OPENNESS

Kiko Correoso

pybonacci.org (kiko@pybonacci.org)

@pybonacci

kikocorreoso

Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world.

Louis Pasteur



In [1]:

    
import os

import matplotlib.pyplot as plt
from matplotlib import rcParams
%matplotlib inline



In [2]:

    
plt.xkcd()
rcParams['font.size'] = 20



In [3]:

    
fig = plt.figure(figsize = (10, 10))
ax = fig.add_subplot(1, 1, 1)
ax.spines['right'].set_color('none')
ax.spines['top'].set_color('none')
ax.spines['left'].set_color('none')
ax.spines['bottom'].set_color('none')
plt.xticks([])
plt.yticks([])
plt.xlim(0, 100)
plt.ylim(0,100)
plt.annotate('Openness', xy=(25, 50), arrowprops=dict(arrowstyle='->'), xytext=(50, 90))
plt.annotate('Openness', xy=(75, 50), arrowprops=dict(arrowstyle='->'), xytext=(50, 90))
plt.annotate('Openness', xy=(50, 65), arrowprops=dict(arrowstyle='->'), xytext=(50, 90))
plt.annotate('Open access', xy=(70, 50), arrowprops=dict(arrowstyle='->'), xytext=(40, 60))
plt.annotate('Open Data', xy=(50, 25), arrowprops=dict(arrowstyle='->'), xytext=(15, 45))
plt.annotate('Open Data', xy=(65, 45), arrowprops=dict(arrowstyle='->'), xytext=(15, 45))
plt.annotate('Open Source', xy=(50, 25), arrowprops=dict(arrowstyle='->'), xytext=(65, 45))
plt.text(40, 20, 'Open Science')
plt.savefig('./misc/openness01.png')



In [4]:

    
fig = plt.figure(figsize = (10, 10))
ax = fig.add_subplot(1, 1, 1)
ax.spines['right'].set_color('none')
ax.spines['top'].set_color('none')
ax.spines['left'].set_color('none')
ax.spines['bottom'].set_color('none')
plt.xticks([])
plt.yticks([])
plt.xlim(0, 100)
plt.ylim(0,100)
plt.annotate('Openness', xy=(25, 50), arrowprops=dict(arrowstyle='->'), xytext=(50, 90))
plt.annotate('Openness', xy=(75, 50), arrowprops=dict(arrowstyle='->'), xytext=(50, 90))
plt.annotate('Openness', xy=(50, 65), arrowprops=dict(arrowstyle='->'), xytext=(50, 90))
plt.annotate('Open access', xy=(70, 50), arrowprops=dict(arrowstyle='->'), xytext=(40, 60))
plt.annotate('Open Data', xy=(50, 25), arrowprops=dict(arrowstyle='->'), xytext=(15, 45))
plt.annotate('Open Data', xy=(65, 45), arrowprops=dict(arrowstyle='->'), xytext=(15, 45))
plt.annotate('Open Source', xy=(50, 25), arrowprops=dict(arrowstyle='->'), xytext=(65, 45))
plt.annotate('Open Source', xy=(80, 35), arrowprops=dict(arrowstyle='->'), xytext=(65, 45))
plt.text(40, 20, 'Open Science')
plt.text(70, 30, 'Open Lab')
plt.savefig('misc/openness02.png')

Open?

Open means anyone can freely access, use, modify, and share for any purpose (subject, at most, to requirements that preserve provenance and openness).

http://opendefinition.org/ (ES: http://opendefinition.org/od/2.0/es/, PT: http://opendefinition.org/od/1.1/pt/)

HOW-TO: open community member

- I try to help in the mail-lists, forums,... (science, programming).

- I blog (http://www.pybonacci.org) and tweet (@pybonacci) about open source and science.

HOW-TO: open community member

- Management of an open community of scientist that program or programmers that make science (https://groups.google.com/forum/#!forum/scipydata-es).

- Some tasks as VP of the Asociación Python España.

(http://www.es.python.org/)

HOW-TO: open community member

- I commit code to some open source projects.

(https://groups.google.com/forum/?fromgroups=#!topic/brython/wW_wMwZUva4)

- I report bugs.

HOW-TO: open community member

- Speaker at some conferences.

- Open Educational resources on github.

(e.g., https://github.com/Python-en-ciencia/Python-cientifico)

HOW-TO: open community member

- Donations to numfocus, wikipedia,...

- Member of open source societies.

Openness - Open Education?

How can we learn?

Traditionally from school, university,...

OPEN EDUCATION!!!

(http://www.wsj.com/articles/SB10001424052702303812904577295930047604846)

OPEN EDUCATION!!!

(http://fortune.com/2015/03/10/american-millennials-are-among-the-worlds-least-skilled/)

OPEN EDUCATION!!!

(http://gao.gov/assets/660/655066.pdf)

How can we learn?

OPEN EDUCATION!!!

Nowadays the paradigm is changing: wikipedia, MOOCs, stackexchange, blog posts, apps in the mobile, lectures from your teachers in electronic format,...

