Resources
Open-source tools, protocols, and workflows for ecologists.
Computational Tools
nanodRop (R Package)
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What it is: A toolkit for reproducible processing of NanoDrop spectral data.
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Who it's for: Any lab manager or student tired of manual Excel copy-pasting.
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Status: Published on Zenodo (v0.0.0.9000).
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BioBERT Fungal Trait Extraction
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What it is: An AI-powered workflow to extract trophic modes (pathogen, saprotroph, etc.) from unstructured literature.
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Who it's for: Researchers conducting large-scale syntheses or meta-analyses in ecology.
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Includes: Fine-tuned model weights and Python notebooks.
Lab Protocols
Axenic Sorghum Seed Production
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The Problem: Growing totally sterile Sorghum for microbiome studies is difficult.
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The Solution: We developed a simple, high-success protocol using common lab reagents.
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Citation: microPublication Biology (2025).
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CUREs Design: Mycology in the Classroom
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The Resource: Curriculum materials for a Course-Based Undergraduate Research Experience (CURE) that led to student co-authored publications.
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Includes: Experimental design templates and data analysis guides for undergraduate mycology courses.
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[Request Materials]
Data Science Education
Carpentries Workshops
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Resources: Lesson plans workshops on OpenRefine, Introduction to R, and data visualization in R.
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Reach out if interested in a data science workshop for your group (no experience necessary!)