Stephen Royle

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

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

Earlier this year I set up a bot on Mastodon. The bot, AlbumsX3, posts an album suggestion twice-a-day. Performance has been good. It has only missed a few posts due – I think – to server glitches. However, I have made a couple of tweaks to upgrade the bot since my last post, so I thought I would detail them here. Preventing duplicate posts   In the last post I wrote:  Well, it wasn’t long before I needed to revisit this issue.

Probot 2: upgrading a Mastodon bot

Caution: this post is for nerds only. I watched this numberphile video last night and was fascinated by the point pattern that was created in it. I thought I would quickly program my own version to recreate it and then look at patterns made by more points. I didn’t realise until afterwards that there is actually a web version of the program used in the video here. It is a bit limited though so my code was still worthwhile.

Realm of Chaos

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

I’m a long-term fan of Weezer. Such was the brilliance of their first two albums that I have stuck with them through thick and thin. And dear me, there has been some very thin music. Nonetheless I own every album – thirteen of them. Among them are six albums entitled “Weezer”.  These records are colloquially referred to by the colour of the album. In chronological order: blue, green, red, white, teal and black.

Say It Ain’t So: using Weezer album cover colours in R

For the past 3.5 yrs I’ve been using Unison to sync files between 3 macs. It works great. In fact, since I installed and set up my profiles for syncing, I’ve not needed to change a thing. Until yesterday. I upgraded to El Capitan on each of the 3 macs. I went to run Unison to sync the days work and – an error. -bash: unison: command not found  Oh dear. I looked in the search path and couldn’t find Unison.

Super Unison

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

A quick tech tip. I usually use Audacity for converting audio files and I have a few simple macros set up in there to make life easy. I had some opus music files which do not play in Apple’s Music app and therefore needed converting to MP3 format. Annoyingly, Audacity 3.1.2 on macOS does not currently import opus files, so I needed to find an alternative.  The command line tool ffmpeg can be used to convert audio files. So how can we do it?

Convertible: using ffmpeg to convert audio files

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’s papers are preprinted?

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’s Eye View: using R to generate inventory maps for lab reagents

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

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

More on the theme of “The Digital Cell”: using quantitative, computational approaches in cell biology. So you want to get started? Well, the short version of this post is:

 Programming

I make no claim to be a computer wizard. My first taste of programming was the same as anyone who went to school in the UK in the 1980s: BBC Basic.

The Digital Cell: Getting Started

An occasional series in esoteric programming issues. As part of a larger analysis project I needed to implement a short program to determine the closest distance of two line segments in 3D space. This will be used to sort out which segments to compare… like I say, part of a bigger project. The best method to do this is to find the closest distance one segment is to the other when the other one is represented as an infinite line.

Adventures in code

Last week, ALM (article-level metric) data for PLoS journals were uploaded to Figshare with the invitation to do something cool with it.  Well, it would be rude not to. Actually, I’m one of the few scientists on the planet that hasn’t published a paper with Public Library of Science (PLoS), so I have no personal agenda here. However, I love what PLoS is doing and what it has achieved to disrupt the scientific publishing system.

Six Plus One

Every Song Ever: Twenty Ways to Listen in an Age of Musical Plenty

Ben Ratliff (Farrar, Straus and Giroux) {.alignleft .size-medium .wp-image-756 loading=“lazy” decoding=“async” attachment-id=“756” permalink=“https://quantixed.org/41lkbxvsugl-

 sx329_bo1204203200

/” orig-file=“https://i0.wp.com/quantixed.org/wp-content/uploads/2016/03/41lkbxvsugl-

 sx329_bo1204203200

.jpg?fit=331%2C499&amp;ssl=1”

My Blank Pages IV: Every Song Ever

Note

: this is not a serious blog post. Neil Hall’s think piece in Genome Biology on the Kardashian index (K-index) caused an online storm recently, spawning hashtags and outrage in not-so-equal measure. Despite all the vitriol that headed Neil’s way, very little of it concerned his use of Microsoft Excel to make his plot of Twitter followers vs total citations!

