I love a nice curated index. wiki’s list of PIC software. Curlie. awesome-* lists.
Here are software that I’ve come across in my travels, and my experiences.
Scientific data management / LIMS / reproducibility scripts
Sumatra
- [x] used
Signac
GitHub - glotzerlab/signac: Manage large and heterogeneous data spaces on the file system.
Writing
Google Drive
I’ve always ended up doing most of my long-form writing in Google Drive - it’s just what I’ve used since growing up. Recently they’ve added some features that make it behave like an outliner.
As of this date, the mechanism to combine and export the whole document, including all tabs, is in the development build only.
LibreOffice
LibreOffice has also added a slightly more limited subset of these features, using the Navigator view and this setting:
Scrivener
Proprietary Windows/OSX-only outliner; no Linux version
Manuskript
Presentations
Created with {Remark.js} using {Markdown} + {MathJax}
https://selipot.github.io/talks/lecture4.pdf need to try this out
LaTex Beamer
Reveal.js - nice feature here over pdf is the speaker notes can be shown on the right
downside is lack of archivability
Git / GitHub
Saves one from having to git pull changes from remote. Helpful if you have a lot of repos to keep updated.
mr register each repo and then alias upd="cd && mr update && cd -"
spack
easybuild
lmod
mamba conda
Writing and editing
Staging ground
Podcasts
VLC has some basic RSS podcast features.
GitHub - m3nu/upodder: simple console/terminal podcast downloader - basic batch downloader tool
Simulation ans numerical codes
X-ray
-
SRW
-
XMI-MSIM
-
msim
-
XRMC
-
Sim-xrf
Charged Particles
https://traceon.org/ - never used but looks interesting, thanks @Chrunchi
Kassiopeia - never used but looks interesting, thanks @manshiro
- SMILEI
XGC XGC - X-Point Included Gyrokinetic Code — X-Point Gyrokinetic Code (XGC) documentation
used by iter
go through programs/ folder
Project management / time management
Redmine
docs/redmine at master · docker-library/docs · GitHub
see demo
no batteries-included support for repeating tasks
Open source
Leantime.io
Lots of ways of tagging new tasks.
Slow AF user interface.
Notion
Apparently folks use this for task tracking. Powerful “paradigm” that I haven’t wrapped my head around properly yet. way beyond CRUD.
Obsidian Tasks
Structured.app
well-designed linear to-do-list app. Used this for a little while but it didn’t quite work for me.
Android app is still WIP but functional.
Home recipe management
PlanToEat
commercial, $50/year. used this for a while. have some qualms with the UX.
Grocy
open-source, selfhosted
Mealie
Open-source, selfhosted. Switched from Mealie to Grocy.
Scientific graphics
MathGL
My go-to if C/C++ is the order of the day. High performance.
Datoviz
Haven’t used this.
VisPy
Disk usage and administration
WinDirStat. The zipped executable option is a nice portable no-install