SSEC Products
Our products range from from open-source software to peer-reviewed publications to workshops and tutorials across academic disciplines. Learn more about our software on our Github.
Open Source Software
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 here.
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 here.
Echopype: Echopype leverages modern cloud computing technologies to support efficient computation of large quantities of ocean sonar data. It was made for this research.
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. Details available here.
Peer-Reviewed Publications
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