BIDS
Berkeley Institute For Data Science
Kathryn (Katy) Huff
Berkeley, CA
May 27, 2016
Science
- builds and organizes knowledge
- tests explanations about the universe
- systematically,
- objectively,
- transparently,
- and reproducibly.
Otherwise it's not science.
Computers
should...
- improve efficiency,
- reduce human error,
- automate the mundane,
- simplify the complex,
- and accelerate research.
But scientists don't use them effectively.
The Hacker Within is Helping
Peer-led organization for scientific computing best practices.
Community
- democratic anarchy
- maximize permissions
- charismatic leadership
- occasional beer
Peer-Driven
- peer teaching and learning
- interdisciplinary normalizes mixed skill levels
- relevant topics
- appeals to the desire to show off
- direct peer-to-peer skill sharing
Software Carpentry is Helping
Software Carpentry Foundation
- NumFOCUS umbrella
- Elected Steering Committee
- Representative, Expert Advisory Council
We make researchers in science, engineering, and medicine more productive by teaching them basic lab skills for scientific computing.
Software Carpentry Workshops
- Two days of hands-on learning
- Scientists teaching scientists
- Instructors are volunteers
- Materials are all open access
- bash --> automate tasks
- python --> build modular code
- git --> track and share work
- SQL --> manage data
- nose --> program defensively
But Why Do They Do It?
- community
- travel
- teaching experience
- teaching = learning
- sensed need
- etc.
Data Science 8
Cathryn Carson, David Culler, etc. databears.berkeley.edu
New Resources
Getting Started
- Chapter 1 - Introduction to the Command Line
- Chapter 2 - Programming Blast Off with Python
- Chapter 3 - Essential Containers
- Chapter 4 - Flow Control and Logic
- Chapter 5 - Operating with Functions
- Chapter 6 - Classes and Objects
Getting It Done
- Chapter 7 - Analysis and Visualization
- Chapter 8 - Regular Expressions
- Chapter 9 - NumPy: Thinking in Arrays
- Chapter 10 - Storing Data: Files and HDF5
- Chapter 11 - Important Data Structures in Physics
- Chapter 12 - Performing in Parallel
- Chapter 13 - Deploying Software
Getting It Right
- Chapter 14 - Building Software Pipelines
- Chapter 15 - Local Version Control
- Chapter 16 - Remote Version Control
- Chapter 17 - Debugging
- Chapter 18 - Testing
Getting It Out There
- Chapter 19 - Documentation
- Chapter 20 - Publication
- Chapter 21 - Collaboration
- Chapter 22 - Licenses, Ownership, and Copyright
- Chapter 23 - Further Musings
Effective Computation Course
- Open source IPython Notebooks
- Project-Driven Course Structure
- Example-Driven In Class Work
- BYO-Science Template
- Alpha-testing, Tiffany Timbers, Simon Fraser
- Beta release soon
github.com/physics-codes/seminar
Acknowledgements
This book was heavily inspired by the work of Software Carpentry and The Hacker Within. We are thrilled to see Effective Computation in Physics come to press and spread the joys of computation further into the physical sciences. In case you were wondering, the cuddly creature on the cover is a bobtail squid.
Acknowledgements
- Anthony M. Scopatz
- Paul P.H. Wilson
- Gregory V. Wilson
- Lorena Barba
- Tiffany Timbers
Links!
THE END
Katy Huff
katyhuff.github.io/2015-05-27-sorma
BIDS for Science Education by Kathryn Huff is licensed under a Creative Commons Attribution 4.0 International License.
Based on a work at http://katyhuff.github.io/2015-05-27-sorma.