Software Development
Quality software is essential for reproducibility, fostering inclusivity, and advancing evolutionary studies. My software projects focus on improving data collection, management, and integration in field-based evolutionary studies and minimizing the technical complexities of genomic analyses. I put ease of use at the center of the software design process. The GUI software incorporates accessibility features. I work toward crafting informative error handling and quality documentation, and I am always open to feedback and collaboration. I ensure cross-platform compatibility whenever feasible, including support for Windows and mobile operating systems.
Software Projects
SEGUL
A cross-platform phylogenomic tool
We develop SEGUL (SEquence and Genomic UtiLities) to address the need for a high-performance and accessible phylogenomic tool. It features a growing list of high-performance, memory-efficient solutions for genomic data exploration, cleaning, filtering, and conversion tasks. We designed SEGUL to handle large-scale phylogenomic datasets involving thousands of loci and hundreds of samples. Additionally, it is capable of handling small Sanger sequences effectively. It scales from smartphones, tablets, and personal computers to high-performance computing clusters. It is available as a command-line app, mobile and desktop GUI, and packages for Rust and Python. Using the SEGUL library in other languages is also possible using the Rust interface, such as in R using extendr. It is a practical solution to typical phylogenomic data analyses and a proof of concept for scalable, cross-platform genomic software.
NAHPU
A cross-platform field catalog for natural history collections
The NAHPU project is a collaborative effort to develop a digital field catalog for natural history collection. We designed it to streamline data collection from fieldwork to the museum database. It minimizes information loss and lack of integration between specimens, collecting efforts, and derivative data (e.g., photographs and sound recording). We aim to foster international collaboration and improved reproducibility through rich, consistent data features and multi-language support. NAHPU features real-time statistics to keep track of specimen records to aid in making decisions in collecting efforts and avoiding over-sampling. The app is in beta. Several field teams tested NAHPU for fieldwork in Brazil, Colombia, Indonesia, Mexico, and the United States. It supports data collection for ornithology and mammalogy, with plans to extend support to other taxa.
ULLAR
An Ultrafast, scaLable, Accessible, and Reproducible pipeline for phylogenomics
ULLAR is currently in the beta development stage. It aims to create a lightweight and scalable pipeline for phylogenomic studies. It requires minimal learning and omits manual config generation and shell scripting. The pipeline uses Rust, which has no runtime dependencies, is memory-safe, and efficiently uses computing resources. In addition to Linux and macOS, typically supported operating systems for bioinformatics, ULLAR will also run natively on Windows for part of the pipeline, allowing more efficient access to hardware than using the Windows Subsystem for Linux.
MDD app
A mobile and desktop app for the ASM's Mammal Diversity Database
The American Society of Mammalogists' Mammal Diversity Database (MDD) app is a mobile and desktop application I developed as part of the MDD curation team. It is currently in beta. The app allows offline access, advanced search, and user-selected export functions for the database. We aim to simplify access to MDD data when access to the internet is limited.