JOSSCast: Open Source for Researchers

#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...

#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 Inn...

<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, 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...

#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...

<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 programming journey, challenges faced, and the role of open-source practices in advancing research.</p> <p>Karelle is a PhD student and the creator of goFlux.</p> <p>You...

#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 Copad...

#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 Quali...

#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...

#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 @k...

#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 La...

#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...

#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 Highlig...

#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...

#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:/...

#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...

#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: ww...

#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 o...

#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 bacteria...

#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 exopl...

#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...

Get ready to dive into the world of open source software for researchers with the new podcast, Open Source for Researchers! Join hosts Arfon Smith and Abby Cabunoc Mayes as they give you a sneak peek of what's to come. Open Source for Researchers launches January 25th, 2024! --- Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS...