Stephen Royle

The Retropie project is a wonderful way to play retro games on a Raspberry Pi (see previous post). A number of handheld units are available to make a convincing retro gaming experience. One of these is the Retroflag GPi case, modelled on Nintendo’s Game Boy. It’s possible to order one of these pre-built and even loaded with games, but where is the fun in that? Here is a quick guide to building one.

Play The Game: Retropie in a Retroflag GPi case

I have a long-running project Raspberry Pi project to make time-lapse movies of a countryside view (see previous posts). It’s been running for over two years and the results are great. The camera takes images every ten minutes and by assembling movies with different time intervals, you can see seasons change, trees growing or the sun setting and snow melting. The sky is mesmerising to watch.

Blue Monday: sampling the sky

The Process_Folder template in Fiji is a wonderful thing. It’s the starting point of most of the ImageJ macros that we use in the lab. However, it has a problem. This post is about how to fix it.

 tl;dr

use this gist instead of the built-in template. The Process_Folder template If you’re reading this, you probably know that the Process_Folder.ijm template is great.

Tips from the Blog XVII: better Process Folder template in Fiji

As I write this, the moderation on major social media platforms has been degraded, and the tools available to the user to curate their feeds are quite poor. So how could we improve our science social media feeds?

Not What You Want: improving a science social media feed

How can we teach “R for cell biologists” rather than teaching R to cell biologists? I’ve noticed that many R training courses will teach R – regardless of who is taking the course – and leave it to the participants to figure out how they can use R in their own discipline.

How can we teach “R for cell biologists” rather than teaching R
 
 to
 
 cell biologists?

I’ve noticed that many R training courses will teach R – regardless of who is taking the course – and leave it to the participants to figure out how they can use R in their own discipline.

Get Better: R for cell biologists

The aim of this post is to look at revisions of bioRxiv preprints. I’m interested how long preprint versions exist on bioRxiv. In other words: how long do revisions to preprints take? The data from bioRxiv is a complex dataset with many caveats as I’ll explain further down, but some interesting details do emerge. Consider this a sketch of the dataset rather than an in-depth analysis. I’ll walk you through the code.

Over and Over: Preprint revisions on bioRxiv

I have been doing paper of the day (#potd) again in 2014. See my previous post about this. My “rules” for paper of the day are: Read one paper each working day. If I am away, or reviewing a paper for a journal or colleague, then I get a pass. Read it sufficiently to be able to explain it to somebody else, i.e. don’t just scan the abstract and look at the figures.

A Day In The Life II

Back of the envelope calculations for this post. An old press release for a paper on endocytosis by Tom Kirchhausen contained this fascinating factoid:  If this is true it is absolutely staggering. Let’s check it out. A synaptic vesicle is ~40 nm in diameter.

Insane In The Brain

Another year, another edition of “the papers I selected for a module that I teach”. Previous selections are grouped here or here.

 The list serves as a snapshot of interesting papers published in the previous 12 months or so.

I hope it is useful to others who are looking for lists of papers to read, for student selections or for anything else.

Papers for MD9A8 &#8211; 2025 edition

Reading about someone else’s recovery-after-injury story can be a bit dull. At least that was my conclusion after pressing delete on my story a moment ago. Having spared you the details, the summary is: I got injured. It hurt. It took me a year to recover because I didn’t tackle the recovery properly.

You Better Run: recovering from injury

We have a new paper out! I am a bit late with this post, since the accepted version went online in December 2020, and the final version appeared a few weeks ago. It will shortly appear in a finished issue of the journal so I can tell myself that I am not too late yet. What’s it about? A complex of TACC3-chTOG-clathrin-GTSE1 is important for stabilising the mitotic spindle during cell division.

Keep A Knockin: new paper using knock-in technology

It’s getting towards the end of the year so it is time to assemble a list of my favourite albums released in 2024. I have sporadically posted lists like this in the past. These twenty albums were the ones I liked the most (and the ones that I thought other people might like to hear). The Lemon Twigs – A Dream Is All We Know   Genre: Power pop | [link]  My favourite record of this year.

What&#8217;s In The Box: Albums of 2024

With the fervour of someone with an n = 1 positive experience, I thought I’d write about what I learned from a recent writing retreat. My University organises one-day events to encourage writing. They’re on-campus, in the neutral territory of the Library, so perhaps calling them “writing retreats” is a little far-fetched. Nonetheless, the idea is to provide a time and space for people to achieve some writing.

