Stephen Royle

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

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

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

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

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

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

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

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

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

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 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

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 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

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.

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

I’m putting this up here in case it is useful for somebody. We capture Z-stacks on a Perkin Elmer Spinning Disk microscope system. I wanted to turn each stack into a single image so that we could quickly compare them. This simple macro does the job. We import the images straight from the *.mvd2 library using the wonderful BioFormats import tool. We open all files as composite hyperstacks.

Tips from the blog VII: Recolour Z-stack and Save Projection

{.alignright .size-medium .wp-image-551 loading=“lazy” decoding=“async” attachment-id=“551” permalink=“https://quantixed.org/jcbdiet/” orig-file=“https://i0.wp.com/quantixed.org/wp-content/uploads/2015/07/jcbdiet.jpg?fit=603%2C2586&amp;ssl=1” orig-size=“603,2586” comments-opened=“1”

Creep Diets: Fewer papers published at JCB

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

Having recently got my head around violin plots, I thought I would explain what they are and why you might want to use them. There are several options when it comes to plotting summary data. I list them here in order of granularity, before describing violin plots and how to plot them in some detail.

Tips from the blog III – violin plots

We have a new paper out! You can access it here. The work was mainly done by Cristina Gutiérrez Caballero, a post-doc in the lab. We had some help from Selena Burgess and Richard Bayliss at the University of Leicester, with whom we have an ongoing collaboration.

 The paper in a nutshell

We found that TACC3 binds the plus-ends of microtubules via an interaction with ch-TOG. So TACC3 is a +TIP.

Sticky End

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.

Belly Button Window

What is your h-index on Twitter? This thought crossed my mind yesterday when I saw a tweet that was tagged #academicinsults It occurred to me that a Twitter account is a kind of micro-publishing platform. So what would “publication metrics” look like for Twitter? Twitter makes analytics available, so they can easily be crunched. The main metrics are

 impressions

and

 engagements

per tweet.

You Know My Name (Look Up The Number)

A colleague once told me that they only review three papers per year and then refuse any further requests for reviewing. Her reasoning was as follows: I publish one paper a year (on average) This paper incurs three peer reviews Therefore, I owe “the system” three reviews.  It’s difficult to fault this logic. However, I think that as a senior scientist with a wealth of experience, the system would benefit greatly from more of her input.

Pay You Back In Time

I noticed something strange about the 2013 Impact Factor data for

 eLife

. Before I get onto the problem. I feel I need to point out that I dislike Impact Factors and think that their influence on science is corrosive. I am a DORA signatory and I try to uphold those principles. I admit that, in the past, I used to check the new Impact Factors when they were released, but no longer.

Strange Things

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

I thought I’d share a procedure for rotating a 2D set of coordinates about the origin. Why would you want do this? Well, we’ve been looking at cell migration in 2D – tracking nuclear position over time. Cells migrate at random and I previously blogged about ways to visualise these tracks more clearly. Part of this earlier procedure was to set the start of each track at (0,0). This gives a random hairball of tracks moving away from the origin.

Round and Round

I was looking at the latest issue of

 Cell

and marvelling at how many authors there are on each paper. It’s no secret that the

 raison d’être

of

 Cell

is to publish the “last word” on a topic (although whether it fulfils that objective is debatable). Definitive work needs to be comprehensive. So it follows that this means lots of techniques and ergo lots of authors.

All This And More

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

 Title of the paper:


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


 In a nutshell:

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

Into The Great Wide Open

Books about the MRC Laboratory of Molecular Biology are plentiful. If you haven’t read any, the best place to start are the books written by some of the Nobelists themselves: “I Wish I’d Made You Angry Earlier” by Perutz, “My Life in Science” by Brenner.

My Blank Pages

How long does it take to publish a paper? I posted the picture below on Twitter to show how long it takes for us to publish a paper.

So Long

Something that has driven me nuts for a while is the bug in FIJI/ImageJ when making montages of image stacks. This post is about a solution to this problem.

 What’s a montage?

You have a stack of images and you want to array them in

 m

rows by

 n

columns. This is useful for showing a gallery of each frame in a movie or to separate the channels in a multichannel image.

Everything In Its Right Place

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

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

 quantixed

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

What’s in the Box: Albums of 2021

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

It is an annual event on

 quantixed

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

Methods papers for MD997 – 2021 Edition

A short follow-up post. Previously, I looked at how to reproduce a Strava feature that compares performance over similar courses. With a few modifications to the code, I was able to analyse a much larger dataset of cycling performance on similar courses. Two courses with the highest number of tracks are shown below. I cycle these courses all the time. Well, I did until the pandemic struck.

Cluster One II: comparing cycling performance on similar courses

Part of a series on the development of Early Career Researchers in the lab. We spent a session discussing how to create a research profile. This led to a second session on CVs. Here is an outline of what we covered. CVs   We talked about different CV formats first of all. We focussed on academic CVs mainly, but we discussed the differences between academic and CVs for jobs outside academia.

Get Better: creating a research profile

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

If you are a cell biologist, you will have noticed the change in emphasis in our field. At one time, cell biology papers were – in the main –

 qualitative

. Micrographs of “representative cells”, western blots of a “typical experiment”… This descriptive style gave way to more

 quantitative

approaches, converting observations into numbers that could be objectively assessed.

The Digital Cell

University of Warwick is a popular conference destination, with thousands of visitors per year. Next time you visit and stay on campus, why not bring your running shoes and try out these routes?

Tips from the blog IX: running route

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

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

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

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

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

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

As 2021 draws to a close, it’s time to check back in on a previous post. As a recap, Garmin Connect offered four challenges to run 3 x 505 km and 1 x 505 km, one in each of the four quarters of 2021. Completing all four would mean

 running 2021 km in 2021

. I used an R script to check my progress throughout the year (available here). Each quarter gave a set of results, the final set for the whole of 2021 is shown here.

Target II: Monitoring a running goal in R

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

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

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?

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

Seles: Tennis coding challenge

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

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. Advocates argue that these tools improve every aspect of science, including the publication process.

No Synths! Use of AI in scientific publications

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

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

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

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?

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

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

 I used R to find the answers.

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

Yet Another Movie: IMDB Top 250 movies

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

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.

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