Python on Science ? Yes, We can.
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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.
Python on Science ? Yes, We can.
- 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!!!
- 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”
- 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
- 34. DEMO (.)
- 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
- 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
- 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
- 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. ??????
- 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!