Retreat To Nowhere: notes on a writing retreat

The IQ Block game is a puzzle where the player must fit eight shapes into a square space. The challenge is to find as many ways as possible to do it. The box says there are

 more than 40 solutions!

So how many are there? I wrote a solver to crack the IQ Block game. The code is available here and a detailed description is at the end of the post. The solver found 264 solutions from 33 placements.

Crackerblocks: computing solutions for IQ Block game

One of the joys of posting a preprint is seeing that people are viewing, downloading and (hopefully) reading your paper. On bioRxiv you can check out the statistics for your paper in the metrics tab. We posted a preprint recently and it clocked up over 1,000 views in the first day or so. This made me wonder: is that a lot of views or not? How does it compare to other preprints in our category?

Exploding, Impacting: looking at bioRxiv preprint view dynamics with R

I jumped ship from Twitter following the Musk takeover in 2022. Seeking an alternative, I joined Mastodon and didn’t look back. Since then, I’ve enjoyed many wonderful interactions and conversations; and I feel a bit sad at what Twitter turned into.

Exodus: moving to Mastodon

It is an annual event on

 quantixed

to post the papers I have selected for MD997 Frontier Techniques and Research Skills in Biomedicine. Previous selections are grouped here. The deal is that each student picks a paper from the list and then uses it to write a “grant application” for a research project. They also present the paper to the class and finally we do a grant panel where projects are scored!

Methods papers for MD997 – 2021 Edition

One of the best features of Strava is the battle to be King (or Queen) of the Mountain. Originally, in cycling, segments were typically climbs or difficult sections of road, and the simple idea, is who can complete the segment in the quickest time. Hence they would be KOM/QOM, King or Queen of the Mountain. Segments quickly expanded to pretty much any section of a course and to include running segments, to separate them from cycling.

King of the Mountain: using R to bag a Strava KOM

I wrote previously about how to archive a Slack workspace. Well, now Slack announced a new policy, effective from August 26th, 2024. Under the new policy, messages and files older than one year in workspaces on the free tier will be

 deleted

. This is in addition to the 90 day limit for viewing content in the workspace. This causes a problem with the solution I outlined previously.

Slacker II: archiving information from a Slack workspace

Previously, I took advantage of a dataset that linked preprints to their published counterparts to look at the fraction of papers in a journal that are preprinted. This linkage can be used to answer other interesting questions. Such as:

 when do authors preprint their papers relative to submission?

And does this differ by journal? There’s a bit of preamble. If you just want to know the answer, click here.

Prehistoric: when do authors preprint their papers?

What’s the best way to make a movie file from microscopy data? Maybe you need to generate a movie for the supplementary info for a paper, or insert one into your electronic lab notebook, or to show in a talk. The problem is that the requirements for each of those is different. This situation is compounded by the fact that there are so many options to make movie files and not much guidance on what is the best method.

Monster Movie: making movie files from microscopy data

This is a rather niche post, but the method can likely be adapted for other use cases. In the lab we have many different cell lines stored in liquid nitrogen. The arrangement is: the vials are in specific positions in a box (10 x 10) there are 13 boxes to a cane we have 5 canes  Ideally, to retrieve the correct vial from the cell store requires a map.

Bird&#8217;s Eye View: using R to generate inventory maps for lab reagents

It is time for my annual post of the papers I selected for a module that I teach (MD9A8, the module formerly known as MD997). Previous selections are grouped here or here.

 The list serves as a snapshot of interesting papers published in the previous 12 months or so.

I hope it is useful to others who are looking for lists of papers to read, for student selections or for anything else.

Papers for MD9A8 – 2024 edition

I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution   The Uniprot IDs can be converted – using the ID Mapping Tool on the Uniprot website – into any number of other IDs.

Tips from the Blog XVI: getting FASTA sequences

2023 has been a great year in running for me. Previous running round-ups are here (2022, 2021).  My two main goals for 2023 were to run 3000 km and also to run 50 HM-or-more distance runs. I managed both with a couple of weeks left. I also bagged new PBs for 5K, 10K and half marathon as well as a handful of segments on Strava. I won no races but I did win two little running competitions at work.

