SSEC Products
Our products range from from open-source software to peer-reviewed publications to workshops and tutorials across academic disciplines. Learn more about SSEC software on our GitHub page.
Open Source Software
CA-Biositing: A web-based tool supporting the development of a circular bioeconomy in California’s Northern San Joaquin Valley, with open source datamodels, pipeline, webservice.
Astrowidget: Interactive radio astronomy visualization for Jupyter that renders radio images on a rotatable celestial sphere reading directly from zarr stores.
Respondent-Driven Sampling app: An open-source web application for conducting Respondent-Driven Sampling (RDS) surveys of unsheltered populations.
Hpyx: Python bindings for HPX (High Performance ParalleX), a C++ Standard Library for Concurrency and Parallelism that implements modern C++ parallelism features defined by the C++ Standard
Phylo2Vec: A high-performance software package for encoding, manipulating, and analysing binary phylogenetic trees.
Biodiversity Horizons: A container ready to use and pre-loaded with an R Package for climate impact predictions, compatible with Apptainer/Singularity for HPC deployment.
Bioethics: A set of tools to help researchers ethically communicate study results to human subjects. It uses AI to generate accessible, eighth-grade-level summaries of clinical research documents, enabling participants to understand research findings while protecting sensitive data.
Offshore Geodesy: GNATSS (Global Navigation Satellite Systems) software for processing seafloor horizontal positioning data. Learn more about the research this software was made for from our news bulletin on Offshore Geodesy.
Braingeneers / Wet AI: Innovative online platform designed to democratize neuroscience education and neuroscience experiments involving cerebral organoids by providing remote access and AI interactivity. Learn more from our news item on Wet AI.
Echopype: Echopype leverages modern cloud computing technologies to support efficient computation of large quantities of ocean sonar data. It was made for the Echopype project.
NoisePy: Python package designed for fast and easy computation of ambient noise cross-correlation functions for noise monitoring and surface wave dispersion analysis for seismology research.
Caustics: GPU-accelerated, automatically differentiable, highly modular lensing pipeline of the future. Click here for details about the Caustics project.
Peer-Reviewed Publications
Aleena: Alignment Agent for Research Software Engineering Collaborations Cordero Core, Landung Setiawan, Carlos Garcia Jurado Suarez, Anshul Tambay, Vani Mandava, Anant Mittal et al.
LLMoxie: Exploring Agentic AI for Scientific Software Development Don Setiawan, Anant Mittal, Cordero Core, Anshul Tambay, Carlos Garcia Jurado Suarez, David A. C. Beck, Andrew J. Connolly, Vani Mandava
Microscale maps of bursting dynamics across human hippocampal slices from epilepsy patients Cordero Core et al.
Phylo2vec: a library for vector-based phylogenetic tree manipulation Don Setiawan et al.
Open-source models for development of data and metadata standards Ariel Rokem, Vani Mandava, Nicoleta Cristea, Anshul Tambay, Andy Connolly et al.
Software Engineering Practices in Academia: Promoting the 3Rs—Readability, Resilience, and Reuse Andrew Connolly, David Beck, Vani Mandava, Sarah Stone et al.
Hiring, Managing, and Retaining Data Scientists and Research Software Engineers in Academia David Beck, Sarah Stone et al.
Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education Cordero Core et al.
Towards an open-source model for data and metadata standards Vani Mandava, Andrew Connolly, Anshul Tambay et al.
Interoperable and scalable echosounder data processing with Echopype Don Setiawan et al.
Pathological microcircuits initiate epileptiform events in patient hippocampal slices Cordero Core et al.
Caustics: A Python Package for Accelerated Strong Gravitational Lensing Simulations Don Setiawan, Cordero Core et al.
Conferences and Workshops
Phylo2Vec Workshop, London, UK Sept 17, 2025.
A workshop for Phylo2Vec, a vector representation for binary trees.
Barcelona Supercomputing Center Workshop, Barcelona, Spain September, 2025.
US-RSE Philadelphia, PA Oct 17, 2025.
LLMaven: Large Language Model based Agentic Verification and Exploration of Natural Inquiry
GNATSS Workshop 2025 Atlanta, GA August 7-8, 2025.
Community Seafloor Global Navigation Satellite Systems: Acoustic (GNSS-A) Transponder Surveying Software Workshop
SciPy 2025 Tacoma, WA July 10, 2025.
Birds of a Feather: AI for Scientific Discovery
US-RSE Albuquerque, NM October 15-17, 2024.
Research Software Engineering as a Service: Approaches to research software engineering
SciPy 2024 Tacoma, WA July 8-14, 2024.
Generative AI Copilot for Scientific Software: a RAG-Based Approach using OLMo
Echostack: A flexible and scalable open-source software suite for echosounder data processing
Xarray: Friendly, interactive, and scalable scientific data analysis