JOSSCast: Open Source for Researchers The Journal of Open Source Software

#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

#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

#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

#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

#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

#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)