Running a marathon is a big deal. It takes a lot of time to train to run a good time, and it takes a while to recover. So, if you’re chasing a marathon PB (personal best) time, you need to choose which Marathon to target wisely. How can we use data to help our decision?

Running a marathon is a big deal. It takes a lot of time to train to run a good time, and it takes a while to recover. So, if you’re chasing a marathon PB (personal best) time, you need to choose which Marathon to target wisely.

 How can we use data to help our decision?

Let’s use R to find out! For the impatient: just show me the marathon data!

Choose Your Fighter: data-driven selection of the best marathon

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.

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

In this post I’ll use R to recap my running data from 2025. Previous round-ups are here (2021, 2022, 2023, not sure why I didn’t post one for 2024…). I had a goal of running a total distance of 3650 km in 2025.

In this post I’ll use R to recap my running data from 2025. Previous round-ups are here (2021, 2022, 2023, not sure why I didn’t post one for 2024…).  I had a goal of running a total distance of 3650 km in 2025. In truth, after running 3500 km in 2024, I decided to aim for less (3000 km), but around springtime, I realised that I was at a similar total to the same point in 2024 and decided to increase the goal.

Running Around: 2025 running dataviz in R

In my previous post, I shared my annual running stats which were generated in R using summary data from Garmin Connect. The code I use to generate these summaries was beginning to get a bit unwieldy, so I have now rebased it into a package.

In my previous post, I shared my annual running stats which were generated in R using summary data from Garmin Connect. The code I use to generate these summaries was beginning to get a bit unwieldy, so I have now rebased it into a package. GarminCSVr – is an R package to look at running data using the activity summaries that can be downloaded from the Garmin Connect website.

Running Around: an R package to analyse Garmin running data

Here we go again! I ran the Mainova Frankfurt Marathon 2025 and wanted to look at the race results. How can we do this using R? I couldn’t see an easy way to download the data, so I used R to scrape them.

Here we go again! I ran the Mainova Frankfurt Marathon 2025 and wanted to look at the race results. How can we do this using R?  I couldn’t see an easy way to download the data, so I used R to scrape them. Note that these times are currently provisional, but they give us a good idea of what happened. The results are available with a search function to find an individual’s results.

Pledging My Time VII

It’s 2026 and so it’s time for another edition of “the papers I selected for a module that I teach”. Previous selections are here (2025, 2024, 2023, 2022). The list serves as a snapshot of interesting papers published in the previous 12 months or so. I hope it’s useful to others who are looking for lists […]

It’s 2026 and so it’s time for another edition of “the papers I selected for a module that I teach”. Previous selections are here (2025, 2024, 2023, 2022).

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

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

Papers for MD9A8 &#8211; 2026 edition

The Green Leek 10.5 km run is a mixed terrain race now in its third year. Today’s was a wet and muddy edition. The chip times were posted this afternoon and using my previous code, I took a look at the results.

The Green Leek 10.5 km run is a mixed terrain race now in its third year. Today’s was a wet and muddy edition. The chip times were posted this afternoon and using my previous code, I took a look at the results. I was a bit disappointed with my time, which was about 24 s slower than last year. Considering that I’m running faster this year than last, I wondered whether the conditions affected my time.

Pledging My Time IV

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.

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

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.

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

Here’s a conundrum. When posting a new preprint, we typically have to juggle up to three DOIs (for the preprint, the code, and the data). How can we cross reference these DOIs?

Here’s a conundrum. When posting a new preprint, we typically have to juggle up to three DOIs (for the preprint, the code, and the data). How can we cross reference these DOIs? The problem

 The preprint

– The manuscript gets deposited to bioRxiv. It takes around 24 h to clear screening and is then assigned a DOI.

 The code

– The code is maintained on GitHub and can be archived at zenodo to get a DOI.

Circlesquare: juggling DOIs when preprinting

If you are into running, chances are that you will be chasing your PB (personal best) times. This post is about using R to search for your PBs, and to monitor them over time. Usually runners target four distances for PBs: 5 km, 10 km, half marathon and full marathon.

If you are into running, chances are that you will be chasing your PB (personal best) times. This post is about using R to search for your PBs, and to monitor them over time. Usually runners target four distances for PBs: 5 km, 10 km, half marathon and full marathon. It’s likely that a PB will come in a race of exactly that distance, but not necessarily. For example, you can hit a 5K PB during a 10K race.

A Pace Far Different: finding best running pace with R

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.

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 saw a fun video on YouTube recently in which some runners attempted to do two parkruns in one day. I don’t mean run the same parkrun course twice, I mean they ran one parkrun at one course and then drove to a different course and ran that one too.

I saw a fun video on YouTube recently in which some runners attempted to do two parkruns in one day. I don’t mean run the same parkrun course twice, I mean they ran one parkrun at one course and then drove to a different course and ran that one too. The challenge was to do both parkruns

 and

beat the last person (the tail walker) on the second course to the finish line.

Close To Me: finding close parkruns

I’ve dabbled a bit with napari – the python-based image viewer – but never needed to use it seriously. I had a real use case so I thought I’d write up the process of how I got going with napari, in case it helps others.

I’ve dabbled a bit with napari – the python-based image viewer – but never needed to use it seriously. I had a real use case so I thought I’d write up the process of how I got going with napari, in case it helps others. My use case   I wanted to overlay tracks onto microscopy images and export them as a movie.

Adventures in Code VII: getting started with napari

I’m a music fan who is anti-streaming and instead I stubbornly maintain a large music collection. At this time of year, streamers receive a round-up of their year’s listening in a “wrapped” report.

