#scientificsoftware

Christian MeestersInterested in <a href="https://fediscience.org/tags/MPI" class="mention hashtag" rel="nofollow noopener" target="_blank">#MPI</a> and <a href="https://fediscience.org/tags/OpenMP" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenMP</a> parallel programming to speed up your scientific applications written in <a href="https://fediscience.org/tags/C" class="mention hashtag" rel="nofollow noopener" target="_blank">#C</a>, <a href="https://fediscience.org/tags/Cpp" class="mention hashtag" rel="nofollow noopener" target="_blank">#Cpp</a>, <a href="https://fediscience.org/tags/Fortran" class="mention hashtag" rel="nofollow noopener" target="_blank">#Fortran</a> or <a href="https://fediscience.org/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#Python</a> (with <a href="https://fediscience.org/tags/numpy" class="mention hashtag" rel="nofollow noopener" target="_blank">#numpy</a>)?Attend our course in <a href="https://fediscience.org/tags/Mainz" class="mention hashtag" rel="nofollow noopener" target="_blank">#Mainz</a> at the Johannes Gutenberg University (<a href="https://fediscience.org/tags/JGU" class="mention hashtag" rel="nofollow noopener" target="_blank">#JGU</a>) for a 4-day course from 1. April to 4. April 2025!See our announcement page for further details and to register: <a href="https://indico.zdv.uni-mainz.de/event/34/" rel="nofollow noopener" translate="no" target="_blank">https://indico.zdv.uni-mainz.de/event/34/</a>Note, it is an on-site course.<a href="https://fediscience.org/tags/RSE" class="mention hashtag" rel="nofollow noopener" target="_blank">#RSE</a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificsoftware</a>

Daniel HuppmannThe <a href="https://mastodon.social/tags/Energy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Energy</a> <a href="https://mastodon.social/tags/Climate" class="mention hashtag" rel="nofollow noopener" target="_blank">#Climate</a> & <a href="https://mastodon.social/tags/Environment" class="mention hashtag" rel="nofollow noopener" target="_blank">#Environment</a> program at <a href="https://mastodon.social/tags/IIASAVienna" class="mention hashtag" rel="nofollow noopener" target="_blank">#IIASAVienna</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" target="_blank">#ScenarioServices</a> & <a href="https://mastodon.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScientificSoftware</a> team.We developed a new <a href="https://mastodon.social/tags/ScenarioExplorer" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScenarioExplorer</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" target="_blank">#opensource</a> packages for scenario analysis, validation & data-management.Step by step towards <a href="https://mastodon.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> and reusable, reproducible analysis...

jonny (good kind)Here's an ~ official ~ release announcement for <a href="https://neuromatch.social/tags/numpydantic" class="mention hashtag" rel="nofollow noopener" target="_blank">#numpydantic</a>repo: <a href="https://github.com/p2p-ld/numpydantic" rel="nofollow noopener" translate="no" target="_blank">https://github.com/p2p-ld/numpydantic</a> docs: <a href="https://numpydantic.readthedocs.io" rel="nofollow noopener" translate="no" target="_blank">https://numpydantic.readthedocs.io</a>Problems: <a href="https://fosstodon.org/@pydantic" class="u-url mention" rel="nofollow noopener" target="_blank">@pydantic</a> 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.<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.This is a standalone part of my work with <a href="https://fosstodon.org/@linkml" class="u-url mention" rel="nofollow noopener" target="_blank">@linkml</a> <a href="https://linkml.io/linkml/schemas/arrays.html" rel="nofollow noopener" 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. plenty of <a href="https://numpydantic.readthedocs.io/en/latest/todo.html" rel="nofollow noopener" target="_blank">todos</a>, but hope ya like it.<a href="https://neuromatch.social/tags/linkml" class="mention hashtag" rel="nofollow noopener" target="_blank">#linkml</a> <a href="https://neuromatch.social/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#python</a> <a href="https://neuromatch.social/tags/NewWork" class="mention hashtag" rel="nofollow noopener" target="_blank">#NewWork</a> <a href="https://neuromatch.social/tags/pydantic" class="mention hashtag" rel="nofollow noopener" target="_blank">#pydantic</a> <a href="https://neuromatch.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScientificSoftware</a>

