Trellisaze: Using Trello for lab organisation

Previously, I wrote a post with tips for new PIs on lab organisation. Since that time, I’ve started using Trello to organise operations in my lab.

Trello is basically a way to track the progress of projects. Collaborative working is built-in. A friend had begun using Trello as she got involved in building an app. It seems that Trello is popular among teams working to develop software. Sure enough, I asked for opinions on Trello via twitter and got a nice email from somebody on the Open Microscopy Environment team on the pros and cons of using Trello. You can see one of their boards in action here, it is after all, open! This convinced me to give it a go. I set up a few boards, invited the lab members and got stuck in.


I set up subject-specific and technique-specific boards (as well as my own to-do list and a board for tasks at home). All lab members are members of Royle Lab group and we have two groups boards – General and Molecular Biology. The General Stuff contains information about lab meetings, one-to-one meetings, orders etc. even photos of lab socials. Molecular Biology, everyone is a member because everybody does some cloning in my group. Then the Membrane Traffic people have a board that the others can’t see etc. I’ll probably move to making them all available to everybody in the group soon. The default is for boards to be closed, i.e. not possible for outsiders to see. You need to add people to your board for them to see it and to work with you.

Part of an example board is shown here:


I’ve redacted parts that we’re not ready to tell the world about just yet. There are many guides online to show you how to get going with Trello. Basically, you have Boards. Within each board you have Lists, the columns that you see above. On a list, you put Cards. On the back of the card you can comment, add checklists, files, links, due dates etc etc. People can be assigned to cards and to provide updates with how it’s going. All of these things can be easily edited as priorities change. For example, I am writing a paper with one person and so we have a list for the paper, with cards for each figure and a card for writing.

I’m happy with how this is working. For example, when writing a paper, myself and the first author used to do an awful lot of rapid communication via email (I’ve previously called this Tiki-taka). It’s best if this was kept out of our Inboxes and organised somewhere. Also, how can we keep track of what still needs doing? Did that experiment get redone with the extra control? Which folder were the tracking experiments in? All of this can be recorded and managed using Trello. You can see the little speech bubble on each card indicating that we are talking to each other.

My tips/notes are:

  • In a team, there will always be some people who take to it and use it avidly, while others don’t engage.
  • To encourage take up, I communicate through Trello to the lab rather than using email.
  • Also, at our weekly one-to-one meetings, we edit cards together.
  • We are just using the free version. I’ve accumulated credits to go gold, but haven’t done so.
  • There are good iOS and Android apps for Trello. Notifications get pushed here if you subscribe to a board, list or card. It will ping you emails too, but you can switch this off.
  • File sharing is still done via our server (or Dropbox for small files), but notifications go on the board.
  • Make cards very specific, cards covering big lab projects will fester and clutter up the list.
  • The help files are incredibly nerdy… they even have a dog called Taco who pops up now and again.

Summary: I recommend Trello (note that other management softwares are available – kanbanflow, slack etc), particularly if you have a large group. Even for new PIs or those with small groups who might be on top of everything, I think there is still something that you’ll get out of it.

The post title is taken from Trellisaze by Slowdive from their Pygmalion LP.

Super Unison

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. My guess is that it got erased during the upgrade (not sure what the problem is). So I re-installed, no big deal. Let’s face it, Unison has changed in those 3.5 years, so I’ll be getting the latest version.

You can get a nice compiled version from @alan_schmitt here. Version 2.48.15 runs on El Capitan. I always run Unison from the command line, but those tools can be installed from this GUI version.

I did this for all 3 macs and checked that Unison was installed by typing

unison -version

All good. I then ran each profile and… command not found. I realised that via ssh, the search path is not the same as via bash. Long story short. I added the following to my profile.


Thank you to @alan_schmitt for the suggestion. This is actually a solution that is specified in the documentation. I thought I’d write this down in case it helps anybody.

Now my profile (syncimac.prf) looks like this

root = /Users/name/Documents/
root = ssh://name@computername.home//Users/name/Documents/
times = true
log = false
ignore = Name .FBCIndex
ignore = Name .FBCLockFolder
ignore = Name {Cache*,.Trash*,.VolumeIcon.icns,.HSicon,Temporary*,.Temporary*,TheFindByContentFolder}
ignore = Name {TheVolumeSettingsFolder,.Metadata,.filler,.idsff,.Spotlight,.DS_Store,.CFUserTextEncoding}
ignore = Name .localized
ignore = Name .fseventsd
ignore = Path .unison

this is saved in ~/.unison/ and I invoke it by running

unison syncimac -ui text

On the first run it detected a Unicode change which I think is due to the new version of Unison. So I needed to ignore the old archives with the flag -ignorearchives. Then it’s fine to run again.

The post title is taken from “Super Unison” by Drive Like Jehu from their LP Yank Crime

Where You Come From: blog visitor stats

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. The number of visitors from each country is probably related to: population of scientists and geographical spread of science people on Twitter (see below). USA is in the lead, followed by UK, Germany, Canada, France, Spain, Australia, etc.

Where do they click from? This is pretty interesting. Most people come here from Twitter (45%), around 20% come via a search on Google (mainly looking for eLife’s Impact Factor) and another ~20% come from the blog Scholarly Kitchen(!). Around 3% come from Facebook, which is pretty neat since I don’t have a profile and presumably people are linking to quantixed on there. 1% come from people clicking links that have been emailed to them – I also value these hits a lot. I guess these links are sent to people who don’t do any social media, but somebody thought the recipient should read something on quantixed. I get a few hits from blogs and sites where we’ve linked to each other. The remainder are a long list of single clicks from a wide variety of pages.

What do they read?

The traffic is telling me that quantixed doesn’t have “readers”. I think most people are one-time visitors, or at least occasional visitors. I do know which posts are popular:

  1. Strange Things
  2. Wrong Number
  3. Advice for New PIs
  4. Publication lag times I and II
  5. Violin plots
  6. Principal Component Analysis

Just like my papers, I’ve found it difficult to predict what will be interesting to lots of people. Posts that took a long time to prepare and were the most fun to think about, have received hardly any views. The PCA post is most surprising, because I thought no-one would be interested in that!

I thoroughly enjoy writing quantixed and I really value the feedback that I get from people I talk to offline about it. I’m constantly amazed who has read something on here. The question that they always ask is “how do you find the time?”. And I always answer, “I don’t”. What I mean is I don’t really have the free time to write this blog. Between the lab, home life, sleep and cycling, there is no time for this at all. The analyses you see on here take only three hours or less. If anything looks tougher than this, I drop it. If draft posts aren’t interesting enough to get finished, they get canned. Writing the blog is a nice change from writing papers, grants and admin. So I don’t feel it detracts from work. One aim was to improve my programming through fun analyses; and I’ve definitely learnt a lot about that. The early posts on coding are pretty cringe-worthy. I also wanted to improve my writing which is still a bit dry and scientific…

My favourite type of remark is when people tell me about something that they’ve read on here, not realising that I actually write this blog! Anyway, whoever you are, wherever you come from; I hope you enjoy quantixed. If you read something here and like it, please leave a comment, tweet a link or email it to a friend. The encouragement is appreciated.

The post title is taken from “Where You Come From” by Pantera. This was a difficult one to pick, but this song had the most apt title, at least.