gistfile1.md

Why / Motivation

• http://programmingforbiologists.org/why-should-you-take-class
• http://www.wired.com/wiredscience/2009/03/why-biology-students-should-learn-how-to-program/
• http://www.mailund.dk/index.php/2009/03/19/automating-scientific-grunt-work/
• http://www.mailund.dk/index.php/highlights/
• http://hackeducation.com/2012/03/17/what-every-techie-should-know-about-education/
  • http://third-bit.com/blog/archives/4462.html
  • http://third-bit.com/blog/archives/4458.html
• http://worrydream.com/KillMath/

Background, Misc

• difference between sage & octave http://sagemath.blogspot.com/2007/12/why-isnt-sage-just-part-of-octave.html

Teaching

• Software Carpentry http://software-carpentry.org/
• Practical Computing for Biologists (Book) http://practicalcomputing.org/
  • EBook
    • http://www.coursesmart.com/9780878933914
  • Ad Flyer
    • http://practicalcomputing.org/files/PCFB_Flyer.pdf
  • TOC
    • http://scans.hebis.de/26/13/09/26130921_toc.pdf
  • Authors give the content as a course
    • https://www.nescent.org/sites/academy/Practical_computing_for_biologists http://practicalcomputing.org/nescent2011
• Programming for Non Computer Scientists
  • http://www.mailund.dk/index.php/2008/06/06/programming-for-non-computer-scientists/
  • discusses teaching computing for scientists, among the actual topics
• Programming as Part of a Science Education
  • http://ask.slashdot.org/story/08/05/29/2242205/programming-as-a-part-of-a-science-education
  • who should learn it? realistic advice.
• Python for Scientists curriculum/course
  • http://enthought.com/training/python_for_scientists.php
• UWash CSSS 569: Visualizing Data
  • "Visual Displays in Quantitative Social Science"
  • http://faculty.washington.edu/cadolph/vis/vis.pdf
  • http://faculty.washington.edu/cadolph/?page=22
• http://www.dalkescientific.com/writings/NBN/
  • Modern Web Applications Development for Bioinformatics
  • Introduction to Programming for Bioinformatics in Python
  • Programming for Bioinformatics in Python
• Key Bioinformatics Computer Skills
  • http://markbieda.wordpress.com/2009/04/21/key-bioinformatics-computer-skills/
• Utah CS 3200 - Introduction to Scientific Computing, Spring 2012
  • http://www.eng.utah.edu/~cs3200/
• USC SCIENTIFIC COMPUTING AND VISUALIZATION (Fall 11)
  • http://cacs.usc.edu/education/cs596.html
• NYU MS Scientific Computing
  • http://www.math.nyu.edu/degree/ms/scicomputing.html
• BU Scientific Computing and Visualization
  • http://www.bu.edu/tech/research/scv/
    • http://www.bu.edu/tech/research/training/tutorials/list/
    • http://www.bu.edu/tech/research/training/presentations/list/
    • http://www.bu.edu/tech/research/training/scv-software-packages/list/
• Florida Dept Scientific Computing
  • http://www.sc.fsu.edu/
• SciPy course
  • http://www.rexx.com/~dkuhlman/scipy_course_01.html
• Tentative NumPy Tutorial
  • http://www.scipy.org/Tentative_NumPy_Tutorial
• Programming for Biologists
  • http://programmingforbiologists.org/
  • http://programmingforbiologists.org/programming-resources
• Software Carpentry
  • http://software-carpentry.org/
  • "Our mission is to help scientists be more productive by teaching them basic computing skills."
  • http://software-carpentry.org/2012/03/what-we-teach-in-two-days/
• Critique of CodeAcademy - Audrey Watters
  • http://www.hackeducation.com/2011/10/28/codecademy-and-the-future-of-not-learning-to-code
• LPTHW learnpythonthehardway and its Udemy with videos
  • http://learnpythonthehardway.org/
  • http://www.udemy.com/learn-python-the-hard-way/