Running Around: 2023 running dataviz in R

What does the life cycle of a scientific paper look like? It stands to reason that after a paper is published, people download and read the paper and then if it generates sufficient interest, it will begin to be cited. At some point these citations will peak and the interest will die away as the work gets superseded or the field moves on. So each paper has a useful lifespan.

Sure To Fall

Bands have been known to declare “No Synths!” on their albums. This statement was a badge of pride indicating that the artists hadn’t used any modern trickery in their recordings. Today, the growing use of artificial intelligence (AI) and large language models (LLMs) in science has created a similar scenario. Advocates argue that these tools improve every aspect of science, including the publication process.

No Synths! Use of AI in scientific publications

In the spirit of “if it took you a while to find out how to do something, write about it”, I will detail a method to approximate the surface area of a 3D shape. Our application here was finding the surface area of a cell but it can be used on any shape. We start with a 3D point set, specified by points of interest in a single cell imaged by 3D confocal microscopy.

Airy Area: approximating surface area of a cell from a 3D point set

In a previous post, I looked at how Google Scholar ranks co-authors. While I had the data available I wondered whether paper authorship could be used in other ways. A few months back, John Cook posted about using Jaccard index and jazz albums. The idea is to look at the players on two jazz albums and examine the overlap.

All The Right Friends II: clustering papers using Google Scholar data

We have a new paper out describing how vesicles move inside cells. The paper in a nutshell  In science-speak   We analysed how small vesicles are transported in cells. In contrast to large vesicles and organelles, which move using motors inside cells, our analysis revealed that passive diffusion is the main mode of small vesicle transport. In normal language   Inside cells, molecules are moved in tiny transport packets called vesicles.

Crosstown Traffic: new paper on vesicle transport

On a scientist’s Google Scholar page, there is a list of co-authors in the sidebar. I’ve often wondered how Google determines in what order these co-authors appear. The list of co-authors on a primary author’s page is not exhaustive. It only lists co-authors who also have a Google Scholar profile. They also have to be suggested to the primary author and they need to accept the co-author to list them on the page.

All The Right Friends: how does Google Scholar rank co-authors?

One of several features that Strava put behind a paywall was the ability to compare performance on similar courses. I miss this comparison tool and wondered how hard it would be to code my own. This post is a walkthrough of how I approached the problem. The code is available here. It uses the trackeR library in R to convert the GPX tracks to a huge dataframe. This is then processed by IgorPro.

Cluster One: comparing running performance on similar courses

Hopefully I will soon break out of this funk of posting about either Mastodon or Twitter. But not yet! This post is to say that:

 I made a static archive of tweets for @quantixed and for @clathrin.

There, you can read all my posts, which ended in 2022. Edit: removed the archives in October 2024. How did I do it and why? I made the archive with this excellent tool written by Darius Kazemi.

Like I Said: archive of tweets

I migrated my personal Mastodon account from mastodon.social to biologists.social recently. If you’d like to do the same, I found this guide very useful. Note that, once you move, all your previous posts are left behind on the old instance. Before I migrated, I downloaded all of my data from the old instance. I thought I’d take a look at what I had posted to see if anything was worth reposting on biologists.social.

Mr. Mastodon Farm: analysing a mastodon ActivityPub outbox.json file

We have an analysis routine for proteomics data written for IgorPro. One output is a

 volcano plot

. These plots show the fold change in one sample compared to another and plot that against a p-value to estimate how reproducible any changes observed are. This post is not about that software, but on the topic of

 how we can recreate this plot in R

. What steps need to be considered?

Step By Step: recreating a volcano plot in R

I’ve posted in the past about analysing race results in R (most recently here). I ran the 2023 MK Marathon and wanted to have a look at the finishing times. The days of race results being made available as a csv or xls for easy analysis seem to be behind us. Instead they tend to be served up on multiple webpages of 50 athletes’ results at a time. Oh no, 29 pages of results and now Download option…. let’s scrape the data!

Pledging My Time VI: scraping and analysis of race results in R

I’m not a big movie person. Nonetheless I have a media library with quite a few films in and I wondered how many “films to see before you die”-type movies I had in the collection, and how many were missing.

 I used R to find the answers.