(http://openstaxcollege.org/, http://www.ck12.org/, http://www.etnassoft.com/biblioteca/, https://www.coursera.org/, https://www.edx.org/,...)

Openness - Open Access

How can we learn?

We learn also from previous work from other people, their methodologies, their conclusions,...

OPEN ACCESS!!!

How can we learn?

OPEN ACCESS!!!

Most of the 2.5 million articles published each year in the world’s 24,000 peer-reviewed journals are closed to many of their potential users, because they cannot afford access.

(http://access.okfn.org/)

How can we learn?

OPEN ACCESS!!!

(http://www.nytimes.com/2015/04/08/opinion/yes-we-were-warned-about-ebola.html)

How can we learn?

OPEN ACCESS!!!

(http://www.bbc.com/news/magazine-22223190)

How can we learn?

OPEN ACCESS!!!

~2/3rds of open access users come from outside of academy

(http://www.slideshare.net/RightToResearch/state-of-oa-us)

How can we learn?

OPEN ACCESS!!!

(http://poeticeconomics.blogspot.com.es/2015/04/dramatic-growth-of-open-access-2015.html)

How can we learn?

OPEN ACCESS!!!

On average, the citation advantage of OA papers is 40.3% while the citation disadvantage is 27% for non-OA papers.

(http://www.science-metrix.com/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf)

How can we learn?

OPEN ACCESS!!!

(http://www.science-metrix.com/files/science-metrix/publications/d_1.8_sm_ec_dg-rtd_proportion_oa_1996-2013_v11p.pdf)

(https://www.openaire.eu/, https://zenodo.org/, https://www.fosteropenscience.eu/, http://figshare.com/about, http://arxiv.org,...)

How can we learn?

OPEN ACCESS!!!

([http://www.washingtonpost.com/blogs/the-switch/wp/2013/12/19/how-one-publisher-is-stopping-academics-from-sharing-their-research/)

Openness - Open Data

How can we learn?

Of course, if we are not working in something theoretical, we need data. We can collect that data or re-use data from others.

OPEN DATA!!!

How can we learn?

OPEN DATA!!!

Transparency.

Innovation.

Reuse, Efficiency.

Costs.

We are ready for the SCIENCE!

But why OPEN SCIENCE?

Mertonian (Robert K. Merton) Norms for modern science:

Communalism all scientists should have equal access to scientific goods (intellectual property) and there should be a sense of common ownership in order to promote collective collaboration.

Universalism all scientists can contribute to science regardless of race, nationality, culture, or gender.

Disinterestedness according to which scientists are supposed to act for the benefit of a common scientific enterprise, rather than for personal gain.

Organized Skepticism Skepticism means that scientific claims must be exposed to critical scrutiny before being accepted.

But why OPEN SCIENCE?

Imagine a world where no-one shared their results.

How would we know what was truth & what was lies or fraud or errors?

Imagine the waste of time and resources if everyone had to replicate results every time.

How would we make progress?

([http://www.slideshare.net/RightToResearch/open-con-mouncedata-41594350)

But why OPEN SCIENCE?

Open access, re-used data, etc, allow others to advance more quickly and easily (and cheaply). They can test the results from others (Science need to be reproduced to be credible), they can analyse the same data from other point of view,...

But why OPEN SCIENCE?

And if the science is open...

everybody in the society, professional or amateur, can access the results, the methodology, the driven data,... MORE IMPACT!!

Potentially drives to open notebook science, open research,... => VICIOUS CIRCLE!!

Knowledge is property of nobody... ETHICAL!!

Can be shared almost inmediately... FASTER PROGRESS

But why OPEN SCIENCE?

Credit / Impact:

altmetric (http://www.altmetric.com/)

-plum (http://www.plumanalytics.com/metrics.html)

-impactstory (https://impactstory.org/)

-twitter, facebook, mentions, blog posts,...

Open Lab

Some tools are a limitation so your results will be limited.

Traditional tools don't update as fast as needed.

Programming is a must for a researcher nowadays!!

We are living an explosion of data, analytics and visualisation tools.

Open Lab

There are a lot of programming languages out there.

But I will like to talk about languages better suited for scientists.

A scientists is not a hacker. Scientists need an easy tool to solve their problems.

And the tool cannot be the problem.

Open Lab

And this is how I arrived to...

Open Lab

We are talking about tools, not religion...

If you don't like Python there are other free tools (Julia, R,...).

Open Lab

Python has libraries for:

Astronomy

Molecular biology

Data analysis

Data visualisation

Cryptography

Numerical Optimisation

Open Lab

Python has libraries for:

GIS

Spatial analysis

Science notebook

Natural language analysis

Solar Physics

Machine Learning

Open Lab

Python has libraries for:

Time series Analysis

Bayesian Analysis

Symbolic Mathematics

Chemistry

Image analysis

And many more (more than 3700 packages tagged as scientific/engineering, [https://pypi.python.org/pypi?:action=browse&show=all&c=385

Live demo of the talk...

Thanks.