JOSSCast: Open Source for Researchers

By The Journal of Open Source SoftwareScience

JOSSCast: Open Source for Researchers episodes

October 03, 2024Modernizing Weather Forecasting with Julia – Milan Klöwer on SpeedyWeather.jl
#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.
43 min
September 19, 2024Tackling the Machine Learning Reproducibility Crisis – KJ Schmidt & Aristana Scourtas on Foundry-ML
#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.
29 min
September 05, 2024Visualize Hypergraphs with Open Source – Brenda Praggastis on HyperNetX
#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.
Brenda is a mathematician and data scientist at the Pacific Northwest National Laboratory.
You can follow HyperNetX on GitHub https://github.com/pnnl/HyperNetX.
Episode highlights:
[01:59] - Interview Begins: Welcome Brenda!
[02:05] - Understanding Hypergraphs
[04:57] - Brenda'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
Links:
JOSS paper: https://joss.theoj.org/papers/10.21105/joss.06016
HyperNetX repository: https://github.com/pnnl/HyperNetX
Docs: https://hypernetx.readthedocs.io/en/latest/
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.
32 min
August 22, 2024Setting the Standard for Audio Data Management – Magdalena Fuentes on Soundata
#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.
33 min
August 08, 2024Greenhouse Gas Flux Analysis Made Easy – Karelle Rheault on goFlux
#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/
Episode highlights:
[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
Links:
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.
33 min
July 25, 2024Data Quality Crafted with Passion – Herminio Vazquez & Virginie Grosboillot on cuallee
#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.
35 min
July 11, 2024Open Source Revolution in Radiotherapy – James Kerns on Pylinac
#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.
40 min
June 27, 2024Humans Think in Graphy Ways – Naomi Arnold and Ben Steer on Raphtory
#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.
37 min
June 13, 2024Text Augmentation for NLP – Kenneth Enevoldsen on Augmenty
#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.
28 min
May 30, 2024From COVID to Commuting – Fred Shone on Population Activity Modeller (PAM)
#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.
31 min

About JOSSCast: Open Source for Researchers

From the publisher's feed

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.

Share JOSSCast: Open Source for Researchers

Sign up to save your podcasts

JOSSCast: Open Source for Researchers

JOSSCast: Open Source for Researchers episodes

About JOSSCast: Open Source for Researchers