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My Favourite Markdown Tools

Recently I have started using markdown for a lot more of my writing. From drafting articles and blog posts to writing cover letters and taking notes, markdown has become my new go-to.

I used to do all my digital writing in office suites such as MS Office and LibreOffice, and whilst I still use them from time to time, I have found that more and more often they are not the right tool for the job.

Markdown is simple enough that it gets out of my way, lightweight enough that I can write in it regardless of what device I’m using, and is simple enough that I never have to worry about corrupted documents and incompatible formats.

I would like to list 3 tools I use regularly to write in markdown.

Apostrophe

Apostrophe is excellent. It is a simple open source markdown editor that gets out of your way. It allows you to write, without worrying about anything else. If you are only going to be writing basic documents and drafts in markdown, without the need to cross-reference or cite, then Apostrophe is the best tool for the job.

Logseq

Logseq is my new favourite note taking application. It is a personal knowledge base (PKB) and whilst it might not be quite as polished or feature rich as the most popular PKB (Obsidian), it is a joy to use.

My old note taking application was Notion. Notion is incredibly powerful and enjoyable to use but it is also proprietary, and I don’t want my notes becoming inaccessible if one day they decide to discontinue the free plan.

I was considering switching to Obsidian because to some extent it solves this issue. It uses markdown and stores files locally so, even if the application stops being developed, all the notes should still be accessible and usable. But if I’m going to go for an open format, I feel like I should go for an open application as well, and so this is the niche that Logseq fills for me.

Like Obsidian, Logseq’s most powerful features are its bidirectional linking and graph view. These allow me to visualise my notes in ways that I just couldn’t before. I still use a physical notepad, but now my digital notes have an advantage, a reason to use them over my notepad for the times when I don’t necessarily need or want an analogue experience.

Zettlr

Zettlr is markdown editor that sort of fills the gap between the note-taking focus of Logseq and the longform writing suitability of Apostrophe. Zettlr is focussed on academic writing, with built in Zotero and JabRef support.

Zettlr is a new addition to my arsenal. I use it for my academic note taking. It helps me draft and plan changes to my thesis, and will likely become my new digital lab-book. To an extent, Zettlr and Logseq are cross-compatible and so I plan to find a way to use them in a complementary way. But thanks to their use of an open format, I can choose to migrate my notes to another platform at any time.

Closing Thoughts

I am still very new to the world of writing in markdown, I’m sure I still have a lot to learn, and I doubt it will ever replace all writing formats for me. I will still write some notes with pen and paper, no doubt I will continue to need to use various office suites for professional work, and I still think LaTeX is superior for thesis writing and academic articles. There are new projects that could replace LaTeX, such as Typst, but they aren’t quite powerful or polished enough yet for me to switch.

I look forward to learning more about markdown and PKBs, and maybe I’ll have some more thoughts on them to share in the future.

An Update

It’s been a while since my last update.

I was diagnosed with an anxiety disorder when I was 18, since then I have had times when it has been pretty easy and times where it has been difficult. Over the last year my mental health has deteriorated significantly, and as a result I have struggled to do many even regular daily tasks, so updating my blog was sort of out of the picture. I not fully back to normal, I still struggle a lot and have worries and concerns about my progress, however I am moving through this and know I will come out the other side.

I finished the lab-based portion of my work at the end of December 2022. My supervisor did suggest applying for an extension due to extenuating circumstances however I wouldn’t have any money to live on, and therefore it unfortunately isn’t an option.

Projects

During my MSc I haven’t really had time for side projects, however a number of the projects that I have undertaken as part of the body of work that I will be submitting in my thesis are interesting as standalone projects and I may write about them here in the future.

Progress

In March I had my first first-author paper published. It is a review article, titled “Mechanical environment for in vitro cartilage tissue engineering assisted by in silico models”, published in Biomaterials Translational. The paper looks at how the mechanical environment affects tissue culture, and how in silico modelling of static and dynamic culturing conditions can be exploited to direct future tissue engineering research.

I am now finishing off my thesis, and will hopefully be moving onto my next adventure soon.

Elbow Tap

Around March last year, the COVID-19 pandemic was becoming of increasing concern in the UK. I was living in my student house at university and trying to avoid unnecessarily catching anything. Students’ houses and especially bathrooms aren’t exactly known for being the cleanest of places, and so I decided that what our bathroom needed was an elbow tap!

Okay, an elbow tap probably wasn’t necessary but I had recently purchased a 3D printer (to help me finish my final year project) and I had not yet learnt that I didn’t need to be printing attachments and modifications for everything in my life… Frankly, I still need to learn that lesson.

So I took to Fusion 360 and started building! I looked at pictures of proper elbow taps on Google images and decided I didn’t need to be making mine that big, just big enough that I could use it easily.

I eyeballed the measurements for the most part, to surprising success. I chose to split it into three parts (the arm and two halves of the clamp).

The 3 parts of the elbow tap

The parts were held together with M3 nuts and bolts, and fitted perfectly on the tap. Unfortunately, I’d failed to consider the fact that the existing tap handle was a perfectly smooth elliptic cylinder and so my attachment would be prone to slipping off. My solution to this was two elastic bands, one holding the attachment to the back of the tap and the other wrapped around the existing handle. This wasn’t exactly an elegant solution, but it worked and so it worked. Below is a picture of the elbow tap in use (along with 3 different bottles of soap for some reason).

Bioprinter… The beginning

A few months ago I decided I wanted to make a low-cost bioprinter, to give myself experience printing hydrogels.

Originally I was trying to decide between a cantilever design and a CoreXY design. The benefit of the former would’ve been its cost-effectiveness and the benefit of the latter would’ve been the speed and accuracy over the standard cartesian printers I am used to.

It is worth noting that, in part due to the pandemic, I have no income at the moment and so I was leaning in favour of building a cantilever printer. When writing up the bill of materials I quickly found that this was going to be rapidly approaching the £150 mark just for the base printer (that I would then be adapting with a Large Volume Extruder), with the mainboard, steppers, and power supply making up the bulk of the cost.

My original Ender 3X cost me £200, and so I assumed that adapting one of those was going to be cost-prohibitive. To my surprise, Creality was now selling the Ender 3 for just £116, and so I decided to order one and change my design.

In this project I am building off of the work laid out in two papers:

M. Kahl et al., “Ultra-Low-Cost 3D Bioprinting: Modification and Application of an Off-the-Shelf Desktop 3D-Printer for Biofabrication,” Front. Bioeng. Biotechnol., vol. 7, no. 184, 2019. doi: 10.3389/fbioe.2019.00184

K. Pusch et al., “Large volume syringe pump extruder for desktop 3D printers,” HardwareX, vol. 3, pp. 49-61, 2018. doi: 10.1016/j.ohx.2018.02.001

I would highly recommend giving them both a read if you are interested in this topic.