@blueobelisk.fosstodon.org.ap.brid.gy
#OpenData, #OpenStandards, #OpenSource for #chemistry https://doi.org/10.1186/1758-2946-3-37 🌉 bridged from https://fosstodon.org/@blueobelisk on the fediverse by https://fed.brid.gy/
CMLXOM 4.14 is out: https://github.com/BlueObelisk/cmlxom/releases/tag/cmlxom-4.14
This release updates three dependencies.
CMLXOM is a Java library for processing CML, implementing the XML object model (XOM) for the Chemical Markup Language (CML).
RE: https://fosstodon.org/@gicrisf/115515504598989643
that sounds useful! are there other #cheminformatics toolkits integrated into #Emacs ?
BChemXtract - a ChemDraw parser and structure extractor - is our first open source software project and is available on @github:
🔗 https://github.com/Beilstein-Institut/BChemXtract
#openscience #opensource #FAIRdata #FAIRchemistry #cheminformatics #GitHub #BeilsteinCheminfoLabs #BChemXtract
Euclid 2.13 is released: https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.13
Minor update that is tested with Java 21 and 25, for which it removed the unused ThriftyList class. It also upgraded dependencies to Log4j 2.25.2 and Commons Lang3 3.19
Euclid is a library of numeric […]
"Getting a DOI on personal blog posts is technically challenging, but possible using services such as The Rogue Scholar (https://docs.rogue-scholar.org/)." https://doi.org/10.1007/s44186-024-00287-w
12.10.2025 07:33 — 👍 8 🔁 11 💬 0 📌 0#compchemsky
Now offers tools to save computed spectra as PNG, PDF, SVG .. or the underlying data.
Found a really nice #opensource #openscience plotting library
25 years Chemistry Development Kit (CDK) and going strong! :) https://doi.org/10.59350/4ce2c-fxh02 https://chem-bla-ics.linkedchemistry.info/2025/09/28/25-years-of-the-chemistry-development-kit.html
Replying to this post will make it show up in my blog.
#openscience #chemistry #opensource
this week, 25 years ago, @steinbeck, @egonw, and @gezelter came together in South Bend., USA and founded the Chemistry Development Kit
#chemistry #openscience
Screenshot of a frame of one of the videos in the linked pull request, showing a chemical structure with various R-groups on the left (code and R group values), and on the right a list of SMILES combinatorial structures generated from the input on the left.
nice new R-group SMILES enumeration feature in the upcoming JChemPaint release, see https://github.com/JChemPaint/jchempaint/pull/225
#openscience #chemistry
pybacting 0.2.15 is released with Bacting 1.0.7 (see also https://social.edu.nl/@egonw/115040533430981814): https://pypi.org/project/pybacting/0.2.15/
pybacting is a Python wrapper around Bacting which provides functionality from the Chemistry Development Kit, OPSIN, Oscar4, BridgeDb, InChI […]
@mike
When #Elsevier sent takedown notices to a few #Harvard authors who posted copies of their articles to their personal web sites (2014), I did an interview with Harvard Library and replied much as you did […]
Oscar4 5.3.0 has been released: https://github.com/BlueObelisk/oscar4/releases/tag/5.3.0
"OSCAR (Open Source Chemistry Analysis Routines) is an open source extensible system for the automated annotation of chemistry in scientific articles. It can be used to identify chemical names, reaction […]
CMLXOM 4.13 is out: https://github.com/BlueObelisk/cmlxom/releases/tag/cmlxom-4.13
This release updates three dependencies.
CMLXOM is a Java library for processing CML, implementing the XML object model (XOM) for the Chemical Markup Language (CML).
Euclid 2.12 is released: https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.12
This release updates three dependencies, including commons-lang3 to 3.18.
Euclid is a library of numeric, geometric and XML routines.
We have recently delivered around 40,000 chemical names to the One Million IUPAC Names project of Egon Willighagen @egonw. A CC0 license provides the community with a free and reusable set of chemical names.
We encourage the community to join us in supporting […]
[Original post on hessen.social]
and follows by CMLXOM 4.12: https://github.com/BlueObelisk/cmlxom/releases/tag/cmlxom-4.12
CMLXOM is a Java library for processing CML, implementing the XML object model (XOM) for the Chemical Markup Language (CML).
