Manuscript | DEZERAECOX

Toolbox talk: Trello

Thu, 30 Aug 2018 12:34:06 +0000

As an early-career researcher, I am still figuring out the best way to get stuff done. Every day it seems like my to-do list gets longer and longer, for every item I tick off two more take its place and I have no doubt it will only get worse. I am all about finding the best, most efficient and connected technologies to help alleviate some unnecessary legwork. After my first , I have decided to write more on the programs, apps and integrations that I use every day starting with one of the newest additions: Trello!

The basics: What the Tr-hell-o is all the fuss about??

Trello is fundamentally a project management application with a simple but sophisticated hierarchical interface consisting of boards, lists and cards. Trello thrives in settings suited to organisation. In the context of Trello, kanban is most often laid out as three stages (lists) - to-do, doing, done - and each element (or card) of a project (board) is represented within a list according to its state of completion. Elements progress through each list, giving a simple, visual overview of the project’s overall state.

This style works well when you work alone on individual projects - but it is also something you could easily accomplish with a chalkboard and some post-it notes. Where Trello really comes into its own is the ability to share and collaborate, such that individual tasks can be assigned to different people, comments can be added to cards specific for that task, and everyone can know at a glance the current big picture.

Trello is free (for the basic version, which is all I have needed thus far!), and accessible via the web interface, PC and iOS apps. It also integrates with all manner of other productivity apps, including GoogleDrive, GitHub, Dropbox, Slack, Evernote, OneDrive… Together, these features enrich the functionality of boards, providing a kind of dashboard from which to tackle projects and giving unparalleled flexibility for teams with diverse computing and file storage preferences.

Trello in action: managing your research projects

First things first: keeping track of experiments. There are many many electronic lab notebooks currently on the market, and I have tried more than my fair share. If you are not stuck in your ways (like I am) I highly recommend shopping around and picking one that you can integrate into your work as soon as possible. Unfortunately, I am a control freak and I am yet to find one that fits seamlessly with my workflow, and so I have resorted to building my own system using Trello!

The basic elements include lists for Ideas, Planned experiments, Lab work in progress, Analysis in progress, Ready to writeup, and Complete. Each new experiment or idea gets a card, for which I quickly note the purpose, reagents to be used, techniques and instrument details, and any pertinent references in the description. I then link this card (using the GoogleDrive powerup) to the folder containing the full experimental plan, results, analysis and write-up. The card then gets moved across the columns (lists) as each stage of the experiment is completed. For similar types of experiments, I have a checklist that allows me to easily track specific small elements of the experiment (e.g. plating cells, collecting results etc). If I complete a particular action for the experiment, I will also note in the comments any details specifically about that action. These comments are date and time stamped, helping to keep track of my activity on a day-to-day basis.

Another awesome Trello feature is the ability to label cards with a customisable category, which appears as a coloured bar on the front of the card. I use this feature here to label experiments with which one of my (many) projects it is specifically associated with.

This brings me to my second board - my project board. This is a board with which I track all of the ongoing projects I am involved in. There are lists for my individual projects (think: first author work), students projects I am involved with, collaborators projects, and ideas to keep in mind. The cards on each of these lists refer to a specific project, which can then also link to another Trello board or card which contains information, ideas and important references specifically for that project. That’s right baby, it’s Trello-ception!

Along similar lines, I have a board for manuscripts which tracks each manuscript I am involved in (cards) as they progress from the first draft to submission to revision to (if I’m lucky!) acceptance. In this case, labels are assigned to indicate my author position, and whether my contribution is required to move the article to the next stage. Individual cards link to additional Trello boards for each manuscript (normally only those for which I am the first author) where I can store more detailed information and ideas, tasks etc in a kanban layout.

By starring the top-level boards for Projects, Manuscripts and my Virtual Lab Book (starring is an inbuilt Trello function that allows you to favourite boards to be displayed at the top of your home page) I can easily get an overview of current progress, then by clicking a specific project or manuscript card I am automatically linked to all the more specific information I might need when working on that project, article or experiment.

The bigger picture: managing your science

When I first started with Trello, the ability to modularly (and very visually) manage and monitor my projects was a great tool. Since then, I have expanded my use of Trello boards to include the peripherals necessary for managing life as an ECR. Things like how to prioritise your workload, manage your short-term and long-term goals and keep on top of your reading list all become easier using Trello. My most recent addition was a prioritisation board, based on the priorities list shared by Corey J. A. Bradshaw in his amazing book “The Effective Scientist” (stay tuned for a book review - I really cannot recommend this book highly enough!). In short, Bradshaw runs through an exemplary list of how to prioritise the many competing interests vying for the time of an academic to get the maximum bang-for-your-buck in terms of career returns. These include things like writing articles, doing experiments (duh), helping students and colleagues, social media and writing grants.

When I first filled in all of the elements of the board, I realised just how unbalanced I have been in allocating time to each of these aspects. It was a great way to put into perspective where I should be spending the majority of my time and revisiting this structured big-picture priority list once a fortnight has helped refocus my research output.

Resources

That’s enough from me for now - if I have convinced you to give Trello a go, there are a couple of handy links below. I have included template examples for each of the board types that I mentioned above: feel free to use, abuse, copy and manipulate them to fit your own workflow, I honestly believe one of the best assets of Trello is it’s customisability - so don’t be afraid to make it your own. Just be sure to let me know if you find it helpful!

