Commits

Giovanni Marco Dall'Olio  committed f079429 Merge

MERGE: weird merge. I dont remember having made changes anywhere else

  • Participants
  • Parent commits 09179a8, fce012a

Comments (0)

Files changed (8)

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ProgrammingforEvolutionaryBiology-Leipzig2012.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ProgrammingforEvolutionaryBiology-Leipzig2012.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/ProgrammingforEvolutionaryBiology-Leipzig2012"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ProgrammingforEvolutionaryBiology-Leipzig2012"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+# -*- coding: utf-8 -*-
+#
+# Programming for Evolutionary Biology - Leipzig 2012 documentation build configuration file, created by
+# sphinx-quickstart on Fri Feb 17 16:41:56 2012.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Programming for Evolutionary Biology - Leipzig 2012'
+copyright = u'2012, Katja Nowick et al'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ProgrammingforEvolutionaryBiology-Leipzig2012doc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'ProgrammingforEvolutionaryBiology-Leipzig2012.tex', u'Programming for Evolutionary Biology - Leipzig 2012 Documentation',
+   u'Katja Nowick et al', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'programmingforevolutionarybiology-leipzig2012', u'Programming for Evolutionary Biology - Leipzig 2012 Documentation',
+     [u'Katja Nowick et al'], 1)
+]

File feedback2013/README.rst

+================================================================
+Analysis of "Programming of Evolutionary Biology" feedback forms
+================================================================
+
+This repository contains code to evaluate the feedback from the "Programming for Evolutionary Biology - Leipzig 2012" course.
+
+Since this is a public repository, the original data files are not included. You need to download them from the google/docs document and export them as a csv file, naming it evaluations.csv.

File feedback2013/evaluations2013.csv

+Timestamp,How would you rate the overall organization of the course? ,"In general, what did you think about the length of the course? ",What did you think of the ratio of teaching versus scientific lectures? ,What topic(s) should we spend more time on? ,Did you get enough help/attention from the TAs (teaching assistants)... ,How would you rate the computer infrastructure? ,How would you rate the room infrastructure and layout? ,How did you find the ratio lectures/exercises? ,How would you rate the quality of the following lectures:  [Linux/Unix intro (3/4) 	],How would you rate the quality of the following lectures:  [High-throughput sequencing (4/4)],How would you rate the quality of the following lectures:  [NGS non-model organisms (5/4 and 6/4)],How would you rate the quality of the following lectures:  [Databases (6/4)],How would you rate the quality of the following lectures:  [Intro to software development (6/4)],How would you rate the quality of the following lectures:  [Visualization (7/4)],How would you rate the quality of the following lectures:  [Introduction to R (7/4 and 8/4)],How would you rate the quality of the following lectures:  [Comparative transcriptomics (9/4)],How would you rate the quality of the following lectures:  [Networks (10/4)],How would you rate the quality of the following lectures:  [Phylogenomics (11/4)],How would you rate the quality of the following lectures:  [Introduction to Perl (13/4 and 14/4)],How would you rate the quality of the following lectures:  [Bioperl (14/4)],How would you rate the quality of the following lectures:  [Population Genomics (15/4)],Do you think the lecture is or will be relevant to your work?  [Linux/Unix intro (3/4) 	],Do you think the lecture is or will be relevant to your work?  [High-throughput sequencing (4/4)],Do you think the lecture is or will be relevant to your work?  [NGS non-model organisms (5/4 and 6/4)],Do you think the lecture is or will be relevant to your work?  [Databases (6/4)],Do you think the lecture is or will be relevant to your work?  [Intro to software development (6/4)],Do you think the lecture is or will be relevant to your work?  [Visualization (7/4)],Do you think the lecture is or will be relevant to your work?  [Introduction to R (7/4 and 8/4)],Do you think the lecture is or will be relevant to your work?  [Comparative transcriptomics (9/4)],Do you think the lecture is or will be relevant to your work?  [Networks (10/4)],Do you think the lecture is or will be relevant to your work?  [Phylogenomics (11/4)],Do you think the lecture is or will be relevant to your work?  [Introduction to Perl (13/4 and 14/4)],Do you think the lecture is or will be relevant to your work?  [Bioperl (14/4)],Do you think the lecture is or will be relevant to your work?  [Population Genomics (15/4)],How would you rate the length of the following lectures:  [Linux/Unix intro (3/4) 	],How would you rate the length of the following lectures:  [High-throughput sequencing (4/4)],How would you rate the length of the following lectures:  [NGS non-model organisms (5/4 and 6/4)],How would you rate the length of the following lectures:  [Databases (6/4)],How would you rate the length of the following lectures:  [Intro to software development (6/4)],How would you rate the length of the following lectures:  [Visualization (7/4)],How would you rate the length of the following lectures:  [Introduction to R (7/4 and 8/4)],How would you rate the length of the following lectures:  [Comparative transcriptomics (9/4)],How would you rate the length of the following lectures:  [Networks (10/4)],How would you rate the length of the following lectures:  [Phylogenomics (11/4)],How would you rate the length of the following lectures:  [Introduction to Perl (13/4 and 14/4)],How would you rate the length of the following lectures:  [Bioperl (14/4)],How would you rate the length of the following lectures:  [Population Genomics (15/4)],Did you feel that the presenter knew his subject well?  [Linux/Unix intro (3/4) 	],Did you feel that the presenter knew his subject well?  [High-throughput sequencing (4/4)],Did you feel that the presenter knew his subject well?  [NGS non-model organisms (5/4 and 6/4)],Did you feel that the presenter knew his subject well?  [Databases (6/4)],Did you feel that the presenter knew his subject well?  [Intro to software development (6/4)],Did you feel that the presenter knew his subject well?  [Visualization (7/4)],Did you feel that the presenter knew his subject well?  [Introduction to R (7/4 and 8/4)],Did you feel that the presenter knew his subject well?  [Comparative transcriptomics (9/4)],Did you feel that the presenter knew his subject well?  [Networks (10/4)],Did you feel that the presenter knew his subject well?  [Phylogenomics (11/4)],Did you feel that the presenter knew his subject well?  [Introduction to Perl (13/4 and 14/4)],Did you feel that the presenter knew his subject well?  [Bioperl (14/4)],Did you feel that the presenter knew his subject well?  [Population Genomics (15/4)],"How would you rate the quality of the following scientific talks? [""Structural Variation"" (Tomas Marques-Bonet) (5/4)]","How would you rate the quality of the following scientific talks? [""Evolution of Behaviour"" (Sarah London) (7/4)]","How would you rate the quality of the following scientific talks? [""Evolution of non-coding RNAs"" (Peter Stadler) (16/4)]","How would you rate the quality of the following scientific talks? [""Genomics of speciation"" (Rui Faria) (17/4)]","Do you think the talk is or will be relevant to your future work?  [""Structural Variation"" (Tomas Marques-Bonet) (5/4)]","Do you think the talk is or will be relevant to your future work?  [""Evolution of Behaviour"" (Sarah London) (7/4)]","Do you think the talk is or will be relevant to your future work?  [""Evolution of non-coding RNAs"" (Peter Stadler) (16/4)]","Do you think the talk is or will be relevant to your future work?  [""Genomics of speciation"" (Rui Faria) (17/4)]","How do you rate the length of these scientific talks? [""Structural Variation"" (Tomas Marques-Bonet) (5/4)]","How do you rate the length of these scientific talks? [""Evolution of Behaviour"" (Sarah London) (7/4)]","How do you rate the length of these scientific talks? [""Evolution of non-coding RNAs"" (Peter Stadler (16/4)]","How do you rate the length of these scientific talks? [""Genomics of speciation"" (Rui Faria) (17/4)]",Did you find the project useful in learning how to do bioinformatics? ,Are you happy with the guidance provided by the TA? ,How would you rate the scope and feasibility of your project? ,Would you like to have more time for the project? ,How many years have you worked in science? ,Did you have programming experience before the course? [Unix],"If yes, in which language?",How did you hear about the course? ,What made you decide to register? ,Were your expectations met?,What do you think you will remember the most? And why? ,Would you recommend this course to your colleagues? , Do you have any general comments about the course? ,Did you have programming experience before the course? [R],Did you have programming experience before the course? [Perl],Did you have programming experience before the course? [SQL],Did you have programming experience before the course? [Python]
+4/19/2013 16:32:26,Good,Just right,"More teaching on programming topics, please","It would be nice to have some more NGS data analysis (for instance, spend a whole day working with raw VCF files and try to figure out the best possible options to filter them - depending on the scientific question...)",It was just right for me,Adequate,good..., Just about right,Good,Good,Average,Good,Good,Good,Very Good,Good,Average,Good,Very Good,Good,Good,Very relevant 	,Probably,I don't know,I don't know,Probably,Probably,Very relevant 	,Probably,I don't know,Probably,Very relevant 	,Probably,Very relevant 	,Too short,Too short,Too long,Just right,Just right,Just right,Just right,Just right,Too long,Just right,Just right,Too short,Too short,Yes,Yes,I don't know,Yes,Yes,,Yes,Yes,I don't know,Yes,Yes,Yes,Yes,Very Good,Very Good,Average,Very Good,Yes,I don't know,No,Yes,Just right,Just right,Too long,Just right,Very,Yes,Our project was too ambitious,It was just right,5-10 years,Some,,Evoldir website, Interesting collection of programming languages and tools,Yes,Perl - it will be extremely useful for data manipulation!,Yes,Thanks for a wonderful time!,Some,Some,None,None
+4/19/2013 16:34:33,Good,Just right,"More teaching on programming topics, please","more programming, for me especially perl. ",It was just right for me,Adequate,"too small, too hot, lack of oxygen!","Too much lecture, too little time for exercises",Very Good,Good,Average,Very Good,Very Good,Very Good,Very Good,Very Good,Good,Good,Very Good,Very Good,Average,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Probably,Probably,Probably,Probably not,I don't know,Very relevant 	,Very relevant 	,Very relevant 	,Probably not,Too short,Just right,Too long,Just right,Just right,Just right,Just right,Too long,Just right,Just right,Just right,Too short,Too long,Yes,Yes,I don't know,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Yes,Yes,I don't know,Good,Good,Very Good,Very Good,I don't know,No,Yes,No,Just right,Too long,Too long,Just right,Very,Yes,Our project found the right balance,It was just right,5-10 years,Some,,Evoldir website,Need to learn for my current project,Yes,That whenever you have problem you can finally find a solution!,Yes,,None,None,None,None
+4/19/2013 16:36:20,Good,Just right,Ratio was just right,"Next gen. sequ. data analyses: mapping to ref. genome, non-model organisms,  RADseq, SNP calling,......... and doing it in exercises with a small dataset!",It was just right for me,Adequate,"room to sticky, bad air, windows did not open","Too much lecture, too little time for exercises",Very Good,Average,Very Poor,Good,Good,Good,Very Good,Good,Average,Average,Very Good,Average,Average,Very relevant 	,Very relevant 	,Very relevant 	,I don't know,I don't know,I don't know,Very relevant 	,Very relevant 	,I don't know,I don't know,Very relevant 	,Very relevant 	,I don't know,Just right,Too short,Too short,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Just right,Too short,Just right,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Good,Good,Very Good,Very Good,I don't know,I don't know,No,Yes,Just right,Just right,Just right,Just right,Very,No,Our project found the right balance,We could have used 1-2 more days,0-5 years,None,,Through a colleague,Need to learn for my current project,Not at all,"different tools available (e.g. bioperl), didn´t know about that before ",Maybe,"I could not concentrate during evening sessions any more; more exercises in NGS data analysis!!!; sometimes exercises went on too fast, Instructors obviously can not imagine, that you need more time for some task, than they do themselves.  (e.g. command we should type in, disappeared after 1 second...); ",Some,None,None,None