Vitamin K

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

Raw Data: A novel on Life in Science

by

 Pernille Rørth

(Springer, 2016) {.alignleft .size-medium .wp-image-786 loading=“lazy” decoding=“async” attachment-id=“786” permalink=“https://quantixed.org/41txjjrwibl-

 sx328_bo1204203200

/” orig-file=“https://i0.wp.com/quantixed.org/wp-content/uploads/2016/03/41txjjrwibl-

 sx328_bo1204203200

.jpg?fit=330%2C499&amp;ssl=1” orig-size=“330,499”

My Blank Pages V: Raw Data

Fans of probability love random processes. And lotteries are a great example of random number generation. The UK National Lottery ran in one format from 19/11/1994 until 7/10/2015. I was talking to somebody who had played the same set of numbers in all of these lottery draws and I wondered what the net gain or loss has been for them over this period.

Wrote for Luck

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’s In The Box: Albums of 2023

The end of the month sees the Coventry Half Marathon. I looked at what constitutes a good time over this course, based on 2015 results. I thought I’d post this here in case any one is interested.

Pledging My Time

There have been calls for journals to publish the distribution of citations to the papers they publish (1 2 3). The idea is to turn the focus away from just one number – the Journal Impact Factor (JIF) – and to look at all the data. Some journals have responded by publishing the data that underlie the JIF (EMBO J, Peer J, Royal Soc, Nature Chem). It would be great if more journals did this.

The Great Curve II: Citation distributions and reverse engineering the JIF

A few days ago, Retraction Watch published the top ten most-cited retracted papers. I saw this post with a bar chart to visualise these citations. It didn’t quite capture what the effect (if any) a retraction has on citations. I thought I’d quickly plot this out for the number one article on the list.

What Difference Does It Make?

My post on the strange data underlying the new impact factor for eLife was read by many people. Thanks for the interest and for the comments and discussion that followed. I thought I should follow up on some of the issues raised in the post. To recap: eLife received a 2013 Impact Factor despite only publishing 27 papers in the last three months of the census window. Other journals, such as Biology Open did not.

Strange Things – update

This is a quick “how to” post. There is a licensed version of PyMol (MacPyMol) available, but the open source version can be installed on a Mac free of charge. The official page has a guide, which is not terribly detailed, and I found this excellent guide which is unfortunately out-of-date.

Installing open source PyMol on a Mac

I’ve generated a lot of code for IgorPro. Keeping track of it all has got easier since I started using GitHub – even so – I have found myself writing something only to discover that I had previously written the same thing. I was thinking that it would be good to make a list of all functions that I’ve written to locate long lost functions.

Adventures in Code V: making a map of Igor functions

It’s been a while since I did some navel-gazing about who reads this blog and where they come from. This week,

 quantixed

is close to 25K views and there was a burst of people viewing an old post, which made me look again at the visitor statistics.

Where You Come From: blog visitor stats

What is the best music to listen to while writing a manuscript or grant proposal? OK, I know that some people prefer silence and certainly most people hate radio chatter while trying to concentrate. However, if you like listening to music, setting an iPod on shuffle is no good since a track by Napalm Death can jump from the speakers and affect your concentration.

Tips from the Blog I

I recently gave a talk at a retreat for new PIs working at QMUL. My talk was focussed on tips for getting started, i.e. the nitty gritty of running an efficient lab. It was a mix of things I’ve been told, worked out for myself or that I’d learned the hard way. PIs are expected to be able to do lots of things that can be full-time jobs in themselves.

Tips from the Blog V: Advice for New PIs

I was searching for the excitation and emission spectra for mNeonGreen. I was able to find an image, but no values for the spectra.

Green is the Colour: mNeonGreen spectra

I put a recent code snippet put up on the IgorExchange. It’s a simple procedure for averaging a set of 1D waves and putting the results in a new wave. The difference between this code and Average Waves.ipf (which ships with Igor) is that this function takes the average of all points in the wave and places this single value in a new wave. You can specify whether the mean or median is used for the average.

Tips from the blog IV – averaging

2016 was the 400 year anniversary of William Shakespeare’s death. Stratford-upon-Avon Rotary Club held the Shakespeare Marathon on the same weekend. Runners had an option of half or full marathon. There were apparently 3.5 K runners. Only 700 of whom were doing the full marathon. The chip results were uploaded last night and can be found here. Similar to my post on the Coventry Half Marathon, I thought I’d quickly analyse the data.

