Marcel Caraciolo is a scientist and CTO who has worked with Python for 7 years. He is interested in machine learning, mobile education, and data. He is the current president of the Python Brazil Association. Caraciolo has created several scientific Python packages and taught Python online. He is now working on applying Python to bioinformatics and clinical sequencing through tools like biopandas.

1. Python
on Science?
Marcel Caraciolo
@marcelcaraciolo
CTO of Genomika Diagnósticos, Scientist, MsC at Computer Science and Data Analysis,
works with Python for 7 years, interested at mobile
education, machine learning and dataaaaa! Current president of Association PythonBrazil.
Recife, Brazil - http://aimotion.blogspot.com
Yes we can!

2. About me
Creator os several scientific python packages including crab
(recsys), benchy and now biopandas
Until last year, Scientist Chief at Atepassar.com
(e-learning social network)
Co-Founder and Instructor of PyCursos, teaching Python on-line
including the famous Masanori’s Python for Zoooommbiesss!!
Interested at Python, mobile, e-learning, machine learning and now
my new acquisition skill: bioinformatics!!!

3. 2014, new challenges!
http://www.genomika.com.br

4. Onde tudo começou…

5. !
Março 2013
!
https://github.com/
marcelcaraciolo/Geo-
Friendship-Visualization

6. What already you know…

7. What already you know…

8. What already you know…

9. What already you know…

17. Putting Science back in Comp Science
Much of the software stack is for systems programming
C++, Java, .NET, ObjC, web, etc.
Complex numbers ? Vectorized primitives ?
Software stack for scientists is not helpful as it should be
FORTRAN, C/C++ is still where many scientists end up

19. High Performance with Big Data

20. Packages for data analysis and visualization

21. Syntax - Gets out of your way !!

22. Community Driven

23. Ready for web applications

24. Which is better Data Analysis language ? R or Python ?
Quora, http://www.quora.com/Data-Analysis/Which-is-the-better-Data-analysis-language-R-or-Python
“Python
is
good
for
data
cleanup,
R
for
sta7s7cal
models”

25. Which is better Data Analysis language ? R or Python ?
Quora, http://www.quora.com/Data-Analysis/Which-is-the-better-Data-analysis-language-R-or-Python
“Python
is
good
for
data
cleanup,
R
for
sta7s7cal
models”
“R
is
quirky
and
weird
but
the
sta7s7cians
love
it
and
there
really
isn’t
any
compelling
reason
to
switch”

26. Which is better Data Analysis language ? R or Python ?
Quora, http://www.quora.com/Data-Analysis/Which-is-the-better-Data-analysis-language-R-or-Python
“Python
is
good
for
data
cleanup,
R
for
sta7s7cal
models”
“R
is
quirky
and
weird
but
the
sta7s7cians
love
it
and
there
really
isn’t
any
compelling
reason
to
switch”
“You’re
running
an
scien7fic
simula7on
on
a
laptop?
Perhaps
you
should
write
it
in
C++/FORTRAN”

27. “You’re(running(an(MCMC(simula2on(on(
a(laptop?(Perhaps(you(should(write(it(in(
C++/FORTRAN”(

28. Numba
just-in-time compiler to LLVM through
@decorators
numba.pydata.org

29. Numba
just-in-time compiler to LLVM through
@decorators*
numba.pydata.org
*
aka
,
fast.
easy

31. Basic packages for data analysis and visualisation

32. NumPy: The foundation of the
Python Data Analysis stack

33. Numpy: Array oriented

34. DEMO (.)

35. Matplotlib
2D plotting library

36. DEMO (…)

37. !
Python Data Analysis toolkit upon Numpy

38. DEMO

39. Upon pandas it started several fork projects
https://github.com/kjordahl/geopandas

40. Upon pandas it started several fork projects
https://github.com/wrobstory/vincent
D3 with Vega

41. Upon pandas it started several fork projects
http://statsmodels.sourceforge.net/
Statistics, regression plots

42. Scikit-learn
Python toolkit for machine learning

43. DEMO (….)

44. Applied Science with Python!

45. Hurricane Detector using GFS Data
Colorado State University
Minwoo Lee
http://conference.scipy.org/scipy2011/slides/lee_hurricane_prediction.pdf

