JOSSCast: Open Source for Researchers

#20: Milan Klöwer joins Arfon and Abby to discuss SpeedyWeather.jl, its development, and its role in climate science. Milan is a Schmidt AI in Science Fellow at the University of Oxford. You can follow Milan on X/Twitter: https://twitter.com/milankloewer bsky: https://bsky.app/profile/milank.bsky.social and at his website milankl.github.io Episode highlights: [01:10] - Introducing Milan Clover [01:56] - Understanding Atmospheric General Circulation Models [05:15] - The Evolution of Weather Prediction [07:23] - SpeedyWeather.jl: A New Approach [20:05] - The Legacy of Fortran in Climate Science [20:51] - Why Julia? [25:35] - Building SpeedyWeather.jl [26:11] - Interactive Modeling with SpeedyWeather.jl [34:07] - The Importance of Open Source in Climate Science [35:29] - Call for Contributors [40:53] - Final Thoughts and Future Plans Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06323 SpeedyWeather.jl repository: https://github.com/SpeedyWeather/SpeedyWeather.jl Milan’s website: milankl.github.io Milan social media: X/Twitter: https://twitter.com/milankloewer bsky: https://bsky.app/profile/milank.bsky.social The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#19: KJ Schmidt & Aristana Scourtas join Arfon and Abby to discuss Foundry-ML, a platform designed to simplify using machine learning datasets, highlighting its development, impacts, and their career advancements post-project. KJ just started a position at the Institute for Genomic Medicine within Nationwide Children's Hospital. Aristana is a Product and Research Manager at The Library Innovation Lab at Harvard Law School. KJ and Aristana both worked on Foundry-ML during their time working at UChicago and Globus. You can follow Aristana on LinkedIn https://www.linkedin.com/in/aristana/ and Twitter/X @aristana_s. You can follow KJ on Twitter/X @kj_schmidt or LinkedIn https://www.linkedin.com/in/schmidtkj/. Episode highlights: [01:54] Beginning of Interview with KJ Schmidt and Aristana Scourtas [02:02] What is Foundry-ML? [04:02] The Role of Globus in Foundry-ML [05:29] Reproducibility in Machine Learning [06:45] Applications and Collaborations [09:15] New Roles and Future Plans [11:01] Maintaining Foundry-ML [12:37] Sustainability in Open Source [13:12] Community Building in Open Source [21:49] Challenges and Lessons Learned [24:28] Publishing in JOSS [25:38] Closing Remarks and Contact Information Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05467 Foundry repository: https://github.com/MLMI2-CSSI/foundry Website: https://foundry-ml.org/ Movement Building from Home KJ on Twitter/X @kj_schmidt or LinkedIn https://www.linkedin.com/in/schmidtkj/ Aristana on LinkedIn https://www.linkedin.com/in/aristana/ and Twitter/X @aristana_s The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

<p>#18: Brenda Praggastis joins Arfon and Abby to discuss HyperNetX, a Python package for modeling complex network data as hypergraphs. Brenda discusses the distinctions between graphs and hypergraphs, their real-world applications, and the collaborative nature of the hypergraph community. She also delves into the open-source development process, the capabilities and limitations of HyperNetX, and the importance of community contribution in advancing hypergraph research. Tune in to learn more about hypergraphs and their growing significance in various research fields.</p> <p>Brenda is a mathematician and data scientist at the Pacific Northwest National Laboratory.</p> <p>You can follow HyperNetX on GitHub <a href="https://github.com/pnnl/HyperNetX">https://github.com/pnnl/HyperNetX</a>.</p> <h3 id="episode-highlights-">Episode highlights:</h3> <p>[01:59] - Interview Begins: Welcome Brenda! [02:05] - Understanding Hypergraphs [04:57] - Brenda&#39;s Journey to Hypergraphs [06:03] - Visualizing Hypergraphs [11:31] - Deep Dive into HyperNetX [19:58] - Applications of Hypergraphs [22:25] - Scalability and Performance of HyperNetX [24:54] - Publishing in JOSS [26:16] - Contributing to HyperNetX</p> <h3 id="links-">Links:</h3> <ul> <li>JOSS paper: <a href="https://joss.theoj.org/papers/10.21105/joss.06016">https://joss.theoj.org/papers/10.21105/joss.06016</a> </li> <li>HyperNetX repository: <a href="https://github.com/pnnl/HyperNetX">https://github.com/pnnl/HyperNetX</a> </li> <li>Docs: <a href="https://hypernetx.readthedocs.io/en/latest/">https://hypernetx.readthedocs.io/en/latest/</a> </li> <li><a href="https://joss.theoj.org/">The Journal of Open Source Software</a> (<a href="https://twitter.com/JOSS_TheOJ">Twitter/X</a>, <a