Stephen Royle

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

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

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

When a preprint is uploaded to bioRxiv, it undergoes screening before it appears online. How long does it take for Affiliates to screen preprints at bioRxiv?

 tl;dr

I used R to look at bioRxiv screening times. Even though bioRxiv has expanded massively, screening happens quickly (in about 24 h). I am a bioRxiv Affiliate – one of the people who does the screening. Preprints wait in a queue to be screened.

Screenager: screening times at bioRxiv

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

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 At some point these citations will peak and the interest will die away as the work gets superseded or the field moves on.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

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

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?

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

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

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

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

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

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

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

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?

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

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

Hot on the heals of the post on how to downsize microscopy movie files, let’s look at ways to shrink the size of a PDF file. There’s several ways to tackle this – suggestions came from this thread on Mastodon.

 Scenario:

you have created a preprint/manuscript/proposal in PDF format.

Smaller: methods to reduce the size of a PDF file

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

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

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

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

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

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

This is a brief review of macOS Mastodon clients that I’ve tried. It is unashamedly incomplete/non-exhaustive, but since the ones I found online from computing magazines literally look at one app, I am ahead of the pack here!

 tl;dr I prefer Ivory on macOS and prior to that, Mastonaut was OK.

For clarity: I have not been asked or received payment to promote any software. Why use an app on desktop/laptop?

Free Bird II: Mastodon macOS clients

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 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

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 have a long-running Raspberry Pi camera project to capture images of the view from a window (more details here). A recent post on mastodon, which showed a keogram, encouraged me to take my PiCam images and turn them into art. The finished product   This is the finished wall art, printed on canvas. Ready to hang on the wall.

Point Me At The Sky: wall art using Raspberry Pi camera images

There are a few one-liners that I use in the shell to do some really nifty stuff. I struggle to quickly find and reuse these and asked for a solution on Mastodon.

Over and Over: quick ways to reuse handy shell one-liners

There’s plenty of guides to getting going on Mastodon, aimed at people leaving Twitter. I just wanted to post a couple of technical points about making the switch that might be of interest to people who maintain webpages with Twitter content (feeds, embeds). Mastodon status updates (feed/timeline)   Twitter provided a widget that meant that an account’s timeline could be embedded on a website.

Free Bird: moving to Mastodon

Please consider this a “supplementary analysis” to my previous post looking at the frequency of tweets from my personal account over the last 12 years. I was curious about what times I was active on Twitter (measured by when I tweeted). Others might be interested in a solution to look at this in R. The code   As in the previous post, we need to get the data into R and then make sure we have a date object to work with.

Any Time At All: tweet frequency around the clock

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

There are lots of ways for runners and cyclists to analyse training data. A key question most fitness enthusiasts want to know is “how am I doing?”. “How you are doing” is referred to as

 form

. Unsurprisingly, form can be estimated in many ways. One method is using training stress scores (acute training load and chronic training load) to assess form as training stress balance.

Form and File: estimating running form in R

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

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

Slack is a wonderful tool for communicating and organising work in teams. Many academic groups are using the free version (since the pricing is simply incompatible with how we are funded). Slack has had a 10,000 message limit for free tier workspaces for many years but they recently changed it to a 90 day limit. This means any messages older than 90 days will no longer be visible.

Slacker: archiving information from a Slack workspace

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

This is a ultra-short post related to sending email via the command line on Linux/Rasperry Pi.  On 30 May 2022, Google disabled the handy feature that allowed less secure sign in to Google accounts. This feature was a handy way to authenticate command-line routines that send email.

I&#8217;ve Gotta Get A Message To You II: fixing SSMTP gmail authorisation

Previously I wrote about latin squares and set a puzzle. Can we make a latin square where all possible pairs are represented in adjacent squares?