Pledging My Time II

I saw this great tweet (fairly) recently:  I thought this was such a great explanation of when to submit your paper. It reminded me of a diagram that I sketched out when talking to a student in my lab about a paper we were writing. I was trying to explain why we don’t exaggerate our findings. And conversely why we don’t undersell our results either. I replotted it below:

Middle of the road: pitching your paper

This year #paperOTD (or paper of the day for any readers not on Twitter) did not go well for me. I’ve been busy with lots of things and I’m now reviewing more grants than last year because I am doing more committee work. This means I am finding less time to read one paper per day. Nonetheless I will round up the stats for this year.

A Day In The Life III

I have a long-running project to make timelapse movies using a Raspberry Pi Zero with camera module. I’m capturing a countryside view and have images for two years. The uptime on the Pi is seriously impressive, but nonetheless I wanted to upgrade the Pi so that it would send me updates of how it’s going, so that I would know if it image capture had failed. Here is my solution.

I’ve Gotta Get A Message To You: automated emails from Raspberry Pi zero

The database clinicaltrials.gov is a web resource of clinical trials around the world. It has a REST API that gives access to clinical trial data. There are some resources available to interact with this resource using R, such as rclinicaltrials and ClinicalTrialsAPI. We were interested at looking clinical trials for rare diseases and particularly whether this year, COVID-19 had affected these trials.

All My Trials: Impact of COVID-19 on rare disease clinical trials

This post is about metrics and specifically the H-index. It will probably be the first of several on this topic. I was re-reading a blog post by Alex Bateman on his affection for the H-index as a tool for evaluating up-and-coming scientists.

Blast Off!

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

We have some macros for ImageJ/FIJI for making figures and blind analysis which could be useful to others. I made an ImageJ Update Site so that the latest versions can be pushed out to the people in the lab, but this also gives the opportunity to share our code with the world. Feel free to add the

 quantixed

ImageJ update site to your ImageJ or FIJI installation. Details of how to do that are here.

Adventures in Code III: the quantixed ImageJ Update site

A bit of navel gazing for this post. Since moving the blog to wordpress.com in the summer, it recently accrued 5000 views.

Belly Button Window

When it comes to measuring the impact of our science, citations are pretty much all we have. And not only that but they only say one thing – yeah – with no context. How can we enrich citation data? Much has been written about how and why and whether or not we should use metrics for research assessment.

“Yeah” Is What We Had

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

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

Over the holidays, I had an idea about looping an animation between two images. I wrote some code to do this in Igor Pro (sorry, no R this time…). This post describes how the code works and how you can make a similar animation. There was a reason to do this animation, but as a proof of principle I used two band logos.

Walk This Way

We have a new paper out. The title is

 New tools for ‘hot-wiring’ clathrin-mediated endocytosis with temporal and spatial precision

. You can read it here. Cells have a plasma membrane which is the barrier between the cell’s interior and the outside world. In order to import material from outside, cells have a special process called endocytosis.

Start Me Up: Endocytosis on demand

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?

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

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

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

I was interested in the analysis by Frontiers on the lack of a correlation between the rejection rate of a journal and the “impact” (as measured by the JIF). There’s a nice follow here at Science Open.

Throes of Rejection: No link between rejection rates and impact?

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

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

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

Following on from the last post about publication lag times at cell biology journals, I went ahead and crunched the numbers for all journals in PubMed for one year (2013). Before we dive into the numbers, a couple of points about this kind of information. Some journals “reset the clock” on the received date with manuscripts that are resubmitted. This makes comparisons difficult.

Waiting to happen II: Publication lag times

This is just a quick tip as it took me a little while to sort this out. In the lab we have two QNAP TS-869 Pro NAS devices. Each was set up with a single RAID6 storage pool and I ran them as a primary and replicant via rsync. We recently bought a bigger server and so the plan was to repurpose one of the NAS boxes to be a Time Machine for all the computers in the lab.

Tips from the blog VIII: Time Machine on QNAP NAS

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

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

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

Quantifying the degree of colocalisation of two signals in microscopy images is very tricky. Lots has been written on this topic, including in my book The Digital Cell. The focus of this post is on

 visualising colocalisation

. One way to look at colocalisation is two think about two sets of objects and how many of each set overlap. This is sometimes referred to as

 co-occupancy

or

 object-based colocalisation

.

Line Up: Waffle plots for colocalisation data

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’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

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

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

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

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.