href="https://blog.joss.theoj.org/">blog</a>)</li> <li>@arfon on (<a href="https://fosstodon.org/@arfon">fosstodon</a>, <a href="https://www.linkedin.com/in/arfon/">Linkedin</a>, <a href="https://github.com/arfon">GitHub</a>, <a href="https://www.arfon.org/">website</a>)</li> <li>@abbycabs on (<a href="https://twitter.com/abbycabs">Twitter/X</a>, <a href="https://hachyderm.io/@abbycabs">hachyderm</a>, <a href="https://bsky.app/profile/abbycabs.bsky.social">bsky</a>, <a href="https://www.linkedin.com/in/abbycabs/">Linkedin</a>, <a href="https://github.com/abbycabs">GitHub</a>, <a href="https://abbycabs.github.io/">website</a>)</li> <li><a href="https://numfocus.org/donate-to-joss">Donate to JOSS</a></li> </ul> <hr> <p>Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work.</p> <p>Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted.</p> <p>New episodes every other Thursday.</p>

#17: Magdalena Fuentes joins Arfon and Abby to discuss her project Soundata. Magdalena shares insights into audio datasets, standardization, and community-driven open-source tools, offering valuable takeaways on reproducibility, dataset management, and open source in machine listening. Magdalena is an Assistant Professor of Music Technology and Integrated Design & Media at New York University (NYU). You can follow Magdalena on Twitter/X @mfu3ntes, GitHub @magdalenafuentes, LinkedIn @mfu3ntes https://www.linkedin.com/in/mfu3ntes/ or at her website magdalenafuentes.com. Episode highlights: [02:02] - Magdalena's Background and Motivation [02:54] - Challenges in Machine Listening [03:48] - Standardizing Audio Data with Soundata [06:58] - Applications and Benefits of Soundata [12:33] - Industry and Academic Use Cases [13:27] - The Broader Landscape of Audio Data Tools [16:37] - Encouraging Community Contributions [21:48] - Maintaining and Evolving Soundata [29:40] - Future Goals and Vision for Soundata Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06634 Soundata repository: https://github.com/soundata/soundata Magdalena on Twitter/X @mfu3ntes https://x.com/mfu3ntes, GitHub @magdalenafuentes https://github.com/magdalenafuentes, LinkedIn @mfu3ntes https://www.linkedin.com/in/mfu3ntes/, website: http://magdalenafuentes.com/ The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

<p>#16: Karelle Rheault joins Arfon and Abby to discuss the development of goFlux, a user-friendly software designed to calculate greenhouse gas (GHG) fluxes. The conversation covers Karelle&#39;s programming journey, challenges faced, and the role of open-source practices in advancing research.</p> <p>Karelle is a PhD student and the creator of goFlux.</p> <p>You can follow Karelle on X/Twitter @KarelleRheault and on LinkedIn <a href="https://www.linkedin.com/in/karelle-rheault-063842105/">https://www.linkedin.com/in/karelle-rheault-063842105/</a></p> <h3 id="episode-highlights-">Episode highlights:</h3> <ul> <li>[02:03] - Karelle&#39;s Journey to Creating goFlux</li> <li>[02:56] - Understanding Greenhouse Gas Fluxes</li> <li>[05:19] - Measurement Techniques and Tools</li> <li>[09:30] - Challenges and Advantages of goFlux</li> <li>[20:20] - Open Source Contributions and Community Support</li> <li>[23:57] - Karelle&#39;s Experience with JOSS</li> <li>[27:00] - Future Plans and Contributions</li> <li>[28:59] - Organizing the Community and Setting Standards</li> <li>[31:27] - Conclusion and Farewell</li> </ul> <h3 id="links-">Links:</h3> <ul> <li>JOSS paper: <a href="https://joss.theoj.org/papers/10.21105/joss.06393">https://joss.theoj.org/papers/10.21105/joss.06393</a> </li> <li>goFlux repository: <a href="https://github.com/Qepanna/goFlux">https://github.com/Qepanna/goFlux</a> </li> <li>goFlux webpage: <a href="https://qepanna.quarto.pub/goflux/">https://qepanna.quarto.pub/goflux/</a> </li> <li>Karelle on X/Twitter <a href="https://x.com/KarelleRheault">https://x.com/KarelleRheault</a>, LinkedIn: <a href="https://www.linkedin.com/in/karelle-rheault-063842105/">https://www.linkedin.com/in/karelle-rheault-063842105/</a>, email: karh [at] ign.ku.dk</li> <li><a href="https://joss.theoj.org/">The Journal of Open Source Software</a> (<a href="https://twitter.com/JOSS_TheOJ">Twitter/X</a>, <a href="https://blog.joss.theoj.org/">blog</a>)</li> <li>@arfon on (<a href="https://fosstodon.org/@arfon">fosstodon</a>, <a href="https://www.linkedin.com/in/arfon/">Linkedin</a>, <a href="https://github.com/arfon">GitHub</a>, <a href="https://www.arfon.org/">website</a>)</li> <li>@abbycabs on (<a href="https://twitter.com/abbycabs">Twitter/X</a>, <a href="https://hachyderm.io/@abbycabs">hachyderm</a>, <a href="https://bsky.app/profile/abbycabs.bsky.social">bsky</a>, <a href="https://www.linkedin.com/in/abbycabs/">Linkedin</a>, <a href="https://github.com/abbycabs">GitHub</a>, <a href="https://abbycabs.github.io/">website</a>)</li> <li><a href="https://numfocus.org/donate-to-joss">Donate to JOSS</a></li> </ul> <hr> <p>Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work.</p> <p>Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted.</p> <p>New episodes every other Thursday.</p>