Christian MeestersTime for a re-<a href="https://fediscience.org/tags/introduction" class="mention hashtag" rel="nofollow noopener" target="_blank">#introduction</a> !I'm a <a href="https://fediscience.org/tags/scicomm" class="mention hashtag" rel="nofollow noopener" target="_blank">#scicomm</a> enthusiast and board member of <a href="https://fediscience.org/tags/Fediscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Fediscience</a>. My background is in <a href="https://fediscience.org/tags/Biophysics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Biophysics</a>, done a Postdoc in <a href="https://fediscience.org/tags/GeneticEpidemiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneticEpidemiology</a>, industry detour, now working in <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a> for some years.Interested in <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a>, <a href="https://fediscience.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>, <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a>, <a href="https://fediscience.org/tags/workflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#workflows</a> (<a href="https://fediscience.org/tags/snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#snakemake</a>), <a href="https://fediscience.org/tags/RDM" class="mention hashtag" rel="nofollow noopener" target="_blank">#RDM</a>, <a href="https://fediscience.org/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificsoftware</a> and <a href="https://fediscience.org/tags/sciencecommunication" class="mention hashtag" rel="nofollow noopener" target="_blank">#sciencecommunication</a> My blog can be found here: blogs.fediscience.org and my more political me can be found at <a href="https://mastodon.m1234.de/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@rupdecat@mastodon.m1234.de</a>.

WeAreSeismicaYou have spent countless hours on your code. It is time for your hard work to pay off. Document and publish your code as a software report with Seismica and let it shine!Find out more at:<a href="https://seismica.library.mcgill.ca/author-guidelines/#publication-types" rel="nofollow noopener" translate="no" target="_blank">https://seismica.library.mcgill.ca/author-guidelines/#publication-types</a><a href="https://mastodon.social/tags/Seismology" class="mention hashtag" rel="nofollow noopener" target="_blank">#Seismology</a> <a href="https://mastodon.social/tags/EarthquakeScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#EarthquakeScience</a> <a href="https://mastodon.social/tags/OpenAcces" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenAcces</a> <a href="https://mastodon.social/tags/Scientificjournals" class="mention hashtag" rel="nofollow noopener" target="_blank">#Scientificjournals</a> <a href="https://mastodon.social/tags/DiamondOpenAccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#DiamondOpenAccess</a> <a href="https://mastodon.social/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificsoftware</a> <a href="https://mastodon.social/tags/peerreviewed" class="mention hashtag" rel="nofollow noopener" target="_blank">#peerreviewed</a>

Daniel HuppmannAre your a <a href="https://mastodon.social/tags/SoftwareDeveloper" class="mention hashtag" rel="nofollow noopener" target="_blank">#SoftwareDeveloper</a> that would like to work on <a href="https://mastodon.social/tags/Climate" class="mention hashtag" rel="nofollow noopener" target="_blank">#Climate</a>-related <a href="https://mastodon.social/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#opensource</a> tools & <a href="https://mastodon.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> solutions?Or are your an <a href="https://mastodon.social/tags/EarlyCareer" class="mention hashtag" rel="nofollow noopener" target="_blank">#EarlyCareer</a> <a href="https://mastodon.social/tags/Researcher" class="mention hashtag" rel="nofollow noopener" target="_blank">#Researcher</a> that prefers programming to paper-writing?The <a href="https://mastodon.social/tags/ScenarioServices" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScenarioServices</a> team at the <a href="https://mastodon.social/tags/IIASA" class="mention hashtag" rel="nofollow noopener" target="_blank">#IIASA</a> <a href="https://mastodon.social/tags/Energy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Energy</a> <a href="https://mastodon.social/tags/Climate" class="mention hashtag" rel="nofollow noopener" target="_blank">#Climate</a> & <a href="https://mastodon.social/tags/Environment" class="mention hashtag" rel="nofollow noopener" target="_blank">#Environment</a> program is hiring a <a href="https://mastodon.social/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScientificSoftware</a> developer to implement new (<a href="https://mastodon.social/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#opensource</a>) user interfaces & <a href="https://mastodon.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> features for our <a href="https://mastodon.social/tags/ScenarioExplorer" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScenarioExplorer</a> infrastructure.👉<a href="https://iiasa.ac.at/employment/job-openings?jh=oj8uz8mtiehwnwyhls5u7b355mdre6b" rel="nofollow noopener" target="_blank">https://iiasa.ac.at/employment/job-openings?jh=oj8uz8mtiehwnwyhls5u7b355mdre6b</a>