I’ve described previously how to get a plain text dump of a Plex database using WebTools-NG. I did that for the Movies library of my Plex Media Server.

Yet Another Movie: IMDB Top 250 movies

I like to set up a standardised directory structure for RStudio projects. The idea came from here. In brief, the structure is: Data/ Output/Data/ Output/Plots/ Script/  My typical workflow is therefore to: select File &gt; New Project in RStudio make a new directory and RProj file then use this R script or these shell commands to setup the directories. So far, so good. However, this process is a bit tedious.

Tips From The Blog XIX: initialising a new RStudio project

It’s a New Year and so it is time to post the papers I have selected for a module that I teach on (MD9A8, the module formerly known as MD997). Previous selections are grouped here or here.

 The list serves as a snapshot of interesting papers published in the previous 12 months or so.

I hope it is useful to others who are looking for lists of papers to read, for student selections or for anything else.

Papers for MD9A8 &#8211; 2023 edition

Another post looking at Twitter data in R. It follows this one and this one. I wanted to look again at my tweeting frequency over the 12 years on Twitter, but this time do it in a calendar view. Something like a GitHub commit calendar would be perfect. I have used a library for this in the past.

Twitcher II: tweet frequency and top tweets

Another post about my time on Twitter. I will post the code in a separate post so that the R-bloggers don’t syndicate this one, which is about

 music

. In my time on Twitter I occasionally posted about what I was listening to. I did this with a #NowPlaying hashtag. I wanted to preserve these tweets – and they can all be found below.

Now Playing

At the time of writing, I have essentially left Twitter. It was a fun ride and without going into what’s happening there now, this is a good opportunity to look at my 12 years on the platform. Early in November, I downloaded my data and locked my Twitter account. This gave me all the data I needed. Using R, a few nifty libraries and the tweets.js file that was part of the download, I could gain quite a lot of insight.

Twitcher: tweet frequency over the years

What was the best year in music? OK, I have to be upfront and say that I thought the answer to this would be 1991. Why? Just a hunch. Nevermind, Loveless, Spiderland, Laughing Stock… it was a pretty good year. I thought it would be fun to find out if there really was a golden year in music. It turns out that it wasn’t 1991.

Very Best Years

Here is a fun post about using colour palettes in R. It starts with a computer game…  After a few years of sporadically playing Super Mario World 2 – Yoshi’s Island on the Retropie, I made it to the final level.

Color Bars

During the pandemic, many virtual seminar programmes have popped up. One series, “Motors in Quarantine”, has been very successful. It’s organised by my colleagues Anne Straube, Alex Zwetsloot and Huong Vu.  Anne wanted to know if attendees of the seminar series were a fair representation of the field. We know the geographical location of the seminar attendees, but the challenge was to find a way to examine research activity at a country level.

Represent: geographical breakdown of a virtual seminar series

Here is a summary of the info I gleaned from asking for recommendations for the best human cell line. These were my criteria:  For context, we currently use a number of human cell lines in the lab: HeLa, RPE1, HCT116, SKOV3; as well as many others in the past: HEK293, DLD-1, U2OS. I consider HeLa to be the almost perfect cell line.

Line Up: recommendations for the best human cell line

By 30th September 2022, I had clocked up a total of over 2000 km of running in 2022. This milestone was a good opportunity to look at how I got to this point. The code is shown below. First, we can make a histogram to look at the distance of runs. From this type of plot it’s clear that my runs this year consist of a lot of 4-5 km runs and then a chunk of 21 km plus.

Get Miles: using treemap to visualise running distances

It’s been a while since I posted a breakdown of half marathon times. The last time seems to have been 2018. I decided to give my old code a clean-up and quickly crunched the numbers from the 2022 Kenilworth Half Marathon. First, the results:  Briefly, the code below reads in a csv file of race results downloaded from the provider.

Pledging My Time V: analysing race results in R

I recently made my first R package and was asked how I did it. The answer of course was: I searched, read, and stumbled around until it was done. But having gone through the process I figured it was worthwhile summarising what I did and what I found tricky. First off, there are a ton of resources out there that describe how to go about building a package.

The Package: learning how to build an R package

We have a new paper out! You can read it here. I thought I would write a post on how this paper came to be and also about our first proper experience with preprinting.

 Title of the paper:


 Non-specificity of Pitstop 2 in clathrin-mediated endocytosis.