#15: Herminio Vazquez & Virginie Grosboillot join Arfon and Abby to discuss cuallee, their Python package designed for data quality checks across multiple data framed APIs. The discussion covers the importance of data quality, the passion behind the project, and the intersection of open-source software in both academia and industry. Herminio is the Director Data Strategy and Analytics at Copado. Virginie is a postdoctoral researcher at the University of Ljubljana. You can follow them both on LinkedIn: Hermino, Virginie Episode highlights: [02:02] - The Story Behind cuallee [03:32] - Guest Backgrounds and Expertise [05:08] - Applications in Bioinformatics [09:27] - Industry Applications and Inspirations [11:21] - Comparing cuallee with Other Tools [23:26] - Open Source Contributions and Community [27:12] - Challenges in Building cuallee [32:17] - Conclusion and How to Get Involved Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06684 cuallee repository: https://github.com/canimus/cuallee Herminio on LinkedIn: https://www.linkedin.com/in/herminio-vazquez-701bb0/ Virginie on LinkedIn: https://www.linkedin.com/in/virginie-grosboillot-7a7b8b23a/ The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#14: James Kerns joins Arfon and Abby to discuss how Pylinac automates quality assurance for radiotherapy, running an open source project while teaching yourself to code, and the growing open source ecosystem for medical physics. James is a technical lead at Radformation, focusing on image analysis. You can follow James on LinkedIn and GitHub. Episode highlights: [00:37] - The Importance of Quality Assurance in Radiotherapy [05:19] - James's Journey into Coding [07:48] - How Pylinac Works [09:56] - Community and Support [16:43] - Commercial Use and Collaboration [19:53] - Transitioning from MATLAB to Python [21:27] - Maintaining Pylinac Over the Years [23:21] - Challenges in Software Development [26:34] - The Importance of Documentation [29:01] - Publishing in JOSS [35:23] - Future of Pylinac and New Projects Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06001 Pylinac repository: https://github.com/jrkerns/pylinac Awesome Medical Physics: https://github.com/jrkerns/awesome-medphys quacc: https://github.com/jrkerns/quaac Radformation: https://www.radformation.com/ James on LinkedIn: https://www.linkedin.com/in/james-kerns/, GitHub: https://github.com/jrkerns The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#13: Naomi Arnold and Ben Steer join Arfon and Abby to discuss their work on Raphtory, THE temporal graph engine for Rust and Python. Other topics include: pomegranates are the graphiest fruit, tracking ship to ship trading, and funding for open source projects through the Tools, Practices and Systems program at the Alan Turing Institute. Naomi is a Postdoctoral Research Associate at Northeastern University London. Ben is the CTO and Co-founder of Pometry. You can follow Naomi on Twitter/X @narnolddd. You can follow Ben on Twitter/X @Raphtory, raphtory.com, and pometry.com. Episode Highlights: [00:00] - Introduction to Open Source for Researchers [00:19] - Meet the Guests: Naomi Arnold and Ben Steer [01:49] - Understanding Temporal Graphs with Raphtory [04:40] - The Origin Story of Raphtory [08:05] - Naming and Evolution of Raphtory and Pometry [12:47] - Raphtory's Applications and Use Cases [19:00] - Transition from Scala to Rust [24:47] - Open Source Journey and Contributions [35:01] - Conclusion and Final Thoughts Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05940 Raphtory repository: https://github.com/Pometry/Raphtory Naomi on Twitter/X: https://twitter.com/narnolddd Raphtory on Twitter/X https://twitter.com/raphtory Raphtory website: https://www.raphtory.com/ Pometry website: https://www.pometry.com/ The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#12: Kenneth Enevoldsen joins Arfon and Abby to discuss Augmenty, a python library for text augmentation, balancing contributor-friendliness