

  A cemetery train line. Cool logo tho.

• Australia 31–0 American Samoa

  A depressing game of football between the Australian and American Samoan national association football teams in an Oceanian qualifying match for the 2002 FIFA World Cup. It broke the world record for the most goals scored in an international football match (both by a team, and a single player with Archie Thompson scoring 13 goals). This ended up resulting in a change to the tournament format to avoid these unbalanced matches like this. Someone posted highlights to youtube.

• List of citogenesis incidents

  Citogenesis, coined in this xkcd, is the process by which someone makes up something on Wikipedia, completely unsourced, which is then picked up by some writer somewhere and repeated with no further research, whose article is then used as a source to justify the original edit in wikipedia. In other words, a source appears out of nowhere! So your teachers had a point! Check the sources that are being cited in Wikipedia.

• List of unusual units of measurement

  A list of unusual units of measurement, such as a horse (not horsepower), a vee (used in the typesetting program groff/troff), a hammer unit (unit of length in the source engine) (maybe i'm chronically online but i somehow didn't think this would show up lol), a jiffy (apparently used in comp sci), a microfortnight, centipawns (measure of the strength of a chess position), and the micromort and microlife (units of risk used in epidemiology, one in a million chance of death, and a half hour of life expectancy respectively).

• Russell Brain, 1st Baron Brain

  Lord Brain (or Baron Brain), was a neurosurgeon, and editor of the journal Brain. He took over as editor of Brain from Henry Head. Brain wrote his thoughts on Head in Brain. Brain also wrote the standard work on neurology, Brain's Diseases of the Nervous System.

  A funny example of nominative determinism. Found out about him from this goofy short video from Medlife Crisis.

• Petrichor and Geosmin

  Another interesting thing I heard from a Hank Green video.

  The smell of rain is known as petrichor. Coined from πέτρᾱ (pétra) meaning 'rock' and ἰχώρ (ikhṓr), the blood of the gods in Greek mythology. This specific term to describe the smell of the earth was coined by Australian researchers Isabel Bear and Dick Thomas in their 1964 paper in Nature, previously described as argillaceous odour.

  The diverse nature of the host materials has led us to propose the name 'petrichor' for this apparently unqie odour which can be regarded as an 'ichor' or 'tenuous essence' derived from rock or stone. This name, unlike the general term 'argillaceous odour', avoids the unwarranted implication that the phenomenon is restricted to clays or argillaceous materials; it does not imply that petrichor is necessarily a fixed chemical entity but rather it denotes an integral odour, variable within a certain easily recognizable osmic latitude. (Bear & Thomas, 1964)

  Geosmin is one of the contributing chemicals to the scent of petrichor, with a distinct musty, earthy odour. It is significant in that it has a very low odour detection threshold for humans, requiring only 4 to 10 ng L^-1 to be detected (orthonasally in water) (Ball et al., 2024).

  References:

  Bear, I. J., & Thomas, R. G. (1964). Nature of Argillaceous Odour. Nature, 201(4923), 993–995. https://doi.org/10.1038/201993a0

  Ball, L., Frey, T., Haag, F., Frank, S., Hoffmann, S., Laska, M., Steinhaus, M., Neuhaus, K., & Krautwurst, D. (2024). Geosmin, a Food- and Water-Deteriorating Sesquiterpenoid and Ambivalent Semiochemical, Activates Evolutionary Conserved Receptor OR11A1. Journal of Agricultural and Food Chemistry, 72(28), 15865–15874. https://doi.org/10.1021/acs.jafc.4c01515

My favourite channels.