+4/19/2013 16:42:27,Average,Just right,"More teaching on programming topics, please",In general there was not enough time for the exercises and the pace was too fast.,It was just right for me,Adequate,The room was too crowded/hot., Just about right,Good,Good,Very Poor,Average,Average,Good,Good,Good,Good,Very Good,Very Good,Average,Good,Probably,Probably,Probably not,Probably,Probably not,Probably,Probably,Probably,I don't know,Probably,Probably,Probably,I don't know,Just right,Just right,Too long,Just right,Just right,Just right,Too short,Too short,Just right,Just right,Just right,Too short,Just right,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Average,Very Good,Very Good,Good,No,I don't know,Yes,Yes,Too long,Just right,Just right,Just right,A little bit,Yes,Our project was too ambitious,We could have used 1-2 more days,>10 years,None,,Evoldir website, Interesting collection of programming languages and tools,Yes,,Maybe,"I think it would be good to have a tighter schedule during the day and no evening sessions. I think that a course that includes evening sessions should not be longer than two weeks as it gets more and more difficult to concentrate. In general, I had the feeling that this is not really a course for total beginners, as we went through the topics way to fast and there was never enough time to finish the exercises. I think it would be better to focus on less topics and cover them more thoroughly.",Some,None,None,Some
+4/19/2013 16:44:17,Good,Just right,"More teaching on programming topics, please",More exercises time. Especially on long exercises. TAs maybe should know what the exercises are before... in networks this was a big issue for me as I couldn't get any help :(.,It was just right for me,Not adequate,Too slow... but large group of people so understandable.,"Too much lecture, too little time for exercises",Very Good,Very Good,Poor,Very Good,Very Good,Very Good,Very Good,Very Good,Very Good,Very Good,Very Good,Good,Average,Very relevant 	,Very relevant 	,Not at all,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Just right,Just right,Too long,Just right,Just right,Just right,Too short,Too short,Too short,Just right,Just right,Too short,Too short,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Very Good,Very Good,Very Good,Very Good,Yes,I don't know,Yes,Yes,Just right,Just right,Too long,Just right,A little bit,No,Our project was too ambitious,We could have used 1-2 more days,0-5 years,A lot,,Facebook,Need to learn for my current project,More than,R and perl were very well thought and I definitely feel more confident in these langauges now.,Yes,"Networks was abit of a disappointment for me, I had big hopes that this would be really useful and in the beginning I found it was but the exercises were too difficult for a beginner. The non-model organism day was very very repetitive and could be thought in a 1/3 of the time. Definitely more time for exercises at the end of lectures. Overall a really really enjoyable experience. I feel comfortable behind the terminal now. Although I don't deal with mapping and such I still found the lectures engaging and hope that I will use the knowledge in future projects. I would definitely recommend the course - and some wonderful friends made :). Thanks guys.",None,None,None,Enough