with maintainability in open source, and which danishes he would eat. Kenneth is a PhD student at Aarhus University and the maintainer of many open source libraries including Augmenty, MTEB, TextDescriptives, ScandEval and more. You can follow Kenneth on X @kcenevoldsen, LinkedIn @kennethenevoldsen, and GitHub @kennethenevoldsen. Episode highlights: [00:00:48] - Discussion on Augmenty and Text Augmentation [00:02:55] - Origins and Development of Augmenty [00:05:51] - Applications and Use Cases of Augmenty [00:12:20] - Community Building and Open Source Contributions [00:15:41] - Maintaining Open Source Projects [00:20:52] - Publishing in JOSS and Final Thoughts [00:25:32] - Conclusion and Outro Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06370 Augmenty repository: https://github.com/KennethEnevoldsen/augmenty DaCy: https://github.com/centre-for-humanities-computing/DaCy spaCy: https://spacy.io/ Multilingual MTEB Project: https://github.com/embeddings-benchmark/mteb Kenneth on Twitter/X, LinkedIn, GitHub The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#11: Fred Shone joins Arfon and Abby to discuss his journey from engineer to economist to data scientist to PhD student, the development of Population Activity Model (PAM) including the evolution from pandemic modeling to broader population activity insights. Fred is a PhD student at the UCL Behaviour and Infrastructure Group (BIG). He built PAM when he was technical lead for the City Modelling Lab at Arup. You can follow Fred on GitHub @fredshone and check out his website https://fredshone.github.io. Episode Highlights [00:01:30] Fred Shone's Background - Fred Shone discusses his journey from civil engineering to economics and data science, leading to his PhD studies. [00:02:24] Origin of PAM - Fred talks about the creation of PAM, originally the Pandemic Activity Modifier, and its evolution to Population Activity Modeller. [00:04:31] Purpose and Application of PAM - Fred explains how PAM was used during the COVID-19 pandemic to model and update transport models quickly. [00:05:39] Behavioral Modeling Insights - Discussion on the necessity of understanding human behavior for policy and business decisions. [00:07:30] Agent-Based Modeling - Fred elaborates on the benefits and challenges of modeling specific individuals in PAM. [00:13:00] Using PAM in PhD Research - Fred mentions how he continues to use PAM for his current research. [00:14:24] Target Audience for PAM - Discussion on the various fields interested in PAM, including transport, energy, and epidemiology. [00:16:08] Internal and External Use of PAM - Fred talks about how Arup and external contributors use and contribute to PAM. [00:19:16] Open Source Software in Industry - The challenges and benefits of publishing open source software from an industry perspective. Links JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06097 PAM repository: https://github.com/arup-group/pam Arup: https://www.arup.com/ Fred on GitHub: https://github.com/fredshone Fred’s website: https://fredshone.github.io/ The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#10: Irea Mosquera-Lois and Seán Kavanagh join Arfon and Abby to discuss releasing software based on important research observations, earning a PhD, and building ShakeNBreak, a defect structure searching method that better identifies low-energy structures. Irea is a PhD Student at Imperial College London. Seán is an Environmental Fellow at Harvard University. You can follow Irea on GitHub @ireaml and X @ireaml. You can follow Seán on GitHub @kavanase, X @Kavanagh_Sean_, and at seankavanagh.com. See the show notes: https://blog.joss.theoj.org/2024/05/josscast-10-defect-structure-searching Episode highlights: [00:03:02] What is a viva? And earning a PhD [00:05:41] Defects in Materials and Their Impact [00:07:20] Understanding ShakeNBreak [00:09:32] Integration with Computational Tools [00:12:46] Benefits of Open Source Contribution [00:17:20] Discovering the Defect Configurational Issue [00:20:23] Peer Review and Publishing Software [00:22:41] Contribute to ShakeNBreak Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.04817 ShakeNBreak repository: https://github.com/SMTG-Bham/ShakeNBreak Mosquera-Lois, I. & Kavanagh, S. R.; Walsh, A.; Scanlon, D. O. Identifying the Ground State Structures of Defects in Solids, npj Comput Mater 9, 25, 2023 https://www.nature.com/articles/s41524-023-00973-1 Irea on (GitHub, Twitter/X) Seán on (GitHub, Twitter/X, website: seankavanagh.com) The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS