Tools, Software & Repositories
An ecosystem of 177+ open-source repositories and 106+ interactive browser tools spanning space biophysics, plant phenomics, fungal genomics, and NASA data exploration.
Curated Flagship Suites
Space Biophysics, CFD & Lunar Systems
Computational fluid dynamics (CFD), habitat microclimate modeling, and lunar environmental simulation tools.
LunarLeaf-CFD
Validated in-browser CFD model of gravity-dependent gas-exchange boundary layers around Arabidopsis leaves in lunar and orbital microenvironments.
LunarFarm-BLSS
What a playable closed loop teaches about closing one: an interactive bioregenerative life support systems (BLSS) architecture simulation.
lunar-lfm-explorer
FAIR exploration toolkit and multi-illumination inference viewer for the NASA-IBM Lunar Foundation Model.
ASTRO-USA-Habitat-Model
Parametric CAD and environmental simulation of the ASTRO-USA Mini-Hab Food Production Module.
Plant Systems Biology & Fungal Atlases
Multi-omics discovery portals, anatomical 3D models, and metabolic pathway decoders for plant and fungal biology.
plant-pathway-atlas
Modernized MapMan, PlantCyc, and ggPlant visualization engine for plant systems biology and cross-species metabolic mapping.
fungal-bgc-atlas
Curated, evidence-linked knowledge base of 609 MIBiG-linked fungal biosynthetic gene clusters with structural annotations.
arabidopsis-atlas
Interactive organ-selectable 3D anatomical atlas of Arabidopsis thaliana grounded in validated structural data.
virtual-root
Open web-based rebuild of SimuPlant / The Virtual Root: cell-based auxin transport and root gravitropism model.
Computer Vision & In-Browser Phenomics
Install-free browser phenotyping tools, machine learning segmentation, and calibration standards for researchers and classrooms.
astroroot
Install-free, in-browser root-image analysis for students and researchers — RootNav GUI and machine learning phenotyping.
cose-fiji
ImageJ 1.54 in the browser with SmartRoot, plant phenotyping presets, and FAIR export with no local installation required.
ABCD_v2
ABCD v2 AstroBotany calibration card: Munsell-defined plant and soil colour chips with ArUco markers for automated computer vision correction.
NASA OSDR & Space Multi-Omics Engines
Harmonized transcriptomic, microbiome, and astronaut biomedical data portals.
toast2
Next-generation DuckDB and Superset rebuild of TOAST (Test Of Arabidopsis Space Transcriptome) for fast spaceflight querying.
SpaceMineralAtlas
Mining NASA LSDA and OSDR for spaceflight mineral-ion and dietary data: multi-omics cross-analysis against NHANES terrestrial populations.
OSDR-Veggie-Nutrition-Dashboard
Interactive nutritional and transcriptomic comparison of salad crops grown on the International Space Station VEGGIE payload.
Full Directory of In-Browser GitHub Pages Tools
These repositories include active GitHub Pages deployments. Click "Launch App" to open each interactive application in your browser.
NASA_GeneLab_MicroArray_Codes
These rough R codes have been used to analyze transcriptomic and plant physiological data as part of the Gilroy NASA GeneLab program at the University of Madison-Wisconsin.
Astronaut_flavenoids_and_biomarkers
JAXA astronaut plasma cell-free RNA data (OSD-530) and iDEP figures. The opposite-forcing flavonoid analysis formerly here was withdrawn on 18 Oct 2026.
Microbiome_of_seedlings_in_space
Planning and workflows for a spaceflight seedling microbiome metagenomics analysis, using raw sequencing data pulled from NASA OSDR.
plant-pathway-atlas
Plant Pathway Atlas: Modernized MapMan, PlantCyc, and ggPlant for Systems Biology and Cross-Species Omics Projection
Lunar-and-Martian-frontier-game-prototype
Lunar and Martian frontier game prototype
OSD615-glycome-cytoskeleton-systems-biology
Open-source scientific repository and interactive web tool.
OSDR_X-species_V2
Cross-species meta-analysis of spaceflight transcriptomics (22 NASA OSDR datasets, 6 species, OrthoDB v12) revealing conserved mitochondrial suppression and organelle-specific responses.
OSDR_sphinx_readthedocs.io
[ARCHIVED → see OSDR_juypter_book.io] OSDR_sphinx_readthedocs
Space_Biology_Education.io
Space Biology and AstroBotany.io has the goal of making space biology data more FAIR. Test website creation methods.
Space_Photography_Guide.io
AstroBiology Photography Training Guide for Transforming to Open Science and Growing Beyond Earth
Training_LLM_game-theory_using_bloodbowl
Exploring the use of LLM’s to design and assist with the playing of board games like blood bowl and warhammer gaming narratives.
Tropism_autodecoder_2026
FAIR pipeline recognizing Arabidopsis spaceflight tropism responses: 1,337 OSDR/GEO samples deconvolved via a Salk single-cell atlas auto-decoder, with DESeq2 meta-analysis and ggPlantMap tissue projections.