+4/19/2013 16:44:58,Good,Too Long,Ratio was just right,,It was just right for me,Adequate,Good.,"Too much lecture, too little time for exercises",Good,Good,Good,Good,Good,Good,Good,Good,Good,Good,Very Good,Good,Average,Very relevant 	,Very relevant 	,Probably not,Probably,I don't know,Probably,Very relevant 	,Probably not,Probably not,Probably not,Very relevant 	,Probably,Probably not,Too short,Too short,Just right,Just right,Just right,Too short,Too short,Just right,Just right,Just right,Too short,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Good,Good,Average,Very Good,No,No,No,No,Just right,Too long,Too long,Just right,Very,Yes,Our project found the right balance,It was just right,0-5 years,None,,Evoldir website, Interesting collection of programming languages and tools,Yes,,Yes,,None,None,None,None
+4/19/2013 16:45:35,Excellent,Just right,"More teaching on programming topics, please",Perl and BioPerl,It was just right for me,Adequate,The room and the faculty are nice and confortable and appropriate for the course ,"Too much lecture, too little time for exercises",Average,Good,Poor,Good,Very Good,Good,Very Good,Very Good,Average,Average,Very Good,Very Poor,Good,Very relevant 	,Very relevant 	,Probably not,Probably,I don't know,Very relevant 	,Very relevant 	,Very relevant 	,Probably,Very relevant 	,Very relevant 	,Very relevant 	,I don't know,Just right,Too long,Too long,Just right,Just right,Just right,Just right,Too short,Just right,Too long,Just right,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Average,Good,Very Good,Very Good,No,No,Yes,I don't know,Too long,Too long,Just right,Just right,A little bit,Yes,Our project found the right balance,It was just right,0-5 years,Some,,Evoldir website, Interesting collection of programming languages and tools,Yes,The nice lectures and practicals ...and the long hours spent at the uni and pubs,Yes,"The TAs/ speakers have a very high scientific standard overall and therefore I consider this course to be very good and particularly updated. We all learnt a lot about very interesting and useful topics from people actually working on these topics (and not old professors). The atmosphere was overall very good and both TAs and participants were overall friendly. There was a lot to be learnt and I think we did the most of these three weeks, but maybe the schedule was too long and exhausting (particularly some of the days). Thank you guys! ",None,None,None,None
+4/19/2013 16:46:11,Average,Too short,"More teaching on programming topics, please",I would have liked a little more time spent on both R and Perl because I felt like many of the modules felt a little rushed and there was never any way to get through most of the examples.  ,It was just right for me,Adequate,"Air movement would be nice.  Other than that, the setup was fine.","Too much lecture, too little time for exercises",Very Good,Good,Good,Good,Good,Average,Very Good,Average,Average,Average,Very Good,Good,Good,Very relevant 	,Very relevant 	,Very relevant 	,Probably,Probably,Probably,Very relevant 	,Probably,I don't know,I don't know,Probably,I don't know,I don't know,Just right,Just right,Just right,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Just right,Too short,Too short,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Good,Very Good,Good,Very Good,I don't know,Yes,I don't know,Yes,Just right,Just right,Too long,Just right,Very,Yes,Our project found the right balance,We could have used 1-2 more days,0-5 years,Some,,Through a colleague,Need to learn for my current project,Yes,I think the introduction to R and Perl will be very helpful going forward for dealing with my RNAseq data that I will have in the future. ,Yes,"I had a very positive experience overall.  The lecturers and the TAs and leaders were all very helpful and made the course fun.  Though I felt a little rushed through some of the topics sometimes, I think that I have a good foundation to begin to work with these tools once I am back home.  I think that having more time for the projects would be ideal but only if the length of the course was increased because I don't think that time should be taken away from any of the introductions.  ",None,None,None,None
+4/19/2013 16:46:45,Good,Just right,"More teaching on programming topics, please","Actual programming and not so many lectures about background info. RAD sequencing, i.e., how to do it, what data you get back, how to analyze it, and not a two hour discussion of the differences between model and non-model organisms (useless).