See the show notes: https://blog.joss.theoj.org/2024/05/josscast-10-defect-structure-searching --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#9: Mats van Es joins Arfon and Abby to discuss reproducible science and the functionality he added to FieldTrip, a MATLAB software toolbox for analyzing brain imaging data. Mats is a cognitive neuroscientist at the University of Oxford. You can follow Mats on Twitter/X @mats_van_es. See the show notes: https://blog.joss.theoj.org/2024/05/josscast-9-reproducibility-in-neuroscience Episode Highlights [00:03:11] Introduction to FieldTrip and reproducescript [00:06:30] Config-Driven Science & Reproducibility [00:11:42] Using MATLAB in Open Source Software [00:21:02] The State of Open Source Software in Neuroscience [00:21:53] Publishing in JOSS [00:23:35] Future Directions and Contributions Links JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05566 FieldTrip repository: https://github.com/fieldtrip/fieldtrip OHBA Software Library or OSL https://github.com/OHBA-analysis/osl OSL Dynamics https://github.com/OHBA-analysis/osl-dynamics Mats on Twitter/X @mats_van_es https://twitter.com/mats_van_es The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS See the show notes: https://blog.joss.theoj.org/2024/05/josscast-9-reproducibility-in-neuroscience --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#8: Giulia Crocioni joins Arfon and Abby to discuss DeepRank2, a deep learning framework for 3D protein structure predictions. Giulia is a Research Software Engineer at the Netherlands eScience Center where she uses different machine learning techniques to develop and contribute to methodologies and applications to answer life sciences research questions. You can follow Giulia on LinkedIn See the show notes: https://blog.joss.theoj.org/2024/04/josscast-8-deep-learning-for-3d-protein-structure-predictions Episode highlights: - [00:02:16] Giulia introduces herself and her work at the Netherlands eScience Centre in the Life Sciences section. - [00:04:09] Introducing DeepRank2: An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants. - [00:10:14] Target audiences (researchers, developers) and applications (drug design, cancer vaccine development) - [00:13:48] Ecosystem overview from complementary projects like AlphaFold, to training data sources, to using PyTorch. - [00:23:27] Open Source & Contributions Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05983 DeepRank2 repository: https://github.com/DeepRank/deeprank2 Netherlands eScience Center: https://www.esciencecenter.nl/ Giulia on LinkedIn: https://www.linkedin.com/in/giulia-crocioni/ The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS See the show notes: https://blog.joss.theoj.org/2024/04/josscast-8-deep-learning-for-3d-protein-structure-predictions --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#7: Jimmy Shen sat down with Arfon and Abby to discuss the role of defect analysis in semiconductor research, the Materials Project, and the development of pymatgen-analysis-defects. Jimmy is a postdoc at the Lawrence Livermore National Laboratory where he tries his best to automate himself away. You can follow Jimmy on GitHub @jmmshn, Linkedin, or on Google Scholar. See the show notes: https://blog.joss.theoj.org/2024/04/josscast-7-adding-defect-analysis-to-the-materials-project Episode Highlights [00:02:19] Introducing pymatgen-analysis-defects and the Materials Project [00:07:09] pymatgen packages [00:07:36] Importance of defects in semiconductor research [00:11:19] Target audiences and alternatives [00:15:11] pymatgen-analysis-defects in the broader open source ecosystem [00:18:15] JOSS review [00:19:12] Contribute to pymatgen-analysis-defects Links JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05941 pymatgen-analysis-defects repository: https://github.com/materialsproject/pymatgen-analysis-defects Jimmy on (GitHub, Linkedin Google Scholar) The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS See the show notes: https://blog.joss.theoj.org/2024/04/josscast-7-adding-defect-analysis-to-the-materials-project --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#6: Marjan Albooyeh and Chris Jones chat with Arfon and Abby about their experience building FlowerMD, an open-source library of recipes for molecular dynamics workflows. Marjan and Chris are both grad students in Dr. Jankowski’s lab at Boise State University where they use molecular dynamics to study materials for aerospace applications and organic solar cells. Before joining the lab, Marjan