Tech Implementation Notes

• http://wiki.python.org/moin/SandboxedPython
• http://fellinlovewithdata.com/guides/tftp-jan-willem-d3-protovis
• Historically, why C/FORTRAN/Python?
  • http://programmers.stackexchange.com/questions/138643/why-is-python-used-for-high-performance-scientific-computing-but-ruby-isnt
• http://sagemath.org/
• JS editors
  • http://ajaxorg.github.com/ace/
  • http://codemirror.net/
• IPython
  • http://ipython.org/index.html
  • http://wiki.ipython.org/Cookbook/Branded_Notebook_Interactive_Tutorial
• IPython Quick Howto: running a public notebook server¶
  • http://ipython.org/ipython-doc/stable/interactive/htmlnotebook.html#quick-howto-running-a-public-notebook-server
  • http://www.quora.com/iPython/How-can-I-connect-to-an-IPython-kernel-running-on-EC2
• Hosting this on Heroku
  • https://github.com/heroku/heroku-buildpack-python
• Where is excellent Python code?
  • http://news.ycombinator.com/item?id=3808057
• installing ipython and superpack on osx
  • http://minrk.posterous.com/install-ipython-qtconsolenotebook-on-osx-lion
  • https://github.com/fonnesbeck/ScipySuperpack
• installing ipython under virtualenv
  • http://www.thisisthegreenroom.com/2011/installing-python-numpy-scipy-matplotlib-and-ipython-on-lion/
• how to do python deps
  • http://carljm.github.com/tamingdeps/
• How to embed ipython in html5
  • http://mail.scipy.org/pipermail/ipython-dev/2012-January/008562.html
  • followup about architecture, yt-project
    • http://mail.scipy.org/pipermail/ipython-dev/2012-April/008928.html
• IPython/D3.js mashup
  • https://github.com/cschin/IPython-Notebook---d3.js-mashup
• IPython 3+hour PyCon tutorial
  • https://plus.google.com/105051551851350439748/posts/cws7WTYFd6E
  • http://ipython.org/presentation.html
  • https://github.com/ipython/ipython-in-depth

What Software

• Python for Scientists curriculum/course
  • http://enthought.com/training/python_for_scientists.php
• R or SciPy
  • http://stackoverflow.com/questions/1944261/when-to-choose-r-vs-scipy
• http://code.google.com/p/scitools/
  • "" SciTools is a Python package containing many useful tools for scientific computing in Python. The package is built on top of other widely used packages such as NumPy, SciPy, ScientificPython, Matplotlib, Gnuplot, etc.
• http://www.bioconductor.org/
  • Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 554 software packages, and an active user community. Bioconductor is also available as an Amazon Machine Image (AMI).
• OEChem TK
  • http://www.eyesopen.com/oechem-tk
  • Programming Library for Chemistry and Cheminformatics
  • OEChem TK is a programming library for chemistry and cheminformatics that is fast and flexible. OEChem TK has many simple yet powerful functions that handle the details of working with small molecules, as well as an expanding number of functions for dealing with proteins. High-level functions provide simplicity while low-level functions provide flexibility.
• Visualization Toolkit
  • http://www.vtk.org/
• ParaView
  • http://www.paraview.org/
  • "" ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.
• Julia Language
  • http://julialang.org/
• Python Sci packages
  • http://www.doughellmann.com/articles/pythonmagazine/completely-different/2007-11-science/
  • http://jblevins.org/log/scipy-overview
  • http://wiki.python.org/moin/NumericAndScientific
• Sequence Manipulation Suite
  • http://bioinformatics.org/sms/
• Pandas - Python Data Analysis, works well with ipython
  • http://pandas.pydata.org/
  • "" pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.

Tutorials

• BioPython tutorials
  • http://biopython.org/DIST/docs/tutorial/Tutorial.html
• BU Scientific Computing and Visualization
  • http://www.bu.edu/tech/research/training/tutorials/list/
  • PDF: IntroSciViz-2.pdf
• NumPy, SciPy
  • http://www.scipy.org/Additional_Documentation

Tools

• How to become a data visualization ninja with 3 free tools for non-programmers
  • http://fellinlovewithdata.com/guides/how-to-become-a-data-visualization-ninja-with-3-free-tools-for-non-programmers
• CoaSim
  • http://users-birc.au.dk/mailund/CoaSim/
• Enthought Python Distribution
  • http://enthought.com/products/epd_free.php
• Tableau Public (Windows)
  • http://www.tableausoftware.com/public

Papers

• John Tukey, "We Need Both Exploratory and Confirmatory"
  • http://www.publicscienceproject.org/wp-content/themes/arras/images/pdf/26.pdf
  • Science doesn't progress as a straight line from question to answer
    • question > design > collection > analysis > answer
      • ...even in the confirmatory case!
    • more often a loop:
      • idea > ( question <-> design ) > collection > analysis > answer
  • Need to teach both exploratory and confirmatory data analysis
  • Need to teach exploratory as an attitude as well as a set of techniques,
    • ...probably before we teach confirmatory
  • "Finding the question is often more important than finding the answer"
  • http://fellinlovewithdata.com/guides/7-classic-foundational-vis-papers