 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 – 2023 edition

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

The scientific response to the COVID-19 pandemic has been astounding. Aside from efforts to generate vaccines, the genomic surveillance of the virus has been truly remarkable. For example, the nextstrain project has sequence many SARS-CoV-2 genomes. In fact, the rapid identification of multiple new strains and mutations by diverse groups of scientists has resulted in a nomenclature crisis.

Os Mutantes: an implausible naming system for SARS-CoV-2 mutants

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

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

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

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

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

I recently did a webinar for ASCB called “From Microscope To Figure”. For posterity, I am re-posting the webinar here with some additional info.

Videotape: From Microscope To Figure

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

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

The coronavirus crisis has meant that scientific meetings and seminars have moved online. This change has led to me wondering:

 why don’t scientists give talks the way that musicians do gigs?

The idea is: after posting a preprint or publishing a paper, a scientist advertises that they will livestream a seminar to explain the work. Attendance is free.

Talkshow: why don’t scientists do gigs?

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’m posting this the morning after generating a graph, and it’s already out-of-date. During the worldwide COVID-19 outbreak, preprint servers such as bioRxiv and medRxiv have again shown that they are the most effective way of communicating science rapidly. A collection of all papers on COVID-19 deposited on these two servers is available here, and it is growing daily.

Take Off: preprints on COVID-19

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

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

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’ve Gotta Get A Message To You II: fixing SSMTP gmail authorisation

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

A new paper means a new paper explainer. This post is all about our new paper on clathrin assembly. Some background info   Endocytosis is the way that cells take up material from the outside world. The cell can make tiny vesicles that bud inwards from the cell surface and pinch off to travel inside the cell. This process is important for lots of things that cells do, so there is a lot of interest in how endocytosis works.

Don’t Let Go The Coat: new paper on clathrin assembly

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

This post follows on from the last post on BBSRC Responsive Mode funding. Another frequent question from applicants is:

 “How much can I ask for?”

One answer is: the same amount as successful grants. This information is freely available and can be downloaded from the UKRI website. All awarded grants can be searched (even those that have completed) using their database.

Notes from a panel II: Value of successful BBSRC grants

I’ve previously written about analysing my iTunes library and about generating Smart Playlists in iTunes. This post takes things a bit further by generating a “perfect playlist” outside of iTunes…

 it is exclusively for nerds

. How can you put together a perfect playlist? What are your favourite songs? How can you tell what they are?

Your Favorite Thing: Algorithmically Perfect Playlist

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

Pull Together: our new paper on “The Mesh”

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 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 post is about a citation analysis that didn’t quite work out. I liked this blackboard project by Manuel Théry looking at the influence of each paper authored by David Pellman’s lab on the future directions of the Pellman lab.

For What It’s Worth: Influence of our papers on our papers

This wonderful movie has repeatedly popped up into my twitter feed.  http://quantixed.org/wp-content/uploads/2018/04/ctenophore.mp4  It was taken by Tessa Montague and is available here (tweet is here).  The movie is striking because of the way that cytokinesis starts at one side and moves to the other. Most model systems for cell division have symmetrical division.  Rob de Bruin commented that “it makes total sense to segregate this way”.

Dividing Line: not so simple division in ctenophores

I thought I’d compile a list of songs related to biomedical science. These were all found in my iTunes library. I’ve missed off multiple entries for the same kind of thing, as indicated.

Science songs

Another post using R and looking at Twitter data. As I was typing out a tweet, I had the feeling that my vocabulary is a bit limited. Papers I tweet about are either “great”, “awesome” or “interesting”. I wondered what my most frequently tweeted words are. Like the last post you can (probably) do what I’ll describe online somewhere, but why would you want to do that when you can DIY in R?  First, I requested my tweets from Twitter.

The Sound of Clouds: wordcloud of tweets using R

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 tracking session generates a TrackMate XML file.

Tracking: announcing new R package TrackMateR

We finally took the plunge and adopted electronic lab notebook (ELNs) for the lab. This short post describes our choice of software. I will write another post about how it’s going, how I set it up and other technical details.

 tl;dr

we are using

 WordPress

as our ELN. First, so you can understand my wishlist of requirements for the perfect ELN. Easy-to-use. Allow adding pictures and notes easily.

quantixed

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

Convertible: using ffmpeg to convert audio files