Stephen Royle

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. How did I do it and why? I made the archive with this excellent tool written by Darius Kazemi.

Like I Said: archive of tweets

I’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”. Weezer’s “Weezer” albums (source: Wikipedia)  These records are colloquially referred to by the colour of the album.


Say It Ain&#8217;t So: using Weezer album cover colours in R

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

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

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. In the most straightforward sense being scooped means that an article appeared online before you managed to get your article online.

Scoop: some practical advice

This post follows on from “Getting Started“.  In the lab we use IgorPRO for pretty much everything. We have many analysis routines that run in Igor, we have scripts for processing microscope metadata etc, and we use it for generating all figures for our papers. Even so, people in the lab engage with it to varying extents. The main battle is that the use of Excel is pretty ubiquitous.


The Digital Cell: Getting started with IgorPRO

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

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

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

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?

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’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

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

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

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

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. and switched (turning them off). On “3” lightbulbs 3, 6, 9 etc. are switched.


Puzzles Like You: Lightbulb puzzle

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

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?

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

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

In early December, Spotify users received a list, known as Spotify Wrapped, of the tracks they listened to most in 2021. As a committed non-streamer, I was a bit envious of these lists; so I decided to assemble my own list using my Music database. This was possible by comparing two snapshots of my Music database in xml format* that were taken in 2020 and yesterday.


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

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

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

In-person science meetings are returning. To the introverts and the carers, the time-poor and the cash-strapped, the climate-conscious and the travel-phobic, the visa-challenged and the real-coffee appreciators, we had our chance; but in-person science meetings are returning. It’s a sad fact that during the pandemic, we failed to make virtual events work as a complete replacement for in-person meetings.


Pleased To Meet Me: returning to in-person meetings

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&#8217;t Let Go The Coat: new paper on clathrin assembly

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


Voice Your Opinion: naming your lab

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


Trellisaze II: Updated guide to using Trello in the lab

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

This post is an update of a previous analysis on quantixed. We have covered publication lag times – the time it takes for a paper go from submitted (received) to accepted and published – a lot on here. It is possible to look at lag times, in R using data from PubMed. Previously my code performed these calculations using an XML file downloaded from the PubMed website.


Ten Years vs The Spread II: Calculating publication lag times in R

As the COVID-19 pandemic continues, different countries are experiencing various restrictions including lockdowns. Some of these restrictions alter our ability to do science: by hindering lab access or taking time away from researchers for homeschooling. So, what impact has the pandemic had on scientific output? One way to look at this – for biology – is to look at newly deposited papers on bioRxiv.


The Rise and Fall: impact of the COVID-19 pandemic on bioRxiv preprints

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 IQ Block game 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

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

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. I would love to… but I don’t subscribe  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… The final level…  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

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&#8217;t scientists do gigs?

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

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

A short tech-tip this week. How can you find a line of code somewhere on your computer? I often find that I need to write a line of code and I can’t remember the exact syntax. To add to the frustration, I can remember writing a similar line before, but can’t remember in which file it was (or for what project, or even when it might’ve been). How can I quickly track that line down? Today I needed to write a LoadWave command in Igor.


Find The Answer Within: using grep to find lost code

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


Get Better: LaTeX and Overleaf

It’s real! I recently received a physical copy of my book,

 The Digital Cell: Cell Biology as a Data Science

. It’s real! It is published by Cold Spring Harbor Laboratory Press and is available here. The official release date is 1st December 2019. As I’ve described before, “The Digital Cell” a handbook to doing cell, developmental and molecular biology in the 21st Century; integrating computational and quantitative approaches.

A Book Like This: The Digital Cell

A quick post this week. I write “this week” in an attempt to convince regular readers that weekly posting will continue. I noticed that

 J. Cell Sci.

give download metrics for their papers and that these downloads are categorised into abstract, full-text and PDF. I was interested in how one of my papers performed.

Yesterday&#8217;s Numbers

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 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

This is a quick set of tips to improve your Twitter experience. YMMV on these tips. Plus I can see Twitter changing things so that they no longer work, but this advice is correct as of today.


