#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's programming journey, challenges faced, and the role of open-source practices in advancing research.

Karelle is a PhD student and the creator of goFlux.

You can follow Karelle on X/Twitter @KarelleRheault and on LinkedIn https://www.linkedin.com/in/karelle-rheault-063842105/

• • [02:03] - Karelle's Journey to Creating goFlux
  • [02:56] - Understanding Greenhouse Gas Fluxes
  • [05:19] - Measurement Techniques and Tools
  • [09:30] - Challenges and Advantages of goFlux
  • [20:20] - Open Source Contributions and Community Support
  • [23:57] - Karelle's Experience with JOSS
  • [27:00] - Future Plans and Contributions
  • [28:59] - Organizing the Community and Setting Standards
  • [31:27] - Conclusion and Farewell

• • JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06393
  • goFlux repository: https://github.com/Qepanna/goFlux
  • goFlux webpage: https://qepanna.quarto.pub/goflux/
  • Karelle on X/Twitter https://x.com/KarelleRheault, LinkedIn: https://www.linkedin.com/in/karelle-rheault-063842105/, email: karh [at] ign.ku.dk
  • 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.

#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.

#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.