was a machine learning researcher. Chris learned to code when the lab’s glove-box went down and he never looked back. You can follow them both on GitHub: Marjan @marjanalbooyeh and Chris @chrisjonesBSU. See the show notes: https://blog.joss.theoj.org/2024/03/josscast-6-streamlining-molecular-dynamics Episode highlights: [00:00:12] Introduction to FlowerMD and its creators, Marjan Albooyeh and Chris Jones. [00:02:54] Explanation of molecular dynamics simulation process and applications. [00:05:10] Insights into FlowerMD's development process and design goals. [00:09:26] Target audience for FlowerMD and its usability for researchers. [00:11:30] Importance of reproducibility in research facilitated by FlowerMD. [00:16:18] Challenges faced building FlowerMD. [00:19:52] Experiences with the JOSS review process. [00:22:39] Contribute to FlowerMD! [00:24:08] Future plans for FlowerMD and building a research community. Links: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05989 FlowerMD repository: https://github.com/cmelab/flowerMD Chris Jones's GitHub profile: @chrisjonesBSU Marjan Albooyeh's GitHub profile: @marjanalbooyeh The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Donate to JOSS See the show notes: https://blog.joss.theoj.org/2024/03/josscast-6-streamlining-molecular-dynamics --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#5: Gui Castelão and Luiz Irber join Arfon and Abby to discuss their work implementing the Gibbs Sea Water Oceanographic Toolbox of TEOS-10 in Rust, and the role of instrument builders in science. Gui is an oceanographer at the Scripps Institution of Oceanography, previously part of the Instrument Developing Group. Luiz is a Computer Science PhD at UC Davis and an avid Rustacean. Gui’s website: www.castelao.net.Luiz’s website: LuizIrber.org See the show notes: https://blog.joss.theoj.org//2024/03/josscast-5-rewrite-in-rust Episode Highlights: [00:01:55] - Introductions to Gui and Luiz and how they got into open source [00:09:18] - GSW-rs – a Rust implementation of the Gibbs SeaWater Oceanographic Toolbox [00:17:13] - Why Rust? [00:19:53] - Instrumentation culture in oceanography (and astronomy!) [00:23:17] - Recognition and credit for software contributions in academia [00:27:47] - Publishing in JOSS [00:31:36] - Contributing to GSW-rs Links Mentioned: JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05988  GSW-rs repository: https://github.com/castelao/GSW-rs  Inception repository: https://github.com/castelao/inception  Gui Castelao's website: castelao.net Luiz Irber's website: LuizIrber.org The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) See the show notes: https://blog.joss.theoj.org//2024/03/josscast-5-rewrite-in-rust --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#4: Nicolas Renaud joins Arfon and Abby to discuss QMCTorch, a PyTorch implementation of real-space Quantum Monte-Carlo simulations of molecular systems, and work to promote research software as a research output. Nico is the head of the Natural Sciences and Engineering section of the Netherlands eScience Center and Senior Researcher at the Quantum Application Lab. He focuses on the intersection of material sciences and machine learning. You can find Nico on GitHub @NicoRenaud or the Research Software Directory ⁠Full show notes and transcript⁠ Episode Highlights [00:02:31] Introduction to QMCTorch – recasting Quantum Monte Carlo as a machine learning problem [00:09:30] Hardware requirements – run it on the cluster [00:11:05] Choosing PyTorch for QMCTorch [00:17:40] The Netherlands eScience Center and promoting research software [00:18:47] Publishing QMCTorch in JOSS [00:19:02] QMCTorch is open for contributions! [00:20:51] Future directions for QMCTorch Links JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05472 QMCTorch code repository: https://github.com/NLESC-JCER/QMCTorch  PyTorch: https://pytorch.org/  A light in the dark: Quantum Monte Carlo meets solar energy conversion Nico on GitHub @NicoRenaud The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) Full show notes and transcript --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#3: Juliette Hayer joins Arfon and Abby to discuss Baargin, an open source tool she created to analyze bacterial genomes, especially those resistant to antibiotics. Juliette is a PhD Researcher at the French Research Institute for Sustainable Development (IRD, Institut de Recherche pour le Développement), at the MIVEGEC research unit, where she implements computational biology methods for bacterial genomics