Building Tools for Neuroimaging
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1. The document discusses various tools and projects developed by Vanessa Sochat at the intersection of neuroimaging, high performance computing, and web technologies. 2. Sochat's goal is to build tools that improve reproducibility in neuroscience research by enabling researchers to easily visualize, share, and deploy analyses. 3. Examples of tools discussed include NeuroVault, PyBrainCompare, MyConnectome, and tools for clinical use like Recovery Log and a prostate application. 4. Sochat's vision is for reproducibility to be more highly valued in graduate training and for reproducibility centers to help researchers deploy tools and analyses easily.
Building Tools for Neuroimaging
- 1. Building Tools for Neuroimaging the intersection of high performance computing, web technology, and fun in graduate school Vanessa Sochat Research Computing Talk October 21, 2015
- 2. Outline Background Why do researchers need tools?
- 3. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience
- 4. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience Vision Reproducibility, tools for researchers
- 5. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience Vision Reproducibility, tools for researchers Discussion
- 6. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience Vision Reproducibility, tools for researchers Discussion
- 7. Why do researchers need tools? Computational Tools
- 8. Science has a reproducibility crisis
- 9. Science has a reproducibility crisis
- 12. pipe dream Computational the reproducible researcher web development computer science skills domain knowledge HPC data analysis skills core ideal organized reproducibility ninja
- 14. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience Vision Reproducibility, tools for researchers Discussion
- 17. NeuroVault Django application hosted on RODEO (TACC) Github/Opbeat Celery to manage tasks Development: Vagrant → Docker Continuous Integration: Travis → Circle Where do we put this? Where / how should data be stored? More complex visualization and analysis?
- 18. Pybraincompare Python module Produces web reports / visualizations Template approach Github D3, canvas Continuous Integration Travis Deployed in NeuroVault (NeuroSynth?) https://github.com/vsoch/pybraincompare
- 19. 150,000+ Values with Canvas Getting data from the user? Hosted on a static site? A better way than a queue? Static application uses data extracted to flat files Canvas queue to render 1000 points/time
- 21. Reproducibility
- 25. MyConnectome Vagrant virtual machine (local or AWS) hosted on Amazon Web Services Github Python, Bash, R, Vagrant Data downloading Standard format for “deployable” repo? Access to web interface Elastic Load Balancing
- 26. Banner-Maker vbmis.com/bmi/project/banner D3 (JavaScript) / CSS / HTML Flask Application Where do we put this?
- 27. Experiments
- 28. Experiments
- 29. Research and Data Analysis
- 32. Noisecloud Matlab code Github Wordpress hosted on bluehost personal (vbmis) MySQL / php API Linked to manuscript Where do we put this?
- 34. Python HPC environment to do analysis HTML / CSS / JavaScript / json / php hosted on personal bluehost (vbmis) Github Challenge: integration of computation Serving a static resource from that How to make this real time?
- 35. Cognitive Phenotypes Django application (MySQL) (was) hosted on AWS Github Where do we put this? Users and permissions Integration with Mechanical Turk
- 36. Web Resources
- 37. Font-Brain https://github.com/vsoch/font-brain Real web font (“font-awesome”) Integration into web, document vision: modern tools for neuroscientists researcher web design tools standard visualizations for reproducibility
- 38. Clinical Tools
- 39. Shiny application in web interface JavaScript / HTML / CSS MySQL Database (Stanford) hosted by research computing Shiny Server Where do I put this? Can deployment be easy?
- 41. Recovery Log https://github.com/vsoch/drain-log Clinical tool hosted on github pages Renders a static data file (visualization/table) This impacted my standard of care Why doesn’t Stanford have tools like this?
- 42. Prostate Shiny ( R ) application hosted on shinyapps.io Where do we put this? Free hosting not reasonable
- 44. Brain-Browser https://youtu.be/KsJ5LOfZHNg NodeJS application runs from command line with “bb”
- 45. Niftindex https://github.com/vsoch/niindex php / .htaccess HTML/JavaScript deployed on personal (bluehost) Can servers be customized for their data?
- 46. Nifti-Drop http://vsoch.github.io/nifti-drop/ Static brain image and NIDM results viewer hosted on github pages Uses FileReader (Chrome) Interactive web tools for neuroscientists Handling large data in browser Reading, exporting standards
- 47. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience Vision Reproducibility, tools for researchers Discussion
- 48. Reproducibility as a Service Graduate Training: -building tools more highly valued -an emphasis is made on reproducible research Reproducibility Center -may be domain specific -provide infrastructure for researchers to deploy tools -could provide “toolization” as a service
- 49. Methods Result Conclusions 1. Researchers need help visualizing, sharing 2. Places to deploy things, easily 3. Deploy an entire analysis instantly 4. Blur the line between desktop & browser 5. Have fun while doing it :) ***
- 50. Outline Background Why do researchers need tools? Projects Spanning HPC, web technology, and neuroscience Vision Reproducibility, tools for researchers Discussion
- 52. Acknowledgements INCF/ Nidash Satra Ghosh Nolan Nichols Jessica Turner Tom Nichols JB Poline David Keator Collaborators Tal Yarkoni Nipy Funding Microsoft Research SGF and NSF Poldracklab Russ Poldrack Chris Gorgolewski Craig Moodie Sanmi Koyejo Patrick Bissett Joke Durnez Ian Eisenberg Mac Shine Joe Wexler BMI Daniel Rubin Russ Altman Mark Musen Rebecca Sawyer Mary Jeanne Nancy Steven Bagley John DiMario