+Comparative pipelines (i.e., existing mapping tools, pros and cons, existing SNP calling tools, pros and cons, and so on)  Actual phylogenomics and not phylogenetics.",It was just right for me,Adequate,"I liked it very much except for... A window in the back of the room would have helped everyone breathe better. Also, I would suggest at the beginning of the course next year you tell everyone to shower frequently and use some kind of deodorant, please.","Too much lecture, too little time for exercises",Very Good,Good,Very Poor,Good,Very Good,Good,Very Good,Good,Very Poor,Very Poor,Very Good,Very Good,Very Poor,Very relevant 	,Very relevant 	,Not at all,Very relevant 	,Probably,Very relevant 	,Very relevant 	,Very relevant 	,Not at all,Not at all,Very relevant 	,Very relevant 	,Not at all,Too short,Too short,Too long,Just right,Too short,Just right,Too short,Too short,Too long,Too long,Too short,Too short,Too long,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,I don't know,No,Yes,Yes,I don't know,Good,Good,Average,Very Good,I don't know,No,No,Yes,Just right,Too long,Too long,Too short,Very,Yes,Our project was too ambitious,We could have used 1-2 more days,>10 years,Some,,Evoldir website, Interesting collection of programming languages and tools,Barely,"Unix, R, Perl, and Bioperl were well explained and the exercises helped fixed the concepts.",Maybe,"I suggest you send the students some reads before the course so they all start at a similar level and no time is wasted on lectures so more time can be devoted to improve our programming skills, which is why we came after all (the course name is ""Programming for Evolutionary Biology). ",Some,None,Some,Some
+4/19/2013 16:48:12,Good,Too Long,"More teaching on programming topics, please","Raw data analysis, different types of alignment & de novo assembly"," I needed more help, but didn't get it",Not adequate,"It was good that everybody had an own computer, but the computational power was way too small.","Too much lecture, too little time for exercises",Average,Good,Very Poor,Good,Good,Average,Average,Average,Poor,Poor,Good,Good,Average,Very relevant 	,Probably,Not at all,Probably,Probably,Probably not,Probably,Probably not,Not at all,Not at all,Probably,Probably not,Probably,Too short,Too short,Too short,Just right,Just right,Just right,Just right,Just right,Too long,Too long,Too short,Just right,Too short,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,I don't know,I don't know,Yes,Yes,No,Good,Good,Poor,Very Good,No,No,No,Yes,Just right,Just right,Too long,Just right,No,No,Our project could have been more ambitious.,We could have used 1-2 more days,5-10 years,Some,,Through a colleague, Interesting collection of programming languages and tools,Barely,I was nice to meet peaople from various countries with different scientific background. ,No,Please concentrate the next time on raw data analysis rather than dealing with finished datasets.,None,Some,None,None
+4/19/2013 16:48:15,Good,Too Long,"More teaching on programming topics, please",More on read mapping with actual practice. ,It was just right for me,Adequate,"The room was too small for the intense programming sessions. We should have split into two groups for longer sessions, with some in the room on the 4th floor. ","Too much lecture, too little time for exercises",Good,Average,Very Poor,Average,Good,Very Good,Very Good,Average,Average,Poor,Very Good,Very Good,Good,Very relevant 	,Very relevant 	,Probably,Probably,Probably not,Probably,Very relevant 	,Not at all,Probably,Very relevant 	,Probably,Probably,Probably,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Just right,Just right,Too long,Just right,Just right,Too long,Yes,Yes,I don't know,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Yes,Yes,I don't know,Good,Good,Poor,Good,Yes,No,No,I don't know,Just right,Too long,Too long,Just right,A little bit,Yes,Our project found the right balance,We had more than time enough,5-10 years,Some,,Through a colleague, Interesting collection of programming languages and tools,Yes,"I think I will remember the intensity of the work schedule. But I will also remember the night activities, especially football and the gym. ",Yes,"It would have been nice to have a half day in the middle of the course for a short break. And it could have been used for another sporting activity or museum. If possible, it would be great to switch restaurants for a different option on a few nights. Or provide a lunch some days and give the evening meal free for personal choice. ",Some,None,None,None
+4/19/2013 16:49:52,Good,Just right,"More teaching on programming topics, please",The differential gene expression part had too much time devoted to statistical models and we ended up not calling DE genes or working with these. I would also have liked that more time was devoted to networks.,It was just right for me,Adequate,Good enough but a room were 30+ people spent ~12h a day should have ventilation.,"Too much lecture, too little time for exercises",Very Good,Very Good,Average,Very Good,Good,Average,Very Good,Good,Average,Poor,Very Good,Average,Very Poor,Very relevant 	,Very relevant 	,I don't know,I don't know,Very relevant 	,Probably,Very relevant 	,Very relevant 	,Probably,Probably not,I don't know,I don't know,Probably not,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Too short,Too short,Too long,Just right,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Good,Very Good,Good,Good,No,No,Yes,No,Too long,Just right,Too long,Just right,Very,Yes,Our project could have been more ambitious.,It was just right,5-10 years,Enough,,googling for bionformatics courses, Interesting collection of programming languages and tools,Yes,The atmosphere was nice and I can see myself keeping in touch with some of the people I meet.,Maybe,"I liked it a lot and would do it again.  