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

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

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

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

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

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: &#8220;The structural basis of&#8230;&#8221; titles for structural  biology papers

I found this great puzzle hidden in an app aimed at children. There are 300 lightbulbs in a row, labelled 1 to 300, each with an on/off switch. We count from 1 to 300 and flick the switches as follows: on “1” all lightbulbs are switched on. On “2” lightbulbs 2, 4, 6, 8 etc.

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?

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&#8217;s in the Box: Albums of 2021

Here is a quick method for checking parity between two directories. Let’s say we have two directories dir1 and dir2. They are large and have thousands of files and subdirectories. How can we check that they have the same contents? I found myself in this situation recently during a server migration.

Tips From The Blog XVI: fast check of two directories

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

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 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

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

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

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 &#8211; 2021 Edition

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

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

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 am giving a talk next week and wanted to update some plots from an old analysis that previously featured on quantixed. The question is: how long does it take for a paper get published? The answer is complex (as previously discussed on quantixed), but we can at least find out using data from PubMed what journals declare as the time from when a paper is received to when it was published. The code is below and can be found here.

Same Time Next Year: crunching PubMed data

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 &#8211; 2020 edition

We have a new paper out! You can access it here. The paper in a nutshell   We have discovered a new class of trafficking vesicle inside cells. These vesicles are very small (30 nm across) and we’ve called them intracellular nanovesicles, or INVs for short. What is a trafficking vesicle? Humans are built from lots of cells.

Tiny Universe: new paper on intracellular nanovesicles

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&#8217;s Play: pi-hole set up for a safer internet

Quaternions are essentially magic. With just four numbers, they can describe the position and orientation of an object in space. For example, the rotation of an object about one axis. Consecutive rotations can also be described by a quaternion.

Rotation: using quaternions in Igor Pro

A while ago, I set up a couple of Raspberry Pi Zero cameras to make long-term time lapse movies. To recap: the idea was to take pictures every ten minutes and turn them into a movie. The process is totally automated so that every day, the photos from each Pi get saved to a server, and then processed into a movie that gradually gets longer and longer. At the end of the week, if the back up went OK, the photos get deleted from the Pi’s SD card.

Calendar: Assessing Raspberry Pi Camera Uptime

This month I spent a lot of time evaluating proposals for BBSRC Committee D. At the same time a number of my colleagues were also preparing BBSRC applications for the next round. A question came up:

 Is it best to put Track Record before Case For Support or vice versa?

If you have no idea what I mean, a brief explanation. The “Case for Support” is a document up to 8 pages which is the meat of a BBSRC Response Mode application.

Notes from a panel: Layout of BBSRC Case for Support

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

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 &#8211; very highly cited papers in biology

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

This week Erick Martins Ratamero and I put up a preprint on vesicle packing. This post is a bit of backstory but please take a look at the paper, it’s very short and simple. The paper started when I wanted to know how many receptors could fit in a clathrin-coated vesicle. Sounds like a simple problem – but it’s actually more complicated.

All That Noise: The vesicle packing problem

A long time ago I posted a little Automator routine to convert Word doc/docx files to PDF. Not long after that, this routine ceased to work due to changes in Microsoft Word (I think). It’s still very useful to convert a whole folder of docx files to PDF in order to avoid Word and just use Preview on the Mac. For committee work or for marking students’ work, I often have a whole folder of docx files and would prefer it if they were in PDF format.

Tips from the blog XI: docx to pdf

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

This post is something of a “how to” guide. The problem is how can you share code with a small team

 and

keep it up-to-date? For ImageJ, the solution is simple. You can make an ImageJ update site and then push any updated code to the user when they startup ImageJ. For IgorPro, there is no equivalent. Typically I send ipf files to someone and they run the code, but I have to resend them whenever there’s an update.

Cloud Eleven: A cloud-based code sharing solution for IgorPro

I’ve previously crunched times for local Half and Full Marathons here on

 quantixed

. Last weekend was the Kenilworth Half Marathon (2018) over a new course. I thought I’d have a look at the distributions of times and paces of the runners. The times are available here. If the Time and Category for finishers are saved as a csv, the script below works to generate the following plots. Aggregated stats for the race are here.

