Maastricht University

Egon Willighagen

Publishing grant proposal is still not very common. The proposal
published in Research Ideas and Outcomes)
(doi:[10.3897/rio.10.e124884](https://doi.org/10.3897/rio.10.e124884))
for the [NWO Open Science grant for the CDK](/2024/04/07/cdk2024.html)
is, however, not the first and hopefully not the last. Interestingly, it
is already cited in (the German) Wikipedia. It is used
[there](https://de.wikipedia.org/wiki/Chemistry_Development_Kit) to
support a statement which tools use the Chemistry Development Kit.


Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

cdk2024 #2: publishing grant proposals

We recently got awarded our
[second](https://chem-bla-ics.blogspot.com/2022/03/bridgedb-nwo-grant-update-1-first-steps.html?q=bridgedb)
NWO Open Science grant
([OSF23.2.097](https://www.nwo.nl/en/projects/osf232097)), this time for
the [Chemistry Development Kit](https://cdk.github.io/) (CDK). "We" here
is me and [Alyanne de Haan](https://orcid.org/0000-0003-0896-0906), René
van der Ploeg, and [Marc Teunis](https://orcid.org/0000-0002-3496-6669)
from Hogeschool Utrecht. The proposal has been submitted for public
dissemination in [RIO Journal](https://riojournal.com/), like [we
did](https://chem-bla-ics.blogspot.com/2022/04/bridgedb-nwo-grant-update-2-building-up.html?q=bridgedb)
with the first NWO Open Science grant.

The project formally started on April 1 but we had our kick-off meeting
in Maastricht on April 4-5. We were joined by Javier and on the second
day by Marvin, and Ozan from our [BiGCaT research
group](https://www.maastrichtuniversity.nl/research/bioinformatics) in
Maastricht. During this hackathon, I gave a (repeat)
[presentation](https://zenodo.org/records/6414204) about the history of
the CDK which also included the problem that software using the CDK does
not always use the most recent version.

And that, upgrading tools using the CDK with the latest CDK version, is
the main topic of this grant (work package 2, WP2). The full proposal
has the focus list of tools, but most of it is also listed in [the issue
tracker](https://github.com/cdk/nwo-openscience-2024/issues) we have set
up as project management tool on GitHub.

Second, we actually hacked together on two first tools, one on our focus
list, but the other that was [requested we have a look at
too](https://github.com/cdk/nwo-openscience-2024/issues/22): SMARTCyp.
The latest version uses [RDKit](https://www.rdkit.org/)
(doi:[10.1093/bioinformatics/btz037](https://doi.org/10.1093/bioinformatics/btz037)),
but the original version uses the CDK
(doi:[10.1021/ml100016x](https://doi.org/10.1021/ml100016x)).

We downloaded the source code of SMARTCyp 2.4.2, started taking
[notes](https://github.com/cdk/nwo-openscience-2024/blob/main/monitoring/smartcyp.md),
Javier [started](https://github.com/cdk/smartcyp) a Maven build
environment, updated a lot of code, but we seem quite close to a version
that can be tested by people that have integrated SMARTCyp in other
tools. This is based on [CDK
2.9](https://github.com/cdk/cdk/releases/tag/cdk-2.9) and if you ignore
the 2D depiction glitch, it looks it was a nice first choice:

![](/assets/images/smartcyp.png)

On a final note, we plan to record carefully our steps, in an open
notebook science approach, with the intention to extract general upgrade
steps. For example, we will update the
[Migration](https://egonw.github.io/cdkbook/migration.html) section of
the [Groovy Cheminformatics with the Chemistry Development
Kit](https://egonw.github.io/cdkbook/).


We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.

Rogue Scholar Posts

cdk2024 #2: publishing grant proposals

cdk2024 #1: NWO Open Science grant for the Chemistry Development Kit