#openscience #cheminformatics
Euclid 2.11 is released: https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.11
Euclid is a library of numeric, geometric and XML routines.
#openscience #cheminformatics
2D chemical depiction of a chemical structure with nine sugar-like rings from the longest IUPAC name found so far, with 626 characters in length.
new: 'One Million IUPAC names #3: the 200 thousand milestone and 1 million IUPAC names" https://doi.org/10.59350/6f7he-kxt56 https://chem-bla-ics.linkedchemistry.info/2025/06/09/one-million-iupac-names.html
"I could not find the time earlier to report (reason) […]
[Original post on social.edu.nl]
new preprint with #opensource #cheminformatics by @Kohulan et al.: "Cheminformatics Microservice V-3: A Web Portal for Chemical Structure Manipulation and Analysis" https://doi.org/10.26434/chemrxiv-2025-xjkxl
"Here, we present Cheminformatics Microservice V3, a significant update to the […]
Screenshot of Ammar's Snorql UI, here wrapped around the Wikidata SPARQL instance by the QLever team, federating with the IDSM SPARQL endpoint for substructure searching, and using CDK Depict to convert the SMILES into 2D depictions in the results tables
oolonek reminded me how cool IDSM is (see https://doi.org/10.1186/s13321-021-00515-1) and works wonderfully in the rich chemistry SPARQL world (see https://doi.org/10.1186/1758-2946-3-15).
Here I mashed up @wikidata, IDSM, QLever, @cdk Depict, and Ammar […]
[Original post on social.edu.nl]
Fwd: "OPSIN's new home is at EMBL-EBI" https://chembl.blogspot.com/2025/05/opsins-new-home-is-at-embl-ebi.html
"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 accessed at:
https://www.ebi.ac.uk/opsin " […]
the @intconfchemstr is held soon. At least two Blue Obelisk members are going to meet up. Who else likes to join?
#openscience #chemistry
Too bad you can't give a Nobel prize to the PDB. How much science and medicine has been enabled because of this open resource?
#OpenScience
The 2025_03_1 release of #RDKit release includes my contribution to speed up part of getting 2D fingerprints for a molecule by ~75x! So if you generate #chemical fingerprints, now is a good time to upgrade.
Reminder that I'm #OpenToWork so if you're hiring for #cheminformatics or […]
"Against common expectations, scientific projects have a longer lifetime than matched non-scientific open-source software projects. We expect our curated attribute-rich collection to support future research on scientific software and provide insights that may help extend longevity of both […]
29.04.2025 13:54 — 👍 1 🔁 2 💬 0 📌 0
Screenshot of the GitHub "commits over time" chart, showing the weekly number of commit, starting in February, and going down until mid March, when it stabilized at around 5 commits per day, each about ~1000 new IUPAC names. Until the week of April 21, then jumping to over 35 commits, reflecting a change in the workflow, as explained in the post.
new blog: "One Million IUPAC names #2: the 100 thousand milestone" https://doi.org/10.59350/dycsw-qeq51 https://chem-bla-ics.linkedchemistry.info/2025/04/27/one-million-iupac-names-2-the-100-thousand-milestone.html
"Two and a half month into the One Million […]
[Original post on social.edu.nl]
but then I also read news like this, which stems me optimistic: "The combined efforts of the recipients are anticipated to create almost 100,000 new quantitative reaction data points which will be published under a CC BY-SA license in the structured ORD format, ready for machine learning by […]
24.04.2025 08:46 — 👍 0 🔁 2 💬 0 📌 0#openscience #cheminformatics dates back to the late nineties with the emerging collaborative development of JChemPaint, Jmol, and the Chemical Markup Language. Sketch of the history by Chris Steinbeck: "The evolution of open science in cheminformatics: a journey from closed systems to […]
05.04.2025 04:30 — 👍 0 🔁 4 💬 1 📌 0CMLXOM 4.11 has been released: https://doi.org/10.5281/zenodo.15108779
"Minor release, reverting to (the newer) xml-apis 1.4.01, updating to Joda time 2.14, and removing unused imports, updating deprecated code, and minimal added JavaDoc."
CMLXOM is a Java library for reading and writing […]