I’m a music fan who is anti-streaming and instead I stubbornly maintain a large music collection. At this time of year, streamers receive a round-up of their year’s listening in a “wrapped” report. Not wanting to miss out, I set about rendering my own annual round-up using R!  If you’d like to see a pick of my favourite albums of 2025, jump here. If you’re here for the R coding, read on!  I am aware that that the audience for this post is small.

What&#8217;s In The Box: Wrapped but not streamed 2025

It’s plot recreation time! In this post, we’ll look at how we can recreate a plot in R. I thought it might be useful to provide the solution but also to detail the process I went through to get there.

It’s plot recreation time! In this post, we’ll look at how we can recreate a plot in R. I thought it might be useful to provide the solution but also to detail the process I went through to get there. We have a FACS plot taken from a BD FACS Aria machine:  Briefly, it’s a histogram of the fluorescence levels of 10000 cells from three different sources.

Let It Flow: recreating a FACS plot with ggplot

The software that we use to do our work is our academic software stack. I often see requests for advice on which software works well. Since recommendations from labs that have road-tested a few options are quite valuable, I thought I would document what we’re currently using and why.

The software that we use to do our work is our

 academic software stack

. I often see requests for advice on which software works well. Since recommendations from labs that have road-tested a few options are quite valuable, I thought I would document what we’re currently using and why. I have tried to note if we’ve switched, tried alternatives and if we’re happy. The lab is Mac-based and we prefer FOSS solutions.

Stacked Up: my academic software stack

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.

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

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.

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

Giving effective feedback is a skill that, like any other, needs to be honed. I wouldn’t claim to be an expert but there are methods in how to give feedback that means that your guidance is more likely to help the person improve. Giving feedback to colleagues on grant applications is particularly tricky.

Giving effective feedback is a skill that, like any other, needs to be honed. I wouldn’t claim to be an expert but there are methods in how to give feedback that means that your guidance is more likely to help the person improve. Giving feedback to colleagues on grant applications is particularly tricky. It’s partly the high stakes involved: people’s livelihoods can be at stake and applicants’ best ideas are laid bare, so care is needed.

Feedback Deficiency: the tricky art of effective peer feedback

Answering the question of what fraction of a journal’s papers were previously available as a preprint is quite difficult to do. The tricky part is matching preprints (from a number of different servers) with the published output from a journal.

Pre Self: what fraction of a journal&#8217;s papers are preprinted?

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?

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

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?

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?

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 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.

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.

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

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.

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

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.

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

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 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 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

There’s plenty of guides to getting going on Mastodon, aimed at people leaving Twitter.

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

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!

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

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.

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

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: Ideally, to retrieve the correct vial from the cell store requires a map.

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

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.

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

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.

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

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.

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

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.

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.

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

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

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.

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?

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.

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

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.

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.

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 like to set up a standardised directory structure for RStudio projects. The idea came from here. In brief, the structure is: My typical workflow is therefore to: So far, so good. However, this process is a bit tedious.

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

I have long admired albums2hear, a Twitter bot that posts albums. You can read a bit more about it here. There was no mastodon equivalent and so I decided to build one. You can follow the bot – currently called Albums Albums Albums (or AlbumsX3) – here.

I have long admired albums2hear, a Twitter bot that posts albums. You can read a bit more about it here. There was no mastodon equivalent and so I decided to build one. You can follow the bot – currently called Albums Albums Albums (or AlbumsX3) – here. Idea behind the bot   The idea is to periodically post an album.

Probot: building a Mastodon bot

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. A handy one-liner might be something like (taken from here): This converts all the flac files in subfolders into mp3 files.

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

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.

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

2022 was my best year for running to date. In 2021, my goal was to run 2021 km. For 2022, I wanted to see if I could run 2500 km and also to run 50 HM-or-more distance runs.

2022 was my best year for running to date. In 2021, my goal was to run 2021 km. For 2022, I wanted to see if I could run 2500 km and also to run 50 HM-or-more distance runs. I managed both and ended the year on a total of 2734 km. I also bagged two PBs for half marathon. Of course, if you subscribe to Strava or VeloViewer or whatever, you can get a nice data visualisation of your year in running.

Running Around: 2022 running dataviz in R

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.

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

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.

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

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?

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

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?

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

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.

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.

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.

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

Sometimes an update causes a chain reaction which borks a system. Here are some notes on how I fixed a SMTP mail issue on my Raspberry Pi camera project.

Sometimes an update causes a chain reaction which borks a system. Here are some notes on how I fixed a SMTP mail issue on my Raspberry Pi camera project. A quick recap: the RPi camera takes pictures every ten minutes, each night the images get sent to a server and each week the transferred images get deleted.

I’ve Gotta Get A Message To You III: fixing SMTP on Raspberry Pi

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.

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.

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

A short post to announce TrackMateR, a new R package to analyse TrackMate XML outputs. Code Instructions Background TrackMate is a plug-in for ImageJ which ships with Fiji. It’s essential for single particle tracking work, particularly for microscopy movies. For example, tracking the movement of fluorescent vesicles inside cells.

A short post to announce TrackMateR, a new R package to analyse TrackMate XML outputs. CodeInstructions Background   TrackMate is a plug-in for ImageJ which ships with Fiji. It’s essential for single particle tracking work, particularly for microscopy movies. For example, tracking the movement of fluorescent vesicles inside cells. A tracking session generates a TrackMate XML file.

Tracking: announcing new R package TrackMateR

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.

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

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

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.

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 &#8211; 2022 edition

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.

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

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.

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

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.

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

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.

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

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.

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.

quantixed

All Together Now

A Day In The Life

So Long

Counting backwards