Jeremy Monat<p>The 2025_03_1 release of <a href="https://fosstodon.org/tags/RDKit" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RDKit</span></a> release includes my contribution to speed up part of getting 2D fingerprints for a molecule by ~75x! So if you generate <a href="https://fosstodon.org/tags/chemical" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chemical</span></a> fingerprints, now is a good time to upgrade.</p><p>Reminder that I'm <a href="https://fosstodon.org/tags/OpenToWork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenToWork</span></a> so if you're hiring for <a href="https://fosstodon.org/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cheminformatics</span></a> or <a href="https://fosstodon.org/tags/scientificSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scientificSoftware</span></a> development, let's talk.</p><p><a href="https://fosstodon.org/tags/chemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chemistry</span></a> <a href="https://fosstodon.org/tags/DrugDiscovery" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DrugDiscovery</span></a> <a href="https://fosstodon.org/tags/pharma" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pharma</span></a> <a href="https://fosstodon.org/tags/PythonForChemists" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PythonForChemists</span></a></p><p><a href="https://github.com/rdkit/rdkit/releases/tag/Release_2025_03_1" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/rdkit/rdkit/release</span><span class="invisible">s/tag/Release_2025_03_1</span></a></p>
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#scientificsoftware
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Christian Meesters<p>Interested in <a href="https://fediscience.org/tags/MPI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MPI</span></a> and <a href="https://fediscience.org/tags/OpenMP" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenMP</span></a> parallel programming to speed up your scientific applications written in <a href="https://fediscience.org/tags/C" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>C</span></a>, <a href="https://fediscience.org/tags/Cpp" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Cpp</span></a>, <a href="https://fediscience.org/tags/Fortran" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Fortran</span></a> or <a href="https://fediscience.org/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Python</span></a> (with <a href="https://fediscience.org/tags/numpy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>numpy</span></a>)?</p><p>Attend our course in <a href="https://fediscience.org/tags/Mainz" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Mainz</span></a> at the Johannes Gutenberg University (<a href="https://fediscience.org/tags/JGU" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>JGU</span></a>) for a 4-day course from 1. April to 4. April 2025!</p><p>See our announcement page for further details and to register: <a href="https://indico.zdv.uni-mainz.de/event/34/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">indico.zdv.uni-mainz.de/event/</span><span class="invisible">34/</span></a></p><p>Note, it is an on-site course.</p><p><a href="https://fediscience.org/tags/RSE" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RSE</span></a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> <a href="https://fediscience.org/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scientificsoftware</span></a></p>
Daniel Huppmann<p>The <a href="https://mastodon.social/tags/Energy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Energy</span></a> <a href="https://mastodon.social/tags/Climate" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Climate</span></a> & <a href="https://mastodon.social/tags/Environment" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Environment</span></a> program at <a href="https://mastodon.social/tags/IIASAVienna" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>IIASAVienna</span></a> had its quarterly meeting last Friday (~100 researchers), so I had to reflect on our role as community data hub and what to present on behalf of the <a href="https://mastodon.social/tags/ScenarioServices" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScenarioServices</span></a> & <a href="https://mastodon.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScientificSoftware</span></a> team.</p><p>We developed a new <a href="https://mastodon.social/tags/ScenarioExplorer" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScenarioExplorer</span></a> front-end last year, and we made a lot of progress with our <a href="https://mastodon.social/tags/opensource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>opensource</span></a> packages for scenario analysis, validation & data-management.</p><p>Step by step towards <a href="https://mastodon.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a> and reusable, reproducible analysis...</p>
Daniel Huppmann<p>Working with <a href="https://mastodon.social/tags/NUTS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NUTS</span></a> administrative EU 🇪🇺 regions is one of the little nuisances in <a href="https://mastodon.social/tags/energysystems" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>energysystems</span></a> modelling and scenario analysis.</p><p>So the <a href="https://mastodon.social/tags/IIASA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>IIASA</span></a> <a href="https://mastodon.social/tags/ScenarioServices" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScenarioServices</span></a> team put together a little <a href="https://mastodon.social/tags/opensource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>opensource</span></a> <a href="https://mastodon.social/tags/python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>python</span></a> utility package so that modelers can focus on <a href="https://mastodon.social/tags/freethemodels" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>freethemodels</span></a> and don’t have to spend too much time on data-wrangling…<br><a href="https://mastodon.social/tags/pysquirrel" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pysquirrel</span></a> <a href="https://mastodon.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScientificSoftware</span></a> <br><a href="https://github.com/iiasa/pysquirrel" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/iiasa/pysquirrel</span><span class="invisible"></span></a></p>
