Jennifer Lin
LightNews LightNews
banner
jhylin.bsky.social
Jennifer Lin
@jhylin.bsky.social
880 followers 230 following 25 posts
Enthusiast in using Python for drug data. Occasionally uses R. Used to be a pharmacist and happened to have a comp/med chem PhD.
Posts Replies Media Videos
jhylin.bsky.social
Notes on integrating Python and R in one place using:

rpy2 - jhylin.github.io/Data_in_life...

reticulate - jhylin.github.io/Data_in_life...
November 11, 2025 at 2:11 AM
Reposted by Jennifer Lin
emilyriederer.bsky.social
The way python and R foster inclusion directly contributes to their success: joyful places to exist, a steady flow of new maintainers, and a delightful collection of niche tools empowered by wildly different expertise coming together

Watch the new python documentary for more on PSF’s work here
The PSF applied a $1.5M grant from the US National Science Foundation (NSF) to make innovative improvements to packaging security — and we were recommended for funding! But as a condition of funding, we were asked to affirm that we wouldn’t undertake any diversity, equity, and inclusion work, whether or not we used the government funds to do so. The PSF simply couldn’t agree to that statement, as facilitating “the growth of a diverse and international community of Python programmers” is written directly into our mission and core to our values, so we withdrew our application. In the end, it wasn’t a hard decision for the PSF to put our community and our values first, but it does mean we lost out on this large funding source. Donations and sponsorship will help us fill the gap, so we can continue supporting the Python ecosystem and living our values.
October 28, 2025 at 12:20 AM
Reposted by Jennifer Lin
iwatobipen.bsky.social
www.unesco.org/en/artificia...
Ethics of Artificial Intelligence
The Recommendation
www.unesco.org
October 3, 2025 at 11:02 PM
Reposted by Jennifer Lin
chembl.bsky.social
ChEMBL 36 is out!

chembl.blogspot.com/2025/09/chem...
ChEMBL 36 is out!
📊 Database Scale 🆕 New Data Sources Src_ID 72 – Chemical Probe data from Scientific Literature NLP and manual extraction from probe-r...
chembl.blogspot.com
September 23, 2025 at 2:42 PM
Reposted by Jennifer Lin
bzdrazil.bsky.social
Check out our new paper available as preprint: chemrxiv.org/engage/chemr...
Enhancing Bioassay Annotations in ChEMBL with Artificial Intelligence
As the volume and diversity of bioactivity data in ChEMBL continues to grow, ensuring that assay metadata is standardized, interoperable, and machine-readable is critical for effective use in cheminfo...
chemrxiv.org
September 18, 2025 at 10:26 AM
Reposted by Jennifer Lin
chris.blue
This looks nice.
GitHub - microsoft/presidio: An open-source framework for detecting, redacting, masking, and anonymizing sensitive data (PII) across text, images, and structured data. Supports NLP, pattern matching, ...
An open-source framework for detecting, redacting, masking, and anonymizing sensitive data (PII) across text, images, and structured data. Supports NLP, pattern matching, and customizable pipelines...
github.com
August 21, 2025 at 7:52 PM
Reposted by Jennifer Lin
baoilleach.bsky.social
Want to work with me on cool stuff? #ukchemjobs #chembl #chemjobs
chembl.bsky.social Chemical Biology Services @chembl.bsky.social · Aug 21
Last chance to apply for this pivotal role, taking our services to the next level. Get in touch by end of Aug if interested...
chembl.bsky.social Chemical Biology Services @chembl.bsky.social · Jul 14
We are inviting applications for a 3-year ARISE2 Postdoctoral Fellowship with the team. Read more on our blog at: chembl.blogspot.com/2025/07/invi...
August 21, 2025 at 6:36 PM
Reposted by Jennifer Lin
ivelasq3.bsky.social
ellmer (for #RStats) and chatlas (for #Python) integrate LLMs directly into your code. They also support local LLMs (like #Ollama) so you can run models on your own machine, in case you have sensitive data, a lack of API access, or cost restrictions.

Check out how here! posit.co/blog/setting...
A white outline of a llama's head, the Ollama logo, is centered against a blue background with a subtle, light blue, bubbly pattern. Around the llama's neck is a thin yellow necklace with two circular pendants. The left pendant is blue with a white 'R' logo, and the right pendant is yellow with a black and yellow Python logo.
August 19, 2025 at 2:35 PM
Reposted by Jennifer Lin
chembl.bsky.social
In support of @egonw.mastodon.social.ap.brid.gy 's 'One Million IUPAC Names' project, we have just released more than 4 million IUPAC names text-mined from patents.

Read more at: chembl.blogspot.com/2025/08/unle...
Unleashing 4 million IUPAC names into the wild
In support of Egon Willighagen's ' One Million IUPAC Names ' project, we have just released more than 4 million IUPAC names text-mined from...
chembl.blogspot.com
August 8, 2025 at 11:23 AM
jhylin.bsky.social
#chemjobs
fayned.bsky.social Darren Fayne @fayned.bsky.social · Jul 23
I'm looking forward to welcoming two new colleagues to the School of Chemical Sciences in Dublin City University, as we are recruiting Assistant Professors in Biochemistry/Chemical Biology and Chemistry with AI. Please see the adverts below and help spread the word. www.dcu.ie/chemistry/va...
August 3, 2025 at 7:10 AM
Reposted by Jennifer Lin
baoilleach.bsky.social
#cheminformatics #chembl #surechembl #chemjobs #chempostdocs
August 2, 2025 at 5:02 PM
Reposted by Jennifer Lin
miketheman.com
Always verify the domain is pypi.org before logging in.