 In a nutshell:

we show that Pitstop 2, a supposedly selective clathrin inhibitor acts in a non-specific way to inhibit endocytosis.

Into The Great Wide Open

Niche tech tips are the cornerstone of this website, and here is another.

 How to upgrade an iTunes/Music library whilst maintaining the database.

I know everyone streams music these days – hence this is likely a very niche tech tip – but I still maintain a large music database on a server. The data in my library is precious (to me) since it tracks my listening habits over 17 years.

Tips From The Blog XVIII: upgrading a Music/iTunes library

Previously I wrote about latin squares and set a puzzle. We can demonstrate this for an n x n latin square where n = 12  In the above images, the normalised latin square only has 12 different pairs out of a possible 66. The density plot shows the pairings in the lower triangle, grey represents 0. A randomly generated latin square (where all rows and all columns feature 1 to 12 exactly once) is shown where all possible pairs are captured.

Latin Quarter II: Colours and Latin Squares

A comment from a referee led me to find a method to describe curvature of membranes. This is a quick write-up of our solution. I couldn’t find a solution readily available in Fiji, so I created one using a combination of Fiji for tracing the curvature and IgorPro to do the fitting. If there is any interest I can convert this code into an all-Fiji routine. The code is simple and a gist is available here.

In Circles: fitting a circle to a curve

As a project idea for a young engineer we wanted to build a

 Raspberry Pi-based Weather Station

. Our last attempt at building something – a sound-responsive LED display – was a failure. So it was important to build something

 really easy

to help us get back on track. Here are some notes. We essentially followed this guide from Adafruit which links out to this guide for the CircuitPython part.

Weather Report: building a weather station

I read about aesthetic uses of Latin Squares on John Cook’s site a few months ago. Since I maintain a resource to use colour tables in Igor Pro, I thought it would be fun to use Latin Squares to display colour tables for easy visualisation. Briefly, I wrote some code to generate a 9 x 9 latin square and assigned the values 1 – 9 to a colour table wave. The results were nice.

Latin Quarter: Colours and Latin Squares

When preparing images for publication, it is good practice to check how accessible they are for colour blind people. Using a simple bit of code, it is possible to check an image – or a whole figure – in ImageJ for accessibility. For example, Figure 1 from our recent paper. Originally looked like this:  Using the script we can see how it appears to people with different types of colour blindness.

Colorblind: Checking figure accessibility for colour blind people

I recently finished

 An Essay on Science and Narcissism

by Bruno Lemaitre. I found this book really insightful and thought I would write some notes about it here. The book was published in 2016 although I only just got around to reading it. You can grab a copy for free here.

My Blank Pages VII: An Essay on Science and Narcissism

Generating movie files for publication can be a bit tricky. We have a protocol for making them for microscopy data, which simplifies things. However, we recently got this question from a journal:  How can we do this? What information is needed for movie files?

Tips From The Blog XVII: determining playback speed of a video

We have a new paper out. It’s about how chromosomes get shared during cell division. The paper in a nutshell  In science-speak   Misaligned chromosomes outside the exclusion zone become *ensheathed *in multiple layers of endomembranes. This event consigns the chromosome to missegregation and generates a micronucleus. In normal language   Cells can make mistakes when they divide.

Alignment Zone: new paper on chromosome missegregation

I found this great puzzle hidden in an app aimed at children. Skip to the solution. If you want to work it out, don’t scroll down! Some blurb as a digression so that you don’t see the solution immediately   The funny thing about this puzzle was that it was far too difficult for a child’s game.

Puzzles Like You: Lightbulb puzzle

A colleague said to me “Everyone is running on fumes with Easter being so late this year.”  Really? Is it late? I admit to being completely perplexed by this religious date and its movement around the calendar. I always feel like I am the last to know when it is, let alone whether it is early or late.  Let’s have a look at what constitutes an early or a late Easter. The data are available here.  This is a quick post with no code example (sorry).

Easter Everywhere: when is Easter Sunday?

I run two pi-holes on my home network (details here). The older of the two was in need of a refresh. Here are some notes on how I did a reinstall. For those that don’t know, a pi-hole is a simple ad-blocking solution. You can donate to the project here. Problem   The pi-hole itself can be easily updated over ssh using pihole -up however the OS also needs occasional updating for security.