jonny (good kind)<p>Here's an ~ official ~ release announcement for <a href="https://neuromatch.social/tags/numpydantic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>numpydantic</span></a></p><p>repo: <a href="https://github.com/p2p-ld/numpydantic" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/p2p-ld/numpydantic</span><span class="invisible"></span></a><br>docs: <a href="https://numpydantic.readthedocs.io" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">numpydantic.readthedocs.io</span><span class="invisible"></span></a></p><p>Problems: <span class="h-card" translate="no"><a href="https://fosstodon.org/@pydantic" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>pydantic</span></a></span> is great for modeling data!! but at the moment it doesn't support array data out of the box. Often array shape and dtype are as important as whether something is an array at all, but there isn't a good way to specify and validate that with the Python type system. Many data formats and standards couple their implementation very tightly with their schema, making them less flexible, less interoperable, and more difficult to maintain than they could be. The existing tools for parameterized array types like nptyping and jaxtyping tie their annotations to a specific array library, rather than allowing array specifications that can be abstract across implementations.</p><p><code>numpydantic</code> is a super small, few-dep, and well-tested package that provides generic array annotations for pydantic models. Specify an array along with its shape and dtype and then use that model with any array library you'd like! Extending support for new array libraries is just subclassing - no PRs or monkeypatching needed. The type has some magic under the hood that uses pydantic validators to give a uniform array interface to things that don't usually behave like arrays - pass a path to a video file, that's an array. pass a path to an HDF5 file and a nested array within it, that's an array. We take advantage of the rest of pydantic's features too, including generating rich JSON schema and smart array dumping.</p><p>This is a standalone part of my work with <span class="h-card" translate="no"><a href="https://fosstodon.org/@linkml" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>linkml</span></a></span> <a href="https://linkml.io/linkml/schemas/arrays.html" rel="nofollow noopener noreferrer" target="_blank">arrays</a> and rearchitecting neurobio data formats like NWB to be dead simple to use and extend, integrating with the tools you already use and across the experimental process - specify your data in a simple <code>yaml</code> format, and get back high quality data modeling code that is standards-compliant out of the box and can be used with arbitrary backends. One step towards the wild exuberance of FAIR data that is just as comfortable in the scattered scripts of real experimental work as it is in carefully curated archives and high performance computing clusters. Longer term I'm trying to abstract away data store implementations to bring content-addressed p2p data stores right into the python interpreter as simply as if something was born in local memory. </p><p>plenty of <a href="https://numpydantic.readthedocs.io/en/latest/todo.html" rel="nofollow noopener noreferrer" target="_blank">todos</a>, but hope ya like it.</p><p><a href="https://neuromatch.social/tags/linkml" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>linkml</span></a> <a href="https://neuromatch.social/tags/python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>python</span></a> <a href="https://neuromatch.social/tags/NewWork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NewWork</span></a> <a href="https://neuromatch.social/tags/pydantic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pydantic</span></a> <a href="https://neuromatch.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScientificSoftware</span></a></p>
Christian Meesters<p>Time for a re-<a href="https://fediscience.org/tags/introduction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>introduction</span></a> !</p><p>I'm a <a href="https://fediscience.org/tags/scicomm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scicomm</span></a> enthusiast and board member of <a href="https://fediscience.org/tags/Fediscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Fediscience</span></a>. My background is in <a href="https://fediscience.org/tags/Biophysics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Biophysics</span></a>, done a Postdoc in <a href="https://fediscience.org/tags/GeneticEpidemiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneticEpidemiology</span></a>, industry detour, now working in <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> for some years.</p><p>Interested in <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a>, <a href="https://fediscience.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a>, <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a>, <a href="https://fediscience.org/tags/workflows" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>workflows</span></a> (<a href="https://fediscience.org/tags/snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>snakemake</span></a>), <a href="https://fediscience.org/tags/RDM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RDM</span></a>, <a href="https://fediscience.org/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scientificsoftware</span></a> and <a href="https://fediscience.org/tags/sciencecommunication" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>sciencecommunication</span></a> </p><p>My blog can be found here: blogs.fediscience.org and my more political me can be found at <span class="h-card" translate="no"><a href="https://mastodon.m1234.de/@rupdecat" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>rupdecat@mastodon.m1234.de</span></a></span>.</p>
Daniel Huppmann<p>The <a href="https://mastodon.social/tags/Energy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Energy</span></a> <a href="https://mastodon.social/tags/Climate" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Climate</span></a> & <a href="https://mastodon.social/tags/Environment" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Environment</span></a> program at <a href="https://mastodon.social/tags/IIASA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>IIASA</span></a> is looking for an <a href="https://mastodon.social/tags/IntegratedAssessment" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>IntegratedAssessment</span></a> modeler to join the <a href="https://mastodon.social/tags/MESSAGEix" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MESSAGEix</span></a> team!</p><p>Come work with us on policy-relevant scenarios and state-of-the-art <a href="https://mastodon.social/tags/opensource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>opensource</span></a> <a href="https://mastodon.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ScientificSoftware</span></a> tools...<br>📝 <a href="https://iiasa.ac.at/employment/job-openings?jh=9vvlm7a64e2n7qejcxg3n0dhyqx528y" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">iiasa.ac.at/employment/job-ope</span><span class="invisible">nings?jh=9vvlm7a64e2n7qejcxg3n0dhyqx528y</span></a></p>
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