Arindam Basu @arinbasu@qoto.org
- Orcid Profile
- https://orcid.org/0000-0003-2326-2292
- Images (pixelfed)
- https://pixelfed.social/i/web/profile/424715601356972526
- Join me in Matrix Chat
- https://matrix.to/#/@arinbasu:qoto.org
Professor, Epidemiologist. Doctor (ENT specialist). Professor of Epidemiology and Environmental Health at the University of Canterbury in New Zealand.
Interests: lego MOCs, wood carving, mountain biking, tramping.
Joined Apr 2022
Call for Carpentries instructors and trainers
Who is a #Carpentries instructor or trainer?
Let's put together a spreadsheet.
Please reply to this post and let's put together our group.
Arindam Basu
boosted
It’s funny, many of the “what you need to know about Mastodon” or “how to learn about the fediverse” pieces are focused on the technology and the implementation, when the hardest thing for people to understand about this context, if they’re used to traditional social media & tech, is that here we have an expectation of _consent_. Consent if you want to be included in a conversation, consent about being amplified, consent in the form of CWs on topics that you want to manage, etc. That’s it! 🎯
I see what you mean. :-), yup.
Several years ago, around 2017-ish, you may recall, there was a massive influx of Japanese language posts across several #mastodon servers, and it was quite interesting to read the posts from, ahem ..., 99% ers.
So good point there!
Many academics tend to be what is referred to as 'laggards' when it comes to adoption of technology, instead looking for 'holes'. Several years ago, a senior academic attacked me in a public forum about open access, arguing why he would have to pay to get published, and ranted about predatory journals.
Well, add to that the complexity of publishers who have figured out a way to make money out of the whole thing.
Arindam Basu
boosted
লে অফের আসল কারণ, কোনো শিল্পেই, ব্যবসা বাঁচানো নয়। লিখলেন প্রতীক #twitter #byjus
https://nagorik.net/opinion/rethinkin-layoffs-amid-darkness-of-twitter-byjus/
Well, knowing a person's prefernces is a little complex in #fediverse, as people can pretty much 'craft' their own timeline, so you can follow whom you want to follow and unless people identify themselves as #Bipoc, or #poc ,
I am curious to know how might you come to the figure of 99.99%? I'd like to use your method to estimate the percentage of various ethnicities in my timeline.
Arindam Basu
boosted
New #preprint from our lab:
kegg_pull: a Software Package for the RESTful Access and Pulling from The Kyoto Encyclopedia of Gene and Genomes
https://www.biorxiv.org/content/10.1101/2022.11.03.515120v1.full
Staff scientist Eric Huckvale's first project has been to write a new #python 📦 to query KEGG's REST API (prelude to other work we want to do w/ KEGG data).
Other stuff we found didn't provide the options we wanted, so you all get to benefit too!
Arindam Basu
boosted
One really big tip: the search bar on your Mastodon dashboard can be used to pull in remote things. People do this for two use-cases:
You can copy and paste any URL to a post on the fediverse, and throw it into your search bar. Your server will pull it in and focus on it, so that you can interact with it.
Every user has what is called a “handle”, which looks a bit like an email address. The format is user@domain.tld. In my case, my handle is sean@social.deadsuperhero.com. Every profile has this thing on it - you can throw that into your search bar, and it will pull up my profile. It’s a very easy way to follow people. In the few edge cases where it fails to load, you can pull in a post instead, then click on their avatar to load the profile manually.
STEM content authoring tools alert: possible ;tldr
[deepnote](https://deepnote.com) is my third favourite. Another great app, web based. Allows writing, and data analysis all at the same time. Think of it like Google Colab notebook, except it allows for `Python`, ‘rstats’ and ‘Julia’ codes to be woven and written up. Markdown content authoring. As with Curvenote and Rstudio, you can post your paper as a well formatted post.
For \(LaTex\), the best tool to write online is @overleaflatex
you can find [Overleaf here](https://overleaf.com)
The best tool to write in \(LaTeX\)
What are your favourite tools?
STEM content authoring tools alert: possible ;tldr
[Rstudio](https://rstudio.cloud) is the next one. Like Curvenote + Jupyter, it is a one stop shop where you can do your data analysis and write your paper and push your blog at the same time. Based on R, and works well for me.
STEM content authoring tools alert: possible ;tldr
## Tools to write and analyse data science
Wanted to post a few tools I have found useful over the years to write papers and analyse data.
First up
[curvenote](https://curvenote.com)
A great tool that integrates jupyter notebook with markdown based text authoring, but more importantly, you can write dynamic text on the editor. It also has a built-in bibtex based reference management system. So, if you keep your analyses in jupyter notebooks, Curvenote offers a Chrome Extension that will enable you to ‘pull in’ version changes in your jupyter notebook into your content authoring space and will let you push your changes to jupyter notebook as well.
Great interface, free tool to host your paper plus if you want, you can push it as a mature webpage.
Great resource, this,
https://qoto.org/@bwbeach/109311485653569994
Bengali language toot alert: tips of using fediverse
হুতোম, এখানে কোট টুট করা যায়, একটু ঘুরিয়ে।
আপনি যে টুট কোট করতে চান, সেখানে ‘Reply’ দিয়ে শুরু করুন। তারপর যাকে উত্তর দিচ্ছেন, তাঁর নামটা না দিলেও চলবে।
আরেক রকম ভাবে করা যায়, যে টুট টিকে কোট করতে চান, তার URL (যেখানে সময় দেয়া আছে, সেখানে ক্লিক করুন, করে টুটের URL টি কপি করে নিন), তারপর আপনার টুটের সার্চ বাক্সয় পেস্ট করুন, করে নিজের কমেন্ট করে টুট করুন। সেভাবেও করা যায়।
এরা কোট টুট ইচ্ছে করে অফ করে রেখেছে, যাতে করে যিনি শুরু করেছেন, তাঁর প্রতি অভব্যতা কেউ না করতে পারে। সে এক জটিল গল্প, 🙂
Arindam Basu
boosted
পয়লা কাজ হলো ভিখিরি কুবেরের বাগান হতে বাবু বিবিদের হেথায় ভাগিয়ে আনা
https://mastodon.social/@quinoa_biryani/109309116690427132
Interesting. I use @curvenote
for my paper writing, and it works very well, integrates perfectly with #jupyterlab
Mighty happy with it.
@ https://curvenote.com
Arindam Basu
boosted
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From the paper,
"Surprisingly, we found that prostate cancer was uniquely genetically associated with
CAD, which may have important implications for cancer screening and integrated treatment
approaches which could target both diseases simultaneously"
Arindam Basu
boosted
Coronary artery disease and prostate cancer share a common genetic risk mediated through Lipoprotein(a) https://www.medrxiv.org/content/10.1101/2022.11.08.22282072
- Orcid Profile
- https://orcid.org/0000-0003-2326-2292
- Images (pixelfed)
- https://pixelfed.social/i/web/profile/424715601356972526
- Join me in Matrix Chat
- https://matrix.to/#/@arinbasu:qoto.org
Professor, Epidemiologist. Doctor (ENT specialist). Professor of Epidemiology and Environmental Health at the University of Canterbury in New Zealand.
Interests: lego MOCs, wood carving, mountain biking, tramping.
Joined Apr 2022