The projects are nice idea and worked well. Some instructors could have spent more time teaching the nity-gritty of programming and not so so much on their work. The quality of the practical part was very uneven and for some excellent well laid out practical there were also a few that were a  bit patchy and hard to understand what and why I was doing. The hotel room was way too small for a 2 week stay, I appreciate that the location was excellent, but I would not minded to stay a bit further away for a roomier room. I liked that we eat in the evening together but the quality was not great for the price - the portions size in particular could change a lot from day to day. Overall, none of the above detract from the fact that this is a very good course, but some aspects could be improved namely improving on some practicals. Good work!",Enough,None,None,Some
+4/19/2013 16:50:54,Excellent,Just right,"More teaching on programming topics, please",I think it would have been better to spend some more time on perl and particularly bioperl could have deserved some more time.,It was just right for me,Adequate,More windows : ))) or a fan , Just about right,Good,Good,Poor,Good,Very Good,Good,Very Good,Very Good,Average,Average,Very Good,Good,Average,Probably,Very relevant 	,Probably not,I don't know,Very relevant 	,Very relevant 	,Very relevant 	,Very relevant 	,Probably,Probably not,Probably,Probably,Probably,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Too short,Too short,Too long,Too short,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Good,Very Good,Good,Very Good,I don't know,Yes,I don't know,I don't know,Just right,Just right,Just right,Just right,Very,Yes,Our project found the right balance,It was just right,>10 years,None,,Through a colleague, Interesting collection of programming languages and tools,Yes,Too early to tell.,Yes,"I think the population genomics class should have been more general and not so human centered to also allow for discussions of how to get the type of data necessary to do the analysis. It should have dealt more with the advantages and pitfalls of working with large data sets compared to maybe single gene approaches. The comparative transcriptome class had a high tempo and covered a lot of ground and could have nicely been a bit longer, while the non-model organism lecture - though important and should be maintained - could have been shorter and more focused. Also the phylogenomic class was more an introduction into the theory of phylogenetics and did not discuss the problems and intricacies of working with large datasets. I think the network class was too much focused on how to draw a figure and it lacked the biological side, which would have maybe been even more interesting. Overall though I think this course was good and gave a very good and diverse introduction and overview of these new tools and leaves us with a good base to explore and use these tools in the future. The TAs were all very knowledgeable, super helpful and were fantastic. Big thanks to all of them, their efforts are much appreciated.",Some,None,None,None
+4/19/2013 16:51:00,Good,Just right,"More teaching on programming topics, please","I think from an objective point of view the ratio was just right but for me, a person who is new with the most of the stuff some programming topics were too short. I would have liked to spend more time with BioPerl and maybe have some options for population genetics analysies in addition to java (CoSi). ",It was just right for me,Not adequate,"I think that the computers were not so good, they crashed quite often and it would be great if you could oraganize more CPU power for Final projects. Otherwise I have no negative things to say about this. ", Just about right,Very Good,Good,Average,Average,Very Good,Good,Good,Good,Very Good,Good,Very Good,Poor,Poor,Very relevant 	,Very relevant 	,Very relevant 	,I don't know,Probably,Very relevant 	,Very relevant 	,Probably,Probably not,Probably not,Very relevant 	,Very relevant 	,Very relevant 	,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Too long,Just right,Just right,Just right,Too short,Too short,Yes,I don't know,I don't know,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Good,Very Good,Good,Very Good,No,No,I don't know,I don't know,Just right,Too long,Too long,Just right,A little bit,No,Our project found the right balance,We could have used 1-2 more days,0-5 years,Some,,Through a colleague, Interesting collection of programming languages and tools,More than,"The best thing that I got out of this course is that I got more familiar with the programming languages like bash, R and Perl. After this course I feel comfortable with bash command line basics and that is really important for me that I can start to use Unix when I go back to work. I think that the second important thing was that I learned to find sites where I can search for help for different programming languages etc. 
