Ideas and Projects
- OpenBases: templates that use Github+CircleCI for easy, reproducible research
- OpenSchemas: Tools to interact with and develop specifications for schema.org
- Stanford Research Computing Lessons: Lessons and tutorials for HPC
- Dinosaur Datasets: Open Source Datasets
- The Scientific Filesystem (scif): a filesystem organization for scientific software and metadata [client] [RRID]
- The Experiment Factory: reproducible experiment containers [library] [RRID]
- The Robots I just needed over 15K of them. Don't judge.
- Pokemon Ascii: avatar generator [Github]
- Service Worker Resource Saved [demo]
- Banner: Custom banner creation (created for a virtual machine for a publication)
- GO: Genetic annotation of behavior (mapping of brain to behaviors via genes)
- Wordfish: tools for finding relationships in corpus from terminologies [details]
- Containershare: containershare for Sherlock
- ContainerTools: suite of tools for containers
- Singularity Registry Global Client: local client to manage Singularity containers.
- Singularity Hub: cloud builders for Singularity containers [software]
- spython: Singularity Python Client
- Singularity Registry: serve your own registry of Singularity containers [software][paper]
- Singularity: developing tools and applications for container based analyses [software]
Visualization and Media
- Cognitive Atlas Matrix: red or blue brain?
- DrainLog: an interactive log for a JP Drain [medical]
- Salted Caramel: never too old for a bedtime story! :)
- MyBrain: My fun visualization project, my first experience with Poldracklab
- Brain-canvas: 150K values in via canvas
- Silhouette: An idea for comparing regional brain maps
- theMAC: Early work for a functional connectivity explorer
- Visualization for Continuous Integration: and other places too [example]
Neuroimaging / Neuroinformatics
- Confusion: optimal classification of fMRI contrast images [cite]
- AuthorSynth: a neuroscience author collaboration network [cite].
- Cognitive Atlas: Version 2.0 with Django/Neo4j [Github]
- NIDM Viewer: view Neuroimaging Data Model results [NeuroVault]
- Nifti-Drop: drop and go nifti in browser
- Nipy: designing a new template for nipy.github.io, eventually deployed to...
- Nipy: nipy org website with continuous integration, gh-pages hosting
- NIDM-API: API for the Neuroimaging Data Model [paper]
- Noisecloud: spatial and temporal features to classify artifact in fMRI [cite].
- Brain-Browser: view brain maps in local web browser
- Nsynth2CA: NeuroSynth to Cognitive Atlas mapping, connected me with my lab! <3
- Niindex: Directory browsing for nifti images [github]
- Font-Brain: web font for neuroscience researchers
- Traits: Mapping of behavioral traits to associated families [research in progress] [github]
- NeuroVault annotation: using hypothes.is, Cognitive Atlas, and NeuroVault APIs
- Neuro2Gene: a project with work not suitable for publication, but a nice web interface
- NeuroVault in Cognitive Atlas [github]
- Potpourri: Mixing up ontologies
- Grid: a "brain grid" prototype to read in a nifti file and render all 200K+ voxels (canvas)
- Courses: the classes I took for my PhD
Early Graduate School
- The Experiment Factory (Legacy): standardizing deployment of behavioral experiments [expfactory.org]
- ICA[ALL]: First work at Stanford using the NYU datasets with Rubin Lab
- Template Matching: for functional brain images
- ConnDB: I have no idea. I think it involved Protege, & I was terrified.
- NDAR: Summarizing data in NDAR
- Pre-graduate school
Pybraincompare Python Package [github]
- Connectogram: to show functional brain network connectivity
- Histogram: Animated histogram
- Scatterplot Compare: interactive scatterplot to compare two images with a brain atlas
- Ontology: Simple tree to show some kind of ontology or graph [d3]
- Quality Analysis (QA): interactive report for fMRI
- make web images out of actual brain data
- Chris Computer: Should have bought a PC...
- Soylent Green
- vsoch.github.io (v1)[github]
- NKG Boston: art gallery, closed.
- GBMAtlas: for glioblastomia multiforme, explore genes and brain anatomy
- Neuropower Tools: for calculating power / sample size.
- Virtual Biomedical Informatics Learning: writing and learning about methods.
- Long: Laboratory of NeuroGenetics (created original design, 2009)
- BRAIN Lab: designed 2011.