and metagenomics to understand the circulation and transmission of antimicrobial resistance. You can find Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer). Episode Highlights [00:02:21] Introduction to Baargin: Juliette explains that Baargin stands for Bacterial Assembly and Antimicrobial Resistance Genes Detection in Nextflow. She developed it to analyze the genomes of drug-resistant bacteria in various environments. [00:06:20] Multiplex Sequencing: Juliette discusses the challenge of assembling genomes for multiple strains simultaneously using high-throughput sequencing technologies. [00:07:21] Next-Gen Sequencing and Assembly: The conversation delves into next-generation sequencing, the assembly of short reads, and the emergence of long-read technologies for comprehensive genome analysis. [00:09:59] Target Audience: Juliette identifies microbiologists as the primary audience for Baargin, emphasizing its user-friendliness for researchers producing genome data. [00:12:50] Nextflow in Bioinformatics: Juliette explains the role of Nextflow in bioinformatics and its popularity, highlighting its benefits for scalable and reproducible workflows. [00:17:03] Open Source Philosophy: Juliette shares her commitment to open source principles, advocating for transparency, reproducibility, and collaborative contributions in research. [00:19:20] Research Using Baargin: Juliette discusses her published studies, including the identification of drug-resistant E. coli transmission in Chile and ongoing projects in Vietnam and Cambodia. [00:20:14] Publishing in JOSS: Juliette describes the benefits of publishing in the Journal of Open Source Software (JOSS), emphasizing the focus on code and transparent review processes. [00:23:27] Documentation Importance: The hosts discuss the significance of documentation in software development, with Juliette highlighting its critical role in ensuring usability. [00:26:03] Contributions and Skills: Juliette welcomes contributions to Baargin, mentioning that comfort with git and Nextflow is essential for potential contributors. [00:28:27] Future Roadmap: Juliette outlines plans for extending Baargin, including adding tools for predicting resistance genes, improving detection of mobile genetic elements, and enhancing multi-locus sequence typing. Links JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05397 Baargin code repository: https://github.com/jhayer/baargin Nextflow: https://www.nextflow.io/ Study using Baargin: Multiple clonal transmissions of clinically relevant extended-spectrum beta-lactamase–producing Escherichia coli among livestock, dogs, and wildlife in Chile: https://doi.org/10.1016/j.jgar.2023.07.009 Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer). The Journal of Open Source Software (Twitter/X, blog) @arfon on (fosstodon, Linkedin, GitHub, website) @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website) --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#2: In this episode of Open Source for Researchers hosts Abby and Arfon explore the world of open source software in astronomy with Dr. Taylor James Bell, a BAER Institute postdoc at NASA Ames. Eureka! is an end-to-end pipeline designed for JWST (James Webb Space Telescope) time series observations. We chat about the motivations behind Eureka!, its unique features, and the democratization of exoplanet science. Join us for an engaging conversation that unveils the complexity of time series observations, the power of open source, and the exciting future of Eureka! and JWST discoveries. --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.

#1: In the first episode of Open Source for Researchers, hosts Arfon and Abby sit down with Eva Maxfield Brown to discuss Speakerbox, an open source speaker identification tool. Originally part of the Council Data Project, Speakerbox was used to train models to identify city council members speaking in transcripts, starting with cities like Seattle. Speakerbox can run on your laptop, making this a cost-effective solution for many civic hackers, citizen scientists, and now .. podcasters! From the advantages of fine-tuning pre-trianed models for personalized speaker identification to the concept of few-shot learning, Eva walks us through her solution. Want to know how this open source project came to life? Tune in to hear about Eva's journey with Speakerbox and publishing in JOSS! --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work. Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted. New episodes every other Thursday.