Electronic Lab books in markdown

--- type: slide title: Electronic Lab books in markdown tags: presentation slideOptions: theme: dark transition: 'fade' spotlight: enabled: true progress: true --- <style> .reveal { font-size: 18px; } </style> # Electronic Lab books in markdown Marcelo Nollmann *version 11/01/2022* --- # Critical issues when considering electronic labooks 1. Easy to use 2. Sharing with others 3. Backup 4. **Revision history** 6. **Long-term format compatibility!** --- # Local word processor (word, openoffice) - Everyone knows how to use it - but it is not always easy to use when you have to write a 200 pages document with figures!  - Difficult to share - No revision history - Format is propietary - **No long-term format compatibility** --- # Online word processor (google docs) <img src="https://i.imgur.com/DwDCQX6.png" width="600"/> - Easy to use, BUT hard to handle in large volumes - Easy to share - Has revision history - Format is propietary - Stored in cloud! - **No long-term format compatibility** --- # Propietary tool (INSERM tool) - Easy to share - Easy to use?? - No revision history - Format is propietary - **No long-term format compatibility** - What happens when the company running it goes under? How do you retrieve the 5-years of data stored in a database format? - Usually their solution is PDFs! --- # Markdown <img src="https://i.imgur.com/z2HUP5r.png" width="500"/> - Easy to use--> requires very basic programming skills - Easy to share: - ownCloud,  - hackMD online,  - HedgeDoc hosted locally! - Revision history using git - Format is open! - **Offers long-term format compatibility as it relies on pure text** --- # Markdown cloud-hosted server Semi-commercial solution hosted online: [hackmd.io ](https://hackmd.io) ![](https://i.imgur.com/n0pXp3M.png) But you can also use on-line editors such as (Dillinger)[https://dillinger.io/] or [StackEdit](https://stackedit.io/app#). --- # Markdown self-hosted server: Hedge-doc Open-source self-hosted: https://hedgedoc.org/ ![](https://i.imgur.com/hIYH2C6.png) --- # Markdown client: obsidian Open-source markdown client: [obsidian.md](https://obsidian.md/) ![](https://i.imgur.com/7pdCx2g.png) --- # Introduction to Markdown There are many applications that support Markdown. I use [Typora](https://www.typora.io/#linux), or [Haroopad](http://pad.haroopress.com/) or [Atom](https://atom.io/) for **offline** editing (my favorite). ![](https://i.imgur.com/OCNyPmi.png) --- # Writing text in markdown ### Headers To write headers of sections you just use '#'. For instance: ```markdown # header 1 ``` # header ```markdown ## header 2 ``` ## header 2 ```markdown ### header 3 ... you get the idea ``` ### header 3 --- # Emphasis This is even easier. For example ```markdown **bold** *italic* ==highlight== 9^th^ H~2~O ``` will appear as **bold**, *italic*, ==highlight==, 9^th^, H~2~O --- # Lists List are done by just using '-' For instance, the following ``` markdown - [ ] work item 1 - [x] sub item 1 - [ ] sub item 2 - work item 2 ``` will appear as - [ ] work item 1 - [x] sub item 1 - [ ] sub item 2 - [ ] work item 2 --- # Lists An ordered list ```markdown 1. item 1 2. item 2 3. item 3 4. item 4 4. etc ``` will look like: 1. item 1 2. item 2 3. item 3 4. item 4 5. etc --- # Images Let's say you have an image, called pinguin.jpeg in your directory ```2019_09_03_Create_Labbook``` You can insert the image by typing ```markdown ![pinguin](./h7P1MWD.jpg) ``` and it will appear as: ![](https://i.imgur.com/h7P1MWD.jpg) You can also add images from the internet by replacing the filename with a link. Make sure you always use relative links! If you don't know what these are, ask around! --- # Tables | | Equipment | fjdfd | | - | -| -| | **as**| sds| sdsd| | **sdsdsdsds**| sdsdsdsdsds| 1111| Tables 1are easy, for instance, do ```markdown | strains | Date | Procedence| | --------|------|----------| |sdsdnk| 20-09-76| Cozzlab| | pyt233| 19-01-81| SherrattLab| ``` will appear as: | strains | Date | Procedence| | --------|------|----------| |sdsdnk| 20-09-76| Cozzlab| | pyt233| 19-01-81| SherrattLab| and so on. --- # Conversion Markdown documents can be easily converted to word, html, latex, pdf using [pandoc](https://pandoc.org/MANUAL.html).