Quotes

In conventional schools, students learn so that they can get good grades. My most important research finding is that young innovators are intrinsically motivated. The culture of learning in programs that excel at educating for innovation emphasize what I call the three P’s—play, passion and purpose. The play is discovery-based learning that leads young people to find and pursue a passion, which evolves, over time, into a deeper sense of purpose. - http://exp.lore.com/post/21379578745/in-conventional-schools-students-learn-so-that

Watering Holes

• Audience: bioinformatician - bioinformatics
• Audience: data visualizer - dataviz, data visualization, data analysis
• Audience: scientist programmer - scientific programming, biology programming, chemistry pro...
• Fell In Love With Data
  • http://fellinlovewithdata.com/about
  • "" I am Enrico Bertini, a data visualization researcher at the Univ. of Konstanz, Germany.
  • "" With FILWD I strive to bridge the gap between academics and practitioners.
  • "" Plus, I love to help people becoming data visualization experts.
  • http://fellinlovewithdata.com/guides/data-vis-beginners-toolkit-1
  • http://fellinlovewithdata.com/guides/data-vis-beginners-toolkit-2
  • http://fellinlovewithdata.com/guides/7-classic-foundational-vis-papers
• TULP interactive
  • http://www.janwillemtulp.com/blog/
• http://www.biology-online.org/search.php?search=programming
• http://delicious.com/tag/programming+biology
• http://delicious.com/search?p=data+visualization
• http://delicious.com/search?p=bioinformatics
• Bioconductor training and mailing list
  • http://www.bioconductor.org/help/course-materials/2012/
  • https://stat.ethz.ch/pipermail/bioconductor/
• http://www.programming4scientists.com/
• http://www.physicsforums.com/showthread.php?t=332618
  • Which language...?
    • http://www.x-rayman.co.uk/xforum/viewforum.php?f=173
    • http://www.macresearch.org/forums/scientific+programming
    • http://biostar.stackexchange.com/questions
• http://ask.sagemath.org/ mathematics
• BEGINNING PYTHON FOR BIOINFORMATICS
  • http://python.genedrift.org/
  • http://web.archive.org/web/20101103003538/http://python.genedrift.org/page/2/
  • http://web.archive.org/web/20080720014040/http://python.genedrift.org/page/3/
  • http://web.archive.org/web/20080907090139/http://python.genedrift.org/page/4/
  • http://web.archive.org/web/20081120004714/http://python.genedrift.org/page/5/
• StackOverflow threads
  • http://stackoverflow.com/questions/tagged/biopython
  • http://stackoverflow.com/questions/tagged/numpy
  • http://stackoverflow.com/questions/tagged/scipy
• BioPython archives
  • http://lists.open-bio.org/pipermail/biopython/
• http://abhishek-tiwari.com/2009/02/30-blogs-about-bioinformatics-and.html
  • _ drill down, cheminfo and bioinfo
• Saaien Tist
  • http://saaientist.blogspot.com/
  • On data visualization, bioinformatics and personal productivity
• IEEE Symposium on Biological Data Visualization
  • http://www.biovis.net/about/
• http://dalkescientific.com/writings/diary/archive/
  • KNIME and beginners
    • http://www.dalkescientific.com/writings/diary/archive/2010/03/16/knime_and_beginners.html
  • Teaching Python for cheminformatics
    • http://www.dalkescientific.com/writings/diary/archive/2008/11/06/teaching_python_for_cheminformatics.html
  • Teaching Python programming for cheminformatics
    • http://www.dalkescientific.com/writings/diary/archive/2008/07/23/teaching.html
• http://third-bit.com/blog/archives/category/teaching
• http://biorelated.com/
• http://markbieda.wordpress.com/
• http://scott.sherrillmix.com/blog/
• http://stackoverflow.com/questions/1671682/the-reading-list-for-scientific-programmer
• http://www.uow.edu.au/~/greg/html/main.html
• http://tldp.org/HOWTO/html_single/Scientific-Computing-with-GNU-Linux/
• http://www.gnu.org/software/gsl/
• http://www.sci.utah.edu/software.html
• BANANA -- Bay Area Numerical Analysis Networking Alliance
  • http://csmr.ca.sandia.gov/mailman/listinfo/banana
• http://www.doughellmann.com/articles/pythonmagazine/completely-different/2007-11-science/
• SciPy Overview
  • http://jblevins.org/log/scipy-overview
• C Titus Brown
  • http://ivory.idyll.org/blog/
• The Hacker Within open source scientific programming
  • http://hackerwithin.org/thw/
• Practical Computing (book) Forums
  • http://practicalcomputing.org/forums