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Blue Obelisk
@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).
Release CMLXOM 4.14 · BlueObelisk/cmlxom
Minor update with upgraded dependencies to Commons IO 2.21, Log4j 2.25.2, and Euclid 2.13. Full Changelog: cmlxom-4.13...cmlxom-4.14
github.com
November 9, 2025 at 10:12 AM
RE: https://fosstodon.org/@gicrisf/115515504598989643

that sounds useful! are there other #Cheminformatics toolkits integrated into #emacs ?
fosstodon.org
November 9, 2025 at 9:43 AM
Reposted by Blue Obelisk
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
November 5, 2025 at 2:00 PM
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 […]
Original post on fosstodon.org
fosstodon.org
November 2, 2025 at 4:37 PM
Reposted by Blue Obelisk
"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
What is Rogue Scholar? – Rogue Scholar Documentation
docs.rogue-scholar.org
October 12, 2025 at 7:34 AM
Reposted by Blue Obelisk
#compchemsky

Now offers tools to save computed spectra as PNG, PDF, SVG .. or the underlying data.

Found a really nice #opensource #openscience plotting library
👀

Coming soon...
September 27, 2025 at 5:04 PM
Reposted by Blue Obelisk
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
25 years of the Chemistry Development Kit
Twenty five years ago the Chemistry Development Kit (CDK) was founded. The Chemistry and Internet (ChemInt2000) had just ended (it ran from 23 to 26 September) and my friend and I had taken the Amtrak night train from Washington to South Bend. At that time there were two leading Java applets for chemistry, JChemPaint and Jmol. I had hacked Chemical Markup Language support into both of them, and Dan Gezelter (Jmol and openscience.org), Christoph Steinbeck (JChemPaint), and me took the opportunity of being in North America to discuss if we could use a common code base. Chris’ _compchem_ had done something similar. Peter Murray-Rust, who had also attended ChemInt2000 like me and Chris did not attend. I do not remember exactly, but I guess we must have met on the 28th and 29th? Maybe already on Wednesday. During this meeting we discussed a common data model (yes, Jmol used the CDK data model at some point) and somewhere during the meeting we wrote down a name for the project. There was the Java Development Kit, so this could be the Chemistry Development Kit. The name stuck. A quick post like this cannot do credit to the history of the CDK, nor of everyone involved in the past or still is. You can browse some of the history of the CDK in my blog and in Chris’ blog. It has been an amazing journey and with a small grant just behind us (with Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht), and all the awesome things ongoing (new JChemPaint, various extensions, upgraded downstream tools), the CDK is alive and kicking. A huge congrats and thanks to everyone (and every company and organization) who contributed code to the CDK with this huge milestone. There are a few people that I want to particularly thank (see the AUTHORS file for all names): Chris, who in the late nineties made a difference with open source in chemistry, Dan, for Jmol and hosting this memorable meeting at Notre Dame University, Rajarshi Guha, who operated _CDK Nightly_ for many years, well before Travis and Google Actions, Stefan, Miguel, Gilleain, and Christian, for many years of contributions to the CDK, and John Mayfield, the current CDK release manager.
github.com
September 28, 2025 at 8:42 AM
Reposted by Blue Obelisk
this week, 25 years ago, @steinbeck, @egonw, and @gezelter came together in South Bend., USA and founded the Chemistry Development Kit

#chemistry #openscience
September 26, 2025 at 10:30 AM
Reposted by Blue Obelisk
nice new R-group SMILES enumeration feature in the upcoming JChemPaint release, see https://github.com/JChemPaint/jchempaint/pull/225

#openscience #chemistry
September 11, 2025 at 11:44 AM
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 […]
Original post on fosstodon.org
fosstodon.org
August 23, 2025 at 10:54 AM
Reposted by Blue Obelisk
@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 […]
Original post on fediscience.org
fediscience.org
August 14, 2025 at 3:38 PM
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 […]
Original post on fosstodon.org
fosstodon.org
August 5, 2025 at 10:36 AM
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).
Release CMLXOM 4.13 · BlueObelisk/cmlxom
Minor update with upgraded dependencies to Commons IO 2.20, Log4j 2.25.1, and Euclid 2.12. Full Changelog: cmlxom-4.12...cmlxom-4.13
github.com
July 20, 2025 at 2:42 PM
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.
Release Euclid 2.12 · BlueObelisk/euclid
Minor update with upgraded dependencies to Commons IO 2.20, Log4j 2.25.1, and Commons Lang3 3.18. Full Changelog: euclid-2.11...euclid-2.12
github.com
July 20, 2025 at 11:51 AM
Reposted by Blue Obelisk
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]
July 17, 2025 at 1:01 PM
Reposted by Blue Obelisk
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]
June 9, 2025 at 10:01 AM
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 […]
Original post on fosstodon.org
fosstodon.org
June 6, 2025 at 7:52 AM
Reposted by Blue Obelisk
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]
May 29, 2025 at 10:16 AM
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 " […]
Original post on fosstodon.org
fosstodon.org
May 16, 2025 at 11:26 AM
the @intconfchemstr is held soon. At least two Blue Obelisk members are going to meet up. Who else likes to join?

#openscience #chemistry
May 11, 2025 at 10:09 AM
Reposted by Blue Obelisk
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
50 years of open access to the PDB has accelerated scientific advances in protein structure architecture and AI/ML prediction tools. #NSFfunded #NSF75
May 8, 2025 at 4:25 PM
Reposted by Blue Obelisk
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 […]
Original post on fosstodon.org
fosstodon.org
May 1, 2025 at 4:17 PM
"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 […]
Original post on fosstodon.org
fosstodon.org
April 29, 2025 at 1:54 PM