Fixing a hole: reinstalling pi-hole

It is an annual event on

 quantixed

to post the papers I have selected for what is now called MD9A8 (the module formerly known as MD997 Frontier Techniques and Research Skills in Biomedicine). Previous selections are grouped here.

Papers for MD9A8 – 2022 edition

A quick post about a puzzle called Wordle that is currently taking over the internet. It’s a mastermind-like game where the object is to guess an unknown 5-letter word. Puzzlers are encouraged to share their results after completing a puzzle. Here is an example for puzzle 192. So how do you know if your performance on today’s puzzle was any good? Why not benchmark your effort against the crowd?

Wordless Song: Benchmarking Wordle performance using R

This recent tweet made me chuckle. It does seem that many structural biology papers have a title that begins “The structural basis of…”. I took a quick PubMed survey to look at its popularity. First a search of "structural basis"[ti] AND "journal article"[pt] gives us the number of research papers with “structural basis” in the title. This plot of the number of papers with this title each year is levelling off.

Untitled: “The structural basis of…” titles for structural  biology papers

Every publication is assembling year-end lists of their selection of the best albums of the year. Well,

 quantixed

did not want to miss out on the fun, so I came up with a list of my favourite 20 albums released in 2021.

What’s in the Box: Albums of 2021

A colleague sent me a coding challenge. This is a short post to describe how I tackled it.  Edit: a follow-up post is here. This is the challenge:  With an eye on b, and since I code fastest in Igor, I went with Igor over python or R. I knew this would lose me major points for c since Igor code is not very compact. It took me 22 minutes to write a solution, slowed down a bit by helping a small person with their homework.

Seles: Tennis coding challenge

Some journals sound like they should be bands. Whereas some journal titles ARE in fact the same as band names. I wondered… how many journal titles are also band names. Let’s find out! The journals cited in PubMed could be downloaded as a text file from here. This list includes every MEDLINE journal – even defunct ones – as well as non-MEDLINE journals where content is is in PMC. This will do for now, but is obviously limited.

Under The Same Name: Journal titles and band names

We have a new paper out! This post is to describe what our paper is about. The paper is free to read, so please take a look if you are interested. Gabrielle Larocque, Daniel J. Moore, Méghane Sittewelle, Cansu Kuey, Joseph H.R. Hetmanski, Penelope J. La-Borde, Beverley J. Wilson, Nicholas I. Clarke, Patrick T. Caswell &amp;

Culture Move: new paper on integrin recycling and cell migration

There are perennial topics of discussion on Science Twitter. An example of this is: should figures be at the end of a manuscript are interspersed in the text. These topics tend not to be resolved because there are strong arguments (and personal preferences) on each side. I am not sure whether it is even possible to get people to agree with you using reasoned argument on Twitter.

Voice Your Opinion: naming your lab

Back in 2015, I wrote a guide to using Trello for lab organisation. I figured it was time for an update because a few things have changed since then and the topic of using Trello for larger labs came up on Twitter. Note that other kanban-style software is available. Basic Trello setup   I set up a lab workspace and invited everyone in the team to it. We have three main boards (described below) that everyone in the workspace can see.

Trellisaze II: Updated guide to using Trello in the lab

PhD students sometimes get the same bad advice on writing their thesis. I call this advice the

 Rule of Three

. Typically, they get told that their thesis: Will take 3 months to write Should have 3 results chapters Should be 300 pages These bits of advice have one thing in common: they are all wrong. If you have been organised (see below), it should not take 3 months to write a PhD thesis.

Rule of Three: advice on writing a PhD thesis

As part of the series on development of early career researchers in the lab, we spent a session (with homework) to learn how to write a document in LaTeX. Like the R session, we spent an hour or so in a room with laptops writing a document and then homework was set, to be completed for the following week. There’s a mix of TeX abilities in the lab.

Get Better: LaTeX and Overleaf

As part of the series on development of early career researchers in the lab, we spent three sessions over three weeks learning the basics of R.  In my book “The Digital Cell”, I advocate R as the main number-crunching software but the R literacy in my lab is actually quite mixed. In order to know how to pitch the training, I conducted a quick poll in our lab Slack workspace to find out what R skills people in the lab already had.

