This document summarizes a talk about teaching basic lab skills for scientific computing using Software Carpentry workshops. The key points are: 1. Software Carpentry's mission is to teach scientists basic coding skills like shell, Git, and Python to help them do research more efficiently. 2. Their teaching method involves live coding, openly licensed lesson materials, and hands-on exercises to keep students engaged. 3. Software Carpentry operates as an open source community with many distributed contributors and instructors around the world.

1. TEACHING BASIC LAB SKILLS FOR RESEARCH
COMPUTING
by Loïc Estève (Inria)
group /
and community /
Strongly inspired from 's talk at Scikit-learn day in June 2016
So ware Carpentry Paris @paris-swc
So ware Carpentry @swcarpentry
Bartosz Telenczuk

2. So ware Carpentry's mission is to help scientists and
engineers get more research done in less time and with less
pain by teaching them basic lab skills for scientific
computing.
MISSION

3. TARGET AUDIENCE
Scientists without prior knowledge
My 2c: mostly beneficial to scientists who have at least a
hint they have problems that programming could solve
better
My 2.5c: even better if you have previous exposure to a
programming language
Truer than life examples at https://so ware-carpentry.org/audience

4. TYPICAL SWC WORKSHOP
shell: 1/2 day
git + github: 1/2 day
Python: 1 day

5. June 2016

6. November 2017

7. workshops worldwide
students trained
863
22353
(as of November 7th, 2017)

8. >
OUR TEACHING METHOD

9. BASIC PRINCIPLES
Live coding
Lessons materials on github with a Creative Commons
licence
Frequent quizzes and hands-on exercises to keep
audience interested/awake
Feed-back: red/green sticky notes, Etherpad during and
a er each session, pre- and post-workshop survey

10. SOFTWARE CARPENTRY AS AN OPEN
SOURCE COMMUNITY

11. COMMON CHARACTERISTICS OF AN OPEN
SOURCE COMMUNITY
inclusive and transparent,
distributed contributors,
working together on an open source "product",
communicating through internet channels.

12. June 2016

13. November 2017

14. 968certified So ware Carpentry instructors
based in 39countries
(as of November 7th, 2017)

15. (http://software-carpentry.org/)
Programming with Python
The best way to learn how to program is to do something useful, so this introduction to Python is built around a common
scientific task: data analysis.
Our real goal isn’t to teach you Python, but to teach you the basic concepts that all programming depends on. We use Python
in our lessons because:
1. we have to use something for examples;
2. it’s free, well-documented, and runs almost everywhere;
3. it has a large (and growing) user base among scientists; and
4. experience shows that it’s easier for novices to pick up than most other languages.
But the two most important things are to use whatever language your colleagues are using, so that you can share your work
with them easily, and to use that language well.
We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first
dozen data sets of their daily inflammation. The data sets are stored in comma-separated values
(file:///home/bartosz/repos/docs/talks/2016-06-15-scikit-learn-day-paris/pages/python-novice-
inflammation/reference.html#comma-separated-values) (CSV) format: each row holds information for a single patient, and the
columns represent successive days. The first few rows of our first file look like this:
0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0
0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1
0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1
0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1
0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1
We want to:
load that data into memory,
calculate the average inflammation per day across all patients, and
157contributors, 350forks,
~1600commits, 230PRs merged,
4000lines of content, 10core lessons

16. OUR LOCAL COMMUNITY

17. Jan Antolik,
Andrew Davison
Loïc Estève,
Eric Bray,
Konrad Hinsen,
Alexandre Gramfort,
Samuel Lelièvre,
Camille Marini,
Marcel Stimberg,
Bartosz Teleńczuk,
Maria Teleńczuk,
Nelle Varoquaux

18. OUR SOFTWARE CARPENTRY WORKSHOPS

19. SWC workshops in Paris area + advanced workshop,
workshops in 2016, students trained,
certified instructors, instructors trained in 2016,
6 1
4 153
10 7

20. PROTO204 TRAINING 24-25 MAY 2016: 50
SEATS SOLD OUT IN A DAY

21. Field of work
PhD student
Other
Reaserch
Staff
Faculty
PostDoc
Stage of career
Female
Male
Gender

22. SWC IN PARIS: LAST 2-YEAR SUMMARY
2016: Instructor training + 4 SWC workshops
2017: 0 SWC workshops
WHAT HAPPENED?
Life happened and priorities took over
Super happy to come and teach at a workshop if we don't
have to bear most of the administrative work
Help needed: room, funding for coffee breaks, food (if
possible), workshop organisation.

23. WHAT IS NEXT?

24. HELP NEEDED!
host a workshop (help needed on the admin side),
web skills + love needed for the paris-swc
become a helper/instructor,
contribute to lessons,
become So ware Carpentry partner
website

26. CONTACT US
Homepage:
GitHub: , ,
email: loic.esteve@inria.fr
paris-swc.github.io
@swcarpentry @paris-swc @lesteve