Pledging My Time III

I’d seen the small multiple artwork of running and cycling routes from Marcus Volz’s R package Strava all over the web. Ads for “posters of your GPS tracks” pop up on Reddit and I’d notice a few #Rstats people put up their posters on Twitter. I’ve had the package bookmarked for a while and this week I finally got round to generating a small multiple poster of some of my cycling routes.

Multiplex: Small multiple artwork from GPX tracks

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

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

As a geek, the added bonus of exercise is the fun that you can have with the data you’ve generated. A recent conversation on Twitter about the accuracy of wrist-based HRMs got me thinking… how does a wrist-based HRM compare with a traditional chest-strap HRM? Conventional wisdom says that the chest-strap is more accurate, but my own experience of chest-strap HRMs is that they are a bit unreliable. Time to put it to the test.

Turn That Heartbeat Over Again: comparing wrist and chest-strap HRM

A while back, the lab moved to an electronic lab notebook (details here and here). One of the drivers for this move was the huge number of hard copy lab note books that had accumulated in the lab over &gt;10 years. Switching to an ELN solved this problem for the future, but didn’t make the old lab note books disappear. So the next step was to archive them and free up some space.

Do It Yourself: Lab Notebook Archiving Project

I recently got a new GPS running watch, a Garmin Fēnix 5. As well as tracking runs, cycling and swimming, it does “activity tracking” – number of steps taken in a day, sleep, and so on. The step goals are set to move automatically and I wondered how it worked. With a quick number crunch, the algorithm revealed itself. Read on if you are interested how it works. The watch started out with a step target of 7500 steps in one day.

Measured Steps: Garmin step adjustment algorithm

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

We have a new paper out! This post is to explain what it’s about. Cancer cells often have

 gene fusions

. This happens because the DNA in cancer cells is really messed up. Sometimes, chromosomes can break and get reattached to a different one in a strange way. This means you get a fusion between one gene and another which makes a new gene, called a gene fusion.

Fusion confusion: new paper on FGFR3-TACC3 fusions in cancer

I’ve returned from the American Society for Cell Biology 2016 meeting in San Francisco. Despite being a cell biologist and people from my lab attending this meeting numerous times, this was my first ASCB meeting. The conference was amazing, so much excellent science and so many opportunities to meet up with people.

Come To California

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.

Rollercoaster: ups and downs of Google Scholar citations

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

We have a new paper out! You can access it here.

 The people

This paper really was a team effort. Faye Nixon and Tom Honnor are joint-first authors. Faye did most of the experimental work in the final months of her PhD and Tom came up with the idea for the mathematical modelling and helped to rewrite our analysis method in R. Other people helped in lots of ways.

Parallel lines: new paper on modelling mitotic microtubules in 3D

Previously I wrote about our move to electronic lab notebooks (ELNs). This post contains the technical details to understand how it works for us. You can even replicate our setup if you want to take the plunge.

 Why go electronic?

Many reasons: I wanted to be able to quickly find information in our lab books.

Notes To The Future

BBC 6Music recently went back in time to 1994. This made me wonder what albums released that year were my favourites. As previously described on this blog, I have this information readily available. So I quickly crunched the numbers. I focused on full-length albums and, using play density (sum of all plays divided by number of album tracks) as a metric, I plotted out the Top 20.

Bateman Writes: 1994

I was recently an external examiner for a PhD viva in Cambridge. As we were wrapping up, I asked “if you were to do it all again, what would you do differently?”. It’s one of my stock questions and normally the candidate says “oh I’d do it so much quicker!” or something similar. However, this time I got a surprise. “I would write my thesis in LaTeX!”, was the reply.  As a recent convert to LaTeX I could see where she was coming from.