VEGGIE_Tom_Red_Blue_Leaves_and_adv_roots
data from the VEGGIE on the ISS from Tomato's grown with Red or Blue light,_Leaves and adventious roots were analysed
arabidopsis-spaceflight-omics
Arabidopsis spaceflight omics meta-analysis: LASSO biomarker panel (NASA OSDR) + scPlantLLM single-cell atlas integration + Ca2+-dominated cell-cell communication. Prepared for npj Microgravity.
astronaut-oncogene-biomarkers
Cross-tissue transcriptomic meta-analysis: spaceflight/microgravity/radiation converge on shared oncogenic programs engaged in tissue-specific directions (NASA OSDR + JAXA; ML + oncogenic scoring; npj Microgravity + Zenodo)
astroroot
Install-free, in-browser root-image analysis for students — RootNav 1 GUI + RootNav 2.0 ML, single or batch, train your own model. Part of AIRI.
deepspace-seed-stress-decoder
FAIR tools (DSRS + GSAD) and a single-cell atlas identifying which Arabidopsis seed cell types and developmental stages are susceptible to deep-space stressors (gravity, radiation, low-oxygen, and more).
fungal-bgc-atlas
Curated, evidence-linked knowledge base of 609 MIBiG-linked fungal biosynthetic gene cluster dossiers — relational database, knowledge graph, and interactive dashboard
madwest-astrobotany
MadWest Rocketry x AstroBotany: a high-school sounding-rocket space-biology program (Arabidopsis qPCR + Populus x ectomycorrhiza timelapse), packaged for NASA OSDR.
tomato-spaceflight-VEG05-APH-SA-integration
Cross-mission integration of two ISS tomato spaceflight RNA-seq studies (OSD-767 x APH/NahG): spaceflight resembles a salicylic-acid-deficient, biotic-defense-primed state.
veg05-integrated-omics
Integrated host transcriptome (OSD-767) × microbiome (OSD-766) multi-omics analysis of ISS VEG-05 tomato: spaceflight dysbiosis and a microbe-driven host defense response.
virtual-root
Open, web-based rebuild of SimuPlant / The Virtual Root: a cell-based auxin transport model for the Arabidopsis root tip (AstroBotany / AIRI Stage VII).
ABCD_v2
ABCD v2 AstroBotany calibration card: Munsell-defined plant & soil colour chips, ArUco DICT_4X4_50 corner markers (IDs 0-3), chip spec, evidence, site + deck
ASTRO-USA-Habitat-Model
Parametric model of the ASTRO-USA Mini-Hab Food Production Module (ICES-2026-251): sourced ledger -> CAD, OpenFOAM CFD, WebXR VR
Aero-leaf-CFD-analysis-adapted-from-blender-ish
Aero leaf CFD analysis adapted from blender-ish
AstroBotany
AstroBotany — a focused hub of plant space-biology projects (a curated subset of the COSE project family).
AstroBotany_calibration_image_sharing_and_analysis
AstroBotany_calibration_image_sharing_and_analysis
AstroRegolith
Open database and growth-anchored reanalysis of plant growth in lunar, Martian and asteroid regolith — NASA OSDR/PSI catalogues, substrate characterisation, and OSD-476 transcriptomes joined to each plant's own growth.
ChromDecode-At
Expression-to-chromatin decoding of the Arabidopsis spaceflight transcriptome (NASA OSDR): code, tables, figures, LaTeX manuscript
CoSE_Cloud
COSE Cloud — the hub / project directory for the CoSE space-biology project family.
DeepSpaceAg
Deep Space Agriculture hub — scoped COSE project family for long-duration plant & crew life support
Hardware_OSDR_review
Which spaceflight biology hardware can be modelled? Metadata audit of NASA SPLASH/OSDR hardware, MI-CFD-HW checklist, verified 0 g/1 g OpenFOAM models
ISS_EDEN
FAIR data repository and interactive GitHub Pages explorer for the EDEN ISS Antarctic space greenhouse biomass production dataset (NASA OSDR OSD-895 / PMC7264257)
LunarFarm-BLSS
What a playable closed loop teaches about closing one — a reproducible study of Lunar Farm as a human-in-the-loop bioregenerative life support model
LunarLeaf-CFD
Validated in-browser CFD model of gravity-dependent gas-exchange boundary layers around Arabidopsis — leaf to canopy to spaceflight hardware (BRIC/CARA/VEGGIE), with an npj-Microgravity draft and full results package.
LunarSims
Original browser simulation games set on the lunar surface, in the spirit of the classic Maxis management sims. Lunar Farm playable now.
Lunar_Red_Alert
Space-Age total conversion of OpenRA — a lunar/vacuum RTS. Independent game (GPLv3), evolved from OpenRA.