Giuseppe BilottaOn an (un)related topic, does anybody have recommendations on a journal whose primary scope is <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/scientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificSoftware</a>? Preference for <a href="https://fediscience.org/tags/CFD" class="mention hashtag" rel="nofollow noopener" target="_blank">#CFD</a>, but more generalist recommendation are welcome too. This manuscript looking for a home is more focused on the actual code (programming strategies etc) than the physics, which makes it a poor fit for journals like CPC and JCP.

Daniel Huppmann<a href="https://fosstodon.org/@danielskatz" class="u-url mention" rel="nofollow noopener" target="_blank">@danielskatz</a> FWIW, here‘s a non-paywalled link: <a href="https://rdcu.be/c6uMN" rel="nofollow noopener" target="_blank">https://rdcu.be/c6uMN</a>I think it‘s great to emphasise the lack of incentives for <a href="https://mastodon.social/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificsoftware</a> development and <a href="https://mastodon.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> more generally), but I believe that the solutions proposed by the authors are too narrow… We need to focus on an incentive structure that focuses on the usability of the tools!

Ben FultonThis article presents a study on the quality and execution of research code from publicly-available replication datasets at the Harvard Dataverse repo. "The infrequent usage and absence of libraries also tell us what researchers are not doing in their projects. In particular, libraries that are used for code testing, such as runit, testthat, tinytest and unitizer, were not present."Yeah, I could have told you that *grumble*<a href="https://www.nature.com/articles/s41597-022-01143-6" rel="nofollow noopener" target="_blank">https://www.nature.com/articles/s41597-022-01143-6</a><a href="https://fosstodon.org/tags/testing" class="mention hashtag" rel="nofollow noopener" target="_blank">#testing</a> <a href="https://fosstodon.org/tags/rse" class="mention hashtag" rel="nofollow noopener" target="_blank">#rse</a> <a href="https://fosstodon.org/tags/rseng" class="mention hashtag" rel="nofollow noopener" target="_blank">#rseng</a> <a href="https://fosstodon.org/tags/ScientificSoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#ScientificSoftware</a>

Christian MeestersTime for an <a href="https://fediscience.org/tags/introduction" class="mention hashtag" rel="nofollow noopener" target="_blank">#introduction</a> ! It's my 3rd or 4th day. Thanks for having me here. 😀 My background: PhD in <a href="https://fediscience.org/tags/Biophysics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Biophysics</a>, PostDoc in <a href="https://fediscience.org/tags/GeneticEpidemiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#GeneticEpidemiology</a>, industry detour, now working in <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a> for ~8y. Interested in <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a>, <a href="https://fediscience.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>, <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a>, <a href="https://fediscience.org/tags/workflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#workflows</a> (<a href="https://fediscience.org/tags/snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#snakemake</a>), <a href="https://fediscience.org/tags/RDM" class="mention hashtag" rel="nofollow noopener" target="_blank">#RDM</a>, <a href="https://fediscience.org/tags/scientificsoftware" class="mention hashtag" rel="nofollow noopener" target="_blank">#scientificsoftware</a> and <a href="https://fediscience.org/tags/sciencecommunication" class="mention hashtag" rel="nofollow noopener" target="_blank">#sciencecommunication</a> . Former scienceblogger (German), now looking for a new plattform, since the current (scienceblogs.de) is closing down.

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