JOSSCast: Open Source for Researchers18 Apr 2024

Deep 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

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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.

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Avsnitt(21)

Modernizing 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 follo...

3 Okt 202442min

Tackling 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 ...

19 Sep 202428min

Visualize Hypergraphs with Open Source – Brenda Praggastis on HyperNetX

<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...

5 Sep 202431min

Setting 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 t...

22 Aug 202432min

Greenhouse Gas Flux Analysis Made Easy – Karelle Rheault on goFlux

<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's pro...

8 Aug 202432min

Data 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 i...

25 Juli 202434min

Open 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 e...

11 Juli 202439min

Humans 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, tracki...

27 Juni 202436min