Tips From The Blog XII: Improving your Twitter experience

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

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

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 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

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&#8217;s Worth: Influence of our papers on our papers

This is the first post at

 quantixed

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

Experiment Zero: Using a Raspberry Pi Zero camera

I’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

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.

Pledging My Time III

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


Ferrous: new paper on FerriTagging proteins in cells

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

 Clathrus ruber

, has a largely hexagonal layout, with pentagons inserted.

Pentagrammarspin: why twelve pentagons?

This deserved a bit of further explanation, due to the stupidity involved. “Debugging is like being the detective in a crime movie where you are also the murderer.” – Filipe Fortes  My code was giving an unexpected result and I was having a hard time figuring out the problem. The unexpected result was that a resampled set of 2D coordinates were not being rotated randomly.


Adventures in Code VI: debugging and silly mistakes

My activity on twitter revolves around four accounts. I try to segregate what happens on each account, and there’s inevitably some overlap. But what about overlap in followers? What lucky people are following all four? How many only see the individual accounts? It’s quite easy to look at this in R.  So there are 36 lucky people (or bots!) following all four accounts.


I&#8217;m not following you II: Twitter data and R

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

As with children’s toys and clothes, books aimed at children tend to be targeted in a gender-stereotyped way. This is a bit depressing.


Inspiration Information: some book recommendations for kids

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


Some Things Last A Long Time II

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

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

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

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?

Lots and lots of lab books and folders. Many reasons: I wanted to be able to quickly find information in our lab books.

Notes To The Future

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.

The Soft Bulletin: Electronic Lab Notebooks

I recently asked on Twitter for any recommendations for software to organise my PDFs. I got several replies, but nothing really fitted the bill. This is a brief summary.

 My situation

I have quite a lot of books, textbooks, cheat sheets, manuals, protocols etc. in PDF format and I need a way to organise them.

The Soft Bulletin: PDF organisation

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

Towards the end of 2015, I started distance running. I thought it’d be fun to look at the frequency of my runs over the course of 2016. Most of my runs were recorded with a GPS watch. I log my cycling data using Rubitrack, so I just added my running data to this. This software is great but to do any serious number crunching, other software is needed.


Colours Running Out: Analysis of 2016 running

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

This is part-tip, part-adventures in code. I found out recently that it is possible to comment out multiple lines of code in Igor and thought I’d put this tip up here.


Tips from the blog X: multi-line commenting in Igor

Molecular Biology of The Cell

, the official journal of the American Society for Cell Biology, recently joined a number of other periodicals in issuing guidelines for manuscripts, concerning statistics and reproducibility.

Blind To The Truth

I’m currently writing two manuscripts that each have a substantial data modelling component. Some of our previous papers have included computer code, but it was straightforward enough to have the code as a supplementary file or in a GitHub repo and leave it at that. Now with more substantial computation in the manuscript, I was wondering how best to describe it. How much detail is required?


The Arcane Model

A couple of recent projects have meant that I had to get to grips more seriously with

 R

and with

 MATLAB

. Regular readers will know that I am a die-hard

 IgorPro

user. Trying to tackle a new IDE is a frustrating experience, as anyone who has tried to speak a foreign language will know. The speed with which you can do stuff (or get your point across) is very slow.

The International Language of Screaming

Today I saw a tweet from Manuel Théry (an Associate Ed at

 Mol Biol Cell

). Which said that he heard that the Editor-in-Chief of MBoC, David Drubin shops for interesting preprints on

 bioRxiv

to encourage the authors to submit to MBoC.

Voice Your Opinion: Editors shopping for preprints is the future

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: Find something that you need to automate and get going!

 Programming

http://www.instruction-manuals.co.uk/imageIM/four/seven/bbc.gif I make no claim to be a computer wizard.

The Digital Cell: Getting Started

Well, the 2015/2016 season was one to forget for Crewe Alexandra. Relegation to League Two (English football’s 4th tier) was confirmed on 9th April with a 3-0 defeat to local rivals Port Vale. Painful. Maybe

 Repeat Failure

is a bit strong. Under Dario Gradi, the Railwaymen eventually broke into League One/Championship (the 2nd Tier) where they punched above their weight for 8 seasons.