46. biological data analysis with python

47. http://www.astropy.org/

48. http://scikit-image.org/

49. NLTK
http://www.nltk.org/

50. IPython:
Interactive Python

51. DEMO (..)

52. DEMO

53. DEMO WITH WAKARI +
DEMO WITH GALLERY NBVIEWER (….)

54. 12. Anaconda Distribution packages
Anaconda:
pulls
it
all
together

55. 12. Anaconda Distribution packages
https://store.continuum.io/cshop/anaconda/
$ conda list
$ conda search
$ conda install <package-name>
$ conda create -n numpy16 ipython-notebook numpy=1.6
$ source activate numpy16
$ source deactivate

56. https://binstar.org/
$ conda install binstar
$ conda build <recipe-dir>
$ conda config --add channels https://conda.binstar.org/username
$ binstar login

57. How do you show your scientific app
to the world ?
One alternative: Yhat

58. How do you show your scientific app
to the world ?
One alternative: Yhat + Heroku

59. DEMO
http://blog.yhathq.com/posts/digit-recognition-with-node-and-
python.html

60. Who is using Scientific Python ?

61. Tools for scientific development

62. Tools for scientific development

63. Getting Started
http://stackoverflow.com/questions/9555635/open-source-enthought-python-alternative
http://fonnesbeck.github.io/ScipySuperpack/
Recent builds of fundamental Python scientific computing packages for OS X
https://code.google.com/p/pythonxy/
Scientific-oriented Python Distribution based on Qt and Spyder
https://store.continuum.io/cshop/anaconda/
Completely free enterprise-ready Python distribution for large-scale data processing, predictive analytics, and
scientific computing
!

64. Scientific python has also several events!
http://conference.scipy.org/

65. …and library community discussion groups
http://www.scipy.org/scipylib/mailing-lists.html
https://groups.google.com/forum/#!forum/pydata
https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
biopython@biopython.org

66. …and library community discussion groups
http://pyscience-brasil.wikidot.com/
https://groups.google.com/forum/#!forum/pyscience-brasil

67. …and library community discussion groups
http://pycursos.com/biblioteca/computacao-cientifica/?filter=lesson

68. Scientific Community is f**ing amazing!
https://www.enthought.com/products/pyxll/
PyXLL - Python for Excel Solution

69. Clinical Sequencing
Flask + Python -Web Dashboard
Python + matplotlib + scipy + numpy - Sequencing
biological and log databases
biopandas in work and sequencing parallel workflow
approaches
What Am I working on ?

70. biopandas
What Am I working on ?
https://github.com/genomika/biopandas

71. Challenges
Reproducible
Research

72. Challenges
“A
rule
of
thumb
among
biotechnology
venture
capitalists
is
that
half
of
published
research
cannot
be
replicated”

73. Challenges
How
do
we
replicate
research
today?

74. Challenges
How
do
we
replicate
research
today?
collaborate
on

75. Challenges
How
do
we
replicate
research
today?
collaborate
on
data
analysis

76. How do we collaborate today ?

77. ??????

79. Project-based interaction

80. Project-based interaction
wakari.io
Browser-­‐based
Python
&
Linux
environment

81. Presente em 22 dos
26 estados

85. Python
on Science?
Marcel Caraciolo
@marcelcaraciolo
CTO of Genomika Diagnósticos, Scientist, MsC at Computer Science and Data Analysis,
works with Python for 7 years, interested at mobile
education, machine learning and dataaaaa! Current president of Association PythonBrazil.
Recife, Brazil - http://aimotion.blogspot.com
Yes we can!