Muscle-Atrophy-Multi-Omics-OSDR
Insights into Muscle Atrophy using Multi-Omics data from NASA OSDR
NMF_review
Near-Null Magnetic Fields in Lunar Plant Biology: The First 5 Days of Growth
OSDR-Veggie-Nutrition-Dashboard
Open-source scientific repository and interactive web tool.
Photorespiration_multiomics_microgravity
A gas-transport model predicts the Arabidopsis spaceflight transcriptome, and illumination separates six flight experiments. Interactive FvCB model, 8 figures, npj manuscript, FAIR tables.
Physics-simulator-for-statolith-modelling-
Physics simulator for statolith modelling, development needed
Rothamsted_BroadBaulk
Rothamsted Broadbalk Explorer: 180+ Years of Continuous Wheat Yields, Climate Overlays & Scientific Data Narratives
Seed_sowing_simulator
Seed_sowing_simulator for investigating tropisms in-silico
Settlers_of_Mars_3D_LLM
Redirect stub — the game moved to Settlers_of_the_Moon_or_Mars.
SpaceMineralAtlas
Mining NASA LSDA and OSDR for spaceflight mineral-ion and dietary data. Real-data reanalysis of the Veggie ICP-OES studies: crop-specific responses, a 1000-fold unit-labelling defect in OSD-655, and what mineral data NASA actually makes available.
Suborbital_Arabidopsis
Open-source scientific repository and interactive web tool.
arabidopsis-atlas
An interactive, organ-selectable 3D atlas of Arabidopsis thaliana grounded in cited structural literature and real NASA OSDR spaceflight transcriptomics.
arabidopsis-drem-osdr
Cell-type-weighted regulatory prior for DREM over NASA OSDR Arabidopsis pseudo-time-series: a single-cell atlas that acts on the model, not just its annotation. SOG1/MYB3R attribution recovered with a built-in sog1-1 knockout control.
arabidopsis-exploration-atmosphere-tabpfn
Decoupling Total Pressure from Hypoxia in Arabidopsis under NASA Exploration Atmospheres via Tabular Foundation Models (TabPFN v2)
arabidopsis-gwas-spaceflight
Open-source scientific repository and interactive web tool.
ares-curation
A FAIR client for NASA's ARES/JSC astromaterials catalogues — Apollo lunar samples, PDS sample photographs, planetary simulants and Astromaterials 3D — and a measured report of which samples each archive actually covers.
astronaut-mineral-final
Astronaut mineral-pathway multi-omics (Inspiration4, AX-1, JAXA CFE) against an NHANES population reference
astroroot-painter
A browser front end for RootPainter's corrective-annotation training loop — astroroot's training/correction companion
clpds-planetary-visualization
Open-source scientific repository and interactive web tool.
cose-arcade
CoSE Arcade — a hub for original lunar/space games and browser-based plant modeling & simulation tools.
cose-fiji
ImageJ 1.54 in the browser with SmartRoot, plant-phenotyping presets and FAIR export. No install.
cose-magbio-3d-report
CoSE MagBio-3D interactive design report: parametric CAD inspector and Biot–Savart field visualiser (design stage, not measured)
dr-richard-barker.github.io
Personal academic CV, public science showcase, and interactive tools portfolio
earth-magnetosphere-4d-viz
Open-source scientific repository and interactive web tool.
infogenius-standalone
Standalone, keyless, browser-native topic research + infographic tool. No Google GenAI. Optional BYO-key AI images. Deployable on GitHub Pages.
lunar-arcade
Original browser games in the spirit of the classic Maxis sims, rebuilt from scratch on the Moon
lunar-magnetic-biology
Open-source scientific repository and interactive web tool.
lunar-mars-magnetic-biology
Open-source scientific repository and interactive web tool.
lunar-regolith-blss-review
From Dust to Bio-Infrastructure: Sintered Regolith Ceramics for Lunar BLSS (npj Microgravity review)
mars-magnetic-biology
Open-source scientific repository and interactive web tool.
microgreen-chamber-cfd
3D internal-flow CFD of a microgreen growth chamber (OpenFOAM v2606) — baseline airflow, buoyancy, and a gravity parametric study
nssdc-cosmic-explorer
Open-source scientific repository and interactive web tool.
osdr-plant-microbiome
FAIR relational + graph database, guild-inference ML and interactive report for NASA OSDR plant-associated microbiome datasets
plant-mitocarta
Plant MitoCarta: Subcellular Digital Doubles, Inter-Organellar Signaling & Cross-Kingdom Synteny
quantum-biology-atlas
Cross-species ontology and SBGN pathway maps for quantum-biological processes: identifier-bound nodes carrying radical-pair/Fe-S/flavin annotations with an explicit evidence tier, plus NASA OSDR data projection. Companion to a near-null magnetic field review.
spaceflight-plant-hardware-cfd
Open-source scientific repository and interactive web tool.