Template boards:

Additional info (from those who’ve said it better than me!):

Happy organising!

Image credit: @sidneyperryphotography via @unsplash

a weekend walk around the Bokeh library

Sun, 13 May 2018 11:13:53 +0000

If you’ve read my , you will know that I (somewhat arrogantly) consider myself “a passionate advocate for the use of programming by life scientists”. This came about following my Cambridge trip during my doctoral degree, in which I began to code analysis programs to derive meaning from the large (tens of gigabyte) datasets that we were collecting on a daily basis. At the time, I first learnt IgorPro - a proprietary language used by the other members of my host lab. While it was a steep learning curve, I was hooked. The power of being able to analyse huge reams of data without a single copy-paste-formula manouver normally completed in spreadsheets? Sign me up! Take out the human error of transferring data from program to program (Excel, GraphPad…) to achieve a result? Tell me more!

After my initial introduction, I quickly went in search of a more versatile language to learn. I disliked the feeling of being locked into the facilities provided within the commercial platform, and was tired of not being able to easily find support for this program online. And so, I met Python. And boy, did we hit it off! Python is easily the most friendly programming language I have come across, it is versatile and open source, the community is amazingly friendly, and I am yet to come across a problem I can’t solve via a quick trip to StackOverflow (seriously, where would I be without you guys?).

Little by little, I have worked on building my skills and I learn a little more each day. For a while now I have been comfortable writing small scripts that assist in my data analysis and plotting needs. However, I was yet to venture into the world of interactive plotting. I have always been intrigued by all of the different ways we can visualise data, and believe interactive plotting is a great way to allow both myself and someone else to explore a dataset. With this in mind, I set out this weekend to explore an interactive plotting library in python - Bokeh.

“Bokeh is an interactive visualization library that targets modern web browsers for presentation… Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.”

Sounds pretty good right? So, I gave it a go. As a test dataset, I decided to recreate the scatter plot from a published by our group for which the supplementary data is readily available. This plot displays the proteins whose cysteine residues significantly changed their reactivity following treatment with the drug Tunicamycin (an inducer of endoplasmic reticulum stress). Below you can find my version of Figure 6b, constructed as it is displayed in the article using Excel and GraphPad.

To recreate this plot in python, I took the raw data and constructed the scatter plot, colouring each datapoint according to the level of significance (as determined by the p-value). I also mapped the gene names associated with each datapoint via the UniProt API (a second learning exercise for this weekend!). This provides a second layer of data which I used to create the interactive feature of the graph - instead of displaying static names for only a few of the genes (which is limited by the need to not overcrowd the plotting area), gene names and ontology information is displayed by hovering over the point of interest. My final product is below - go ahead, give it a try! I found it super simple to embed the output here, plus there is also some handy toolbars provided by Bokeh out of the box that allow the plot to be saved to png or svg from the current view.

Bokeh Plot

I must say, I have been thoroughly impressed so far. Bokeh makes it extremely easy to build simple plots from existing pandas dataframes (think: spreadsheets) and to overlay interactivity without too much extra hassle. It offers the ability to completely customise the plots and layouts with widgets and extra functionality, although I think even the standard plotting elements I used here look pretty stunning in comparison to the original version!

So, here it is - my first passionate post about the benefits of programming for life scientists. Even if you take away the amazing benefits of reproducibilty, shareability, scalability and efficiency - the sheer ability to easily produce stunning visualisations that can be shared is a great asset. If you haven’t jumped on the programming bandwagon yet, what are you waiting for??

Manuscript: The sticky cell savers

Wed, 14 Mar 2018 09:01:25 +0000

All great wines and whiskys are matured, some for many many years. Ageing in this way allows time for complex chemical interactions that improves their quality. Although the maturation process for my latest scientific publication wasn’t quite as long as a quality (traditionally 12 - 21 years, in case you were curious), there were times where it felt as though I was never going to get to crack open the barrel! But, we are - and with that, the remainder of my PhD research is finally published.

I will do my best to not bore you with the details, and instead try to distil 4 years of research, experiments, writing, revisions, more experiments and more revisions into a succinct description of why this paper is important. But first, if you haven’t already found it, I recommend looking here for a little context.

AIM: To examine the ability of the small heat shock molecular chaperone proteins to interact with higher order aggregates (oligomers and fibrils) of alpha-synuclein, whose aggregation is associated with Parkinson’s Disease.

NOTABLE METHODS: Single molecule total internal reflection fluorescence (TIRF) microscopy - allows us to visualise directly the chaperone proteins interacting with fibrillar alpha-synuclein, reactive oxygen cell toxicity assay to monitor the impact of fibrillar alpha-synuclein on live cells in the presence and absence of chaperone.

THE BEST BITS: Directly visualising the interaction between a small heat shock molecular chaperone protein and alpha-synuclein fibrils. While this wasn’t the version that made it into the manuscript, it’s one of my personal favourite science images so far!

TIRF image of fibrils (blue, green, yellow), with bound chaperone (red)

TAKE HOME MESSAGE: Small heat shock proteins have multiple mechanisms of interacting with potentially toxic proteins. These molecular chaperones are well-suited to intervening at various stages in the aggregation pathway to protect cells from toxicity.

If you’d like to read the full article, or maybe check out a few more pretty pictures, you can find it .