Get Better: R for absolute beginners

I thought I would start add a blog to our lab website. The plan is to update maybe once a week with content that is too long for twitter but doesn’t fit in the categories on the lab website. I’m thinking extra analysis, paper commentaries, outreach activities etc. Let’s see how it goes.  First up: how do you count the number of words or characters in a text file?  Microsoft Word has a nice feature for doing this, but poor old TextEdit does not.

Counting backwards

Part of a series on the development of Early Career Researchers in the lab. The idea for the CV clinic came from the lab themselves. We had previously had a session on creating a research profile and a large part of that session was spent looking at CVs. We scrutinised some anonymised CVs and suggested improvements to them. From this, the idea came to put everyone’s CVs through the same treatment!

Get Better: CV Clinic

How can we contribute to the development of early career researchers in a lab environment? I’m talking about how people in the lab acquire “soft skills” or “get better” in ways that are parallel to doing research. This sort of training can get overlooked in the chase for new results and the excitement of doing biomedical research. I’m testing out a strategy to develop the skills of people in the lab. It’s an experiment.

Get Better: early career researcher development

I run a Masters module called MD997. Over six weeks, students have to write a grant proposal and then assess their peers’ proposals at a mock grant panel. Each student bases their proposal on a paper. They present that paper to the class and then they write their proposal using the paper as a springboard. I refreshed my paper list this year to consist of solely papers published (or posted on bioRxiv) in 2019. The previous list is here.

Methods papers for MD997 – 2020 edition

I wrote a short opinion piece for the December Newsletter for the American Society for Cell Biology (ASCB). The content is reproduced below, or you can read the newsletter version here on page 14 of the PDF.

The theme of this year’s ASCB|EMBO Meeting is Cell Biology for the 21st Century. So what skills are essential for a cell biologist to master in the 21st century?

Modern Cell Biology Is Computational

This is a follow up to a previous post. Despite what the title says, it is what we wanted. Our paper on dongles has just been published in Journal of Cell Science. The previous post on

 quantixed

, explained all about the paper and the background to it. The journal featured our paper as a research highlight and they also interviewed first author, Cansu Küey.

Not What You Want II

I have been running a pi-hole to block ads on my home network for a while. It’s great! Not only are ads blocked, but it speeds up internet browsing because… the ads do not load. I wondered if it would be possible to use a pi-hole to make a child-safe internet experience to protect the little people in the house. Sure, there are ways to do this in most routers but they are not ideal.

Child’s Play: pi-hole set up for a safer internet

A while back I visited

 Artistes &amp; Robots

in Paris. Part of the exhibition was on the origins of computer-based art. Nowadays this is referred to as

 generative art

, where computers generate artwork according to rules specified by the programmer.

Turn A Square: generative aRt

Garmin Connect has a number of plots built in, but to take a deeper dive into all your fitness data, you need to export a CSV and fire up R. This post is a quick guide to some possibilities for running data.  There’s a few things that I wanted to look at. For example, how does my speed change through the year? How does that compare to previous years? If I see some trends, is that the same for short runs and long runs?

Garmonbozia: Using R to look at Garmin CSV data

We have a new preprint out – it is a cautionary tale about using GFP nanobodies in cells. This short post gives a bit of background to the work. Please read the paper if you are interested in using GFP nanobodies in cells, you can find it here.

 Paper in a nutshell:

Caution is needed when using GFP nanobodies because they can inhibit their target protein in cells.

Not What You Want: our new paper on a side effect of GFP nanobodies

Our lab is international. People born all over the world have come to work in my group. I’m proud of this fact, especially in the current political climate. I’ve previously used the GoogleMaps API to display a heat map on our lab webpage. It shows where in the world people in the lab come from. This was OK, but I wanted to get an R based solution to make this graphic to make it easier to automate updates.

All Around The World: Maps and Flags in R

I read this recent paper about very highly cited papers and science funding in the UK. The paper itself was not very good, but the dataset which underlies the paper is something to behold, as I’ll explain below. The idea behind the paper was to examine very highly cited papers in biomedicine with a connection to the UK. Have those authors been successful in getting funding from MRC, Wellcome Trust or NIHR?

