JOSSCast: Open Source for Researchers

By The Journal of Open Source SoftwareScience

JOSSCast: Open Source for Researchers episodes

May 16, 2024Defect Structure Searching – Irea Mosquera-Lois and Seán Kavanagh on ShakeNBreak
#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

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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.
27 min
May 02, 2024Reproducibility in Neuroscience – Mats van Es on FieldTrip reproducescript
#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.
27 min
April 18, 2024Deep Learning for 3D Protein Structure Predictions – Giulia Crocioni on DeepRank2
#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.
29 min
April 04, 2024Adding Defect Analysis to the Materials Project – Jimmy Shen on pymatgen-analysis-defects
#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.
23 min
March 21, 2024Streamlining Molecular Dynamics – Marjan Albooyeh and Chris Jones on FlowerMD
#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.
27 min
March 07, 2024Rewrite in Rust – Gui Castelão and Luiz Irber on Gibbs SeaWater Oceanographic Toolbox in Rust
#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.
37 min
February 22, 2024Applying ML to Quantum Monte Carlo Simulations – Nicolas Renaud on QMCTorch
#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.
23 min
February 08, 2024Studying Superbugs – Juliette Hayer on Baargin
#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.
31 min
January 25, 2024 Astronomy in the Open – Dr. Taylor James Bell on Eureka!
#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.
31 min
January 25, 2024 Eva Maxfield Brown on Speakerbox – Open Source Speaker Identification for Political Science
#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!

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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.
22 min

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