Repeat Failure: Crewe Alexandra F.C.

Raw Data: A novel on Life in Science

by

 Pernille Rørth

(Springer, 2016) I was keen to read this “lab lit” novel written by renowned cell biologist Pernille Rørth. I’d seen lots of enthusiastic comments about the book, and it didn’t disappoint.

My Blank Pages V: Raw Data

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

Ben Ratliff (Farrar, Straus and Giroux) A non-science book review for today’s post. This is a great read on “how to listen to music”. There have been hundreds of books published along these lines, the innovation here however is that we now live in an age of musical plenty.

My Blank Pages IV: Every Song Ever

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. The breakdown of runners by category for the 2015 event. Male Senior (MSEN) category has the most runners, constituting a wide age grouping. There were 3565 runners in total, 5 in an undetermined category and 9 DNFs.


Pledging My Time

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


Get Better: CV Clinic

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?

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!

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 read this article on the BBC recently about alcohol consumption in the UK. In passing it mentions how many people in the UK are teetotal. I found the number reported – 21% – unbelievable so I checked out the source for the numbers. Sure enough, ~20% of the UK population are indeed teetotal (see plots). The breakdown by gender and age is perhaps to be expected. There are fewer teetotal men than women.


Lemonade Secret Drinker: sober statistics

Our recent paper on “the mesh” in kinetochore fibres (K-fibres) of the mitotic spindle was our first adventure in 3D electron microscopy. This post is about some of the new data analysis challenges that were thrown up by this study. I promised a more technical post about this paper and here it is, better late than never.


Parallel Lines: Spatial statistics of microtubules in 3D

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 do the readers of quantixed come from?

Well, geographically they come from all around the world.

Where You Come From: blog visitor stats

A couple of years ago, a colleague sent me this picture* to say “who put J Cell Biol on a diet?”. I joked that maybe they publish too many autophagy papers and didn’t think much more of it.  Recently, Ron Vale put up this very interesting piece on bioRxiv discussing what it takes to publish a paper in the field of cell biology these days. In the main, he questions whether this is now out of reach of many trainees in our labs.


Creep Diets: Fewer papers published at JCB

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

 Title of the paper:

The mesh is a network of microtubule connectors that stabilizes individual kinetochore fibers of the mitotic spindle

 What’s it about?

When a cell divides, the two new cells need to get the right number of chromosomes. If this process goes wrong, it is a disaster which may lead to disease e.g. cancer.

Pull Together: our new paper on &#8220;The Mesh&#8221;

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 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. Statistics is a topic that many people find difficult to grasp. I think there are a couple of reasons for this that I’ll go into below.

My Blank Pages II: Statistics Done Wrong

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

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

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

In this post I’ll describe a computational method for splitting two sides of a cell biological structure. It’s a simple method that relies on

 principal component analysis

, otherwise known as PCA.

Division Day: using PCA in cell biology

Back of the envelope calculations for this post. An old press release for a paper on endocytosis by Tom Kirchhausen contained this fascinating factoid:  The equivalent of the entire brain, or a football field of membrane, is turned over every hour  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

I was talking to a speaker visiting our department recently. While discussing his postdoc work from years ago, he told me about the identification of the sperm factor that causes calcium oscillations in the egg at fertilisation. It was an interesting tale because the group who eventually identified the factor – now widely accepted as PLCzeta – had earlier misidentified the factor, naming it oscillin.


Half Right

A bit of navel gazing for this post. Since moving the blog to wordpress.com in the summer, it recently accrued 5000 views. Time to analyse what people are reading…  The most popular post on the blog (by a long way) is “Strange Things“, a post about the eLife impact factor (2824 views). The next most popular is a post about a Twitter H-index, with 498 views.


Belly Button Window

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.


quantixed

Over and Over: Preprint revisions on bioRxiv

The Rise and Fall: impact of the COVID-19 pandemic on bioRxiv preprints

Scoop: some practical advice

Some Things Last A Long Time II

Methods papers for MD997