One With The Freaks – very highly cited papers in biology

I really dislike being asked “how big is your lab?”. The question usually arises at scientific meetings when you are chatting to someone during a break. Small talk can lead to some banal questions being asked, and that’s fine, but when this question is asked seriously, the person asking really just wants to compare themselves to you in some way.

Small Talk: How big is your lab?

This is the first post at

 quantixed

about Raspberry Pi computing. Pi Zero is a minimalist Raspberry Pi that can be coupled to a camera. With this little rig, you can make time-lapse footage amongst other things. I’ve set up a couple of these now. One was to make a time-lapse movie of some plants growing through a plastic maze. The results were pretty good and I thought I’d upload the video and a brief how-to guide.

Experiment Zero: Using a Raspberry Pi Zero camera

I’ve been following the tweets from an account called Albums You Must Hear @Albums2Hear. Each tweet is an album recommended by the account owner. I’m a sucker for lists of Albums That I Must Hear Before I Die since I’m always interested in new (or not so new) music recommendations.

Til I Die: Seeking new music

It’s getting towards the end of the year so it is time to assemble a list of my favourite albums released in 2023. I have sporadically posted lists in the past e.g. here.

What&#8217;s In The Box: Albums of 2023

We have a new paper out. It’s not exactly news, because the paper has been up on bioRxiv since December 2016 and hasn’t changed too much. All of the work was done by Nick Clarke when he was a PhD student in the lab. This post is to explain our new paper to a general audience.

Ferrous: new paper on FerriTagging proteins in cells

This post has been in my drafts folder for a while. With the World Cup here, it’s time to post it! It’s a rule that a 3D assembly of hexagons must have at least twelve pentagons in order to be a closed polyhedral shape. This post takes a look at why this is true. First, some examples from nature. The stinkhorn fungus

 Clathrus ruber

, has a largely hexagonal layout, with pentagons inserted.

Pentagrammarspin: why twelve pentagons?

This deserved a bit of further explanation, due to the stupidity involved. My code was giving an unexpected result and I was having a hard time figuring out the problem. The unexpected result was that a resampled set of 2D coordinates were not being rotated randomly. I was fortunate to be able to see this otherwise I would have never found this bug and probably would’ve propagated the error to other code projects.

Adventures in Code VI: debugging and silly mistakes

I read about Antonio Sánchez Chinchón’s clever approach to use the Travelling Salesperson algorithm to generate some math-art in R. The follow up was even nicer in my opinion, Pencil Scribbles. The subject was Boris Karloff as the monster in Frankenstein. I was interested in running the code (available here and here), so I thought I’d run it on a famous scientist.

Frankly, Mr. Shankly

So

 quantixed

occasionally gets correspondence from other researchers asking for advice. A recent email came from someone who had been “scooped”. What should they do? Before we get into this topic we have to define what we mean by being scooped. You were working on something that someone else was also working on – maybe you knew about this or not and vice versa – but they got their work out before you did.

Scoop: some practical advice

Many projects in the lab involve quantifying circular objects. Microtubules, vesicles and so on are approximately circular in cross section. This quick post is about how to find the diameter of these objects using a computer. So how do you measure the diameter of an object that is approximately circular? Well, if it was circular you would measure the distance from one edge to the other, crossing the centre of the object.

Esoteric Circle

I have just finished reading this excellent book,

 Statistics done wrong: a woefully complete guide

by

 Alex Reinhart

. I’d recommend it to anyone interested in quantitative biology and particularly to PhD students starting out in biomedical science.

My Blank Pages II: Statistics Done Wrong

Back in 2014, I posted an analysis of the time my lab takes to publish our work. This post is very popular. Probably because it looks at the total time it takes us to publish our work. It was time for an update. Here is the latest version.

Some Things Last A Long Time II

To validate our analyses, I’ve been using randomisation to show that the results we see would not arise due to chance. For example, the location of pixels in an image can be randomised and the analysis rerun to see if – for example – there is still colocalisation. A recent task meant randomising live cell movies in the

 time dimension

, where two channels were being correlated with one another.

The Second Arrangement

In the UK there is an advertising disclaimer that “the value of your investments may go down as well as up.” Since papers are our main commodity in science and citations are something of a return, surely the “value” of a published paper only ever increases over time. Doesn’t it?  I think this is true when citations to a paper are tracked at a conventional database (Web of Science for example). Citations are added and very rarely taken away.