Read more: blog.pypi.org/posts/2025-0...
PyPI Users Email Phishing Attack - The Python Package Index Blog
PyPI Users are receiving emails detailing them to log in to a fake PyPI site.
blog.pypi.org
July 28, 2025 at 2:35 PM
Reposted by Jennifer Lin
wpwalters.bsky.social
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
July 22, 2025 at 1:40 PM
Reposted by Jennifer Lin
posit.co
Announcing Orbital for Python! For Scikit-learn users, this tool transforms your ML pipelines into SQL queries, letting predictions run directly in your database without a #Python environment.

Learn more: posit.co/blog/introdu...
A white stylized serpent or "S" curve with a circular head and dot for an eye, is centered on a dark blue circle. Behind the circle is a dark blue background with lighter blue vertical lines of varying heights, resembling an audio waveform.
July 14, 2025 at 2:11 PM
Reposted by Jennifer Lin
chembl.bsky.social
We would very much appreciate people taking the time to fill our impact survey. This helps makes the case for support for our resources. Survey closes on July 16th.
July 11, 2025 at 12:29 PM
Reposted by Jennifer Lin
chembl.bsky.social
The ChEMBL-og: Support ChEMBL - EMBL-EBI user survey! chembl.blogspot.com/2025/06/supp...
Support ChEMBL - EMBL-EBI user survey!
If our data resources have ever been of use to you, here’s your chance to give back! EMBL-EBI’s impact survey aims to understand the usage,...
chembl.blogspot.com
June 25, 2025 at 10:31 AM
Reposted by Jennifer Lin
marimo.io
You can now use marimo with quarto from Posit!

With the marimo-quarto plugin you get reactive execution as well as our suite of widget are all available from blogs that want to use it.

For a demo, check our latest YT video:
youtu.be/scuGmtv81S0
Introducing: the marimo-quarto plugin!
We made a new plugin!You can learn more about all of this by checking out these two links:https://github.com/marimo-team/quarto-marimohttps://quarto.org/Repo...
www.youtube.com
June 23, 2025 at 4:59 PM
Reposted by Jennifer Lin
lelandmcinnes.bsky.social
But most importantly you can build this yourself using open source tools. A notebook with full end-to-end code is here: gist.github.com/lmcinnes/951...

You can use the same tools and techniques to build a map for your own data.
Interactive Data Map of Wikipedia
Interactive Data Map of Wikipedia. GitHub Gist: instantly share code, notes, and snippets.
gist.github.com
June 22, 2025 at 3:36 PM
Reposted by Jennifer Lin
chembl.bsky.social
In collaboration with Dr Daniel Lowe, we are delighted to announce that the new home of the OPSIN web service is at EMBL-EBI. This well-known service converts systematic IUPAC names to structure.

Read more on our post: chembl.blogspot.com/2025/05/opsi...
OPSIN's new home is at EMBL-EBI
We are delighted to announce that the OPSIN web app has become a member of the Chemical Biology Services here at EMBL-EBI and can be acces...
chembl.blogspot.com
May 17, 2025 at 6:57 AM
Reposted by Jennifer Lin
me-datapoint.bsky.social
New release of my "Hands-on Introduction to Data Science with Python" textbook!

Contains many text edits and figure updates. For instance, in the sections on Clustering and Machine Learning.

All fully #opensource and #openaccess. Figures are #CCBY.

--> florian-huber.github.io/data_science...
May 14, 2025 at 8:10 PM
jhylin.bsky.social
Here's the expanded CYP-ADRs dataset on adverse drug reactions for cytochrome P450 substrates (drugs) with ideas behind this work.

Dataset: github.com/jhylin/Adver...

Ideas: jhylin.github.io/Data_in_life...

#prescription_drugs #cytochromep450 #adverse_reactions #cheminformatics
April 27, 2025 at 11:40 PM
Reposted by Jennifer Lin
veit-schiele.de
🎉 Yeah, uv 0.6.15 supports PEP751, pylock.toml with
• uv export -o pylock.toml
• uv pip compile -o pylock.toml -r requirements.in
• uv pip sync pylock.toml
• uv pip install -r pylock.toml
github.com/astral-sh/uv...
#Python
Release 0.6.15 · astral-sh/uv
Release Notes This release includes preliminary support for the pylock.toml file format, as standardized in PEP 751. pylock.toml is an alternative resolution output format intended to replace requi...
github.com
April 22, 2025 at 6:56 AM
Reposted by Jennifer Lin
baoilleach.bsky.social
Over on LinkedIn, I am polling people on whether they are interested in attending a ChEMBL UGM in person or remote. Leave a message here or follow the link if interested. (Stupid LI, you need to view desktop version of this site if on phone):
www.linkedin.com/posts/noel-o...
Noel O'Boyle posted on LinkedIn
Noel O'Boyle posted on LinkedIn
www.linkedin.com
April 4, 2025 at 6:00 AM
Reposted by Jennifer Lin
mathspp.com
Don't use the method `replace` to remove punctuation from a Python string.

Instead, use the method `translate`.

This is much more efficient and more general.

The method `translate` expects a “translation table” in a specific format, but `maketrans` builds it for us.
Diagram showing how to use the string method `translate` to remove punctuation from a string. You can remove punctuation from a string in Python with ease. Instead of using the method `replace` repeatedly to remove one punctuation character at a time, you can use the method `translate`. The method `translate` expects a “translation table”, but `maketrans` builds it for us. The string method translate expects a “translation table”, which we build with the auxiliary class method maketrans. The third argument is a string of characters we want to delete. Full code: import string s = "Hello, world!" print(s.translate(str.maketrans("", "", string.punctuation))) # Hello world
March 15, 2025 at 5:55 PM