+All in all, I feel my self much more comfortable with Unix now than before the course, eventhough I know that most of the people in the course were more skillful in using programming laguages, I am still very happy about how I progressed. I will definitely apply the things that I have learned during this course to my work. ",Yes,"TA's were kind, motivated and helpful. I noticed that some of the TA's don't necessarily have very much experience in ""team leading"" and maybe that would be something to improve. But this conserns mostly the young TA's and because of that it is totally understandable. Programming skills of every TA were great and so was the attitude <3 Course is quite long and very intensive but still I would not make it any shorter maybe I would add a one day. I really enjoyed myself and I am very pleased that I got this opportunity to participate to this course. For me everything I learned will be very useful.",None,None,None,None
+4/19/2013 16:52:36,Excellent,Just right,"More teaching on programming topics, please","mapping using different tools, SNP calling, VCF tools",It was just right for me,Adequate,adeguate,"Too much lecture, too little time for exercises",Very Good,Very Good,Average,Good,Very Good,Very Good,Very Good,Good,Poor,Very Poor,Very Good,Very Good,Poor,Very relevant 	,Very relevant 	,I don't know,I don't know,I don't know,Very relevant 	,Very relevant 	,I don't know,I don't know,Probably not,Very relevant 	,Very relevant 	,I don't know,Too short,Too short,Too long,Just right,Too short,Just right,Too short,Too short,Just right,Too long,Too short,Too short,Too short,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Very Good,Good,Average,Very Good,Yes,No,No,I don't know,Too short,Just right,Too long,Just right,Very,Yes,Our project found the right balance,We could have used 1-2 more days,0-5 years,None,,Evoldir website, Interesting collection of programming languages and tools,Yes,The lectures about R and Perl. the instructors were able to manage the time in a perfect balance between lectures and time for practice. Although I wish we had more days to learn those languages.,Yes,,None,None,None,None
+4/19/2013 16:52:37,Good,Just right,"More teaching on programming topics, please","at least take the time for every topic which is needed - it is a pity when the lecturer has to speed through interesting parts of the presentation like in Bioperl or the end of the Gene Expression Lecture ",It was just right for me,Adequate,"Need more windows (to opem) or AC!!! But otherwise fine.", Just about right,Average,Average,Poor,Very Good,Average,Good,Good,Very Good,Good,Average,Very Good,Average,Poor,Probably,Very relevant 	,Probably not,Probably,I don't know,Probably,Very relevant 	,Very relevant 	,I don't know,Probably not,Very relevant 	,I don't know,Probably not,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Too short,Just right,Too long,Just right,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Good,Very Good,Good,Very Good,No,No,I don't know,No,Just right,Just right,Too long,Just right,A little bit,Yes,Our project could have been more ambitious.,It was just right,0-5 years,Some,,Through a colleague,Need to learn && Interesting collection,Yes,"Programming lectures and exercises in Perl and R - because I (hope to) need them for my daily work in particular and because we learned about the general logic behind programming, which might help with planning further bioinformatic projects Gene Expression Analysis - because it is my actual project Visualization -  because you can improve your plots (and thus the presentation of your data) by following simple rules ",Yes,"Not to have a organized lunch was great, because it gave the opportunity to explore the city. But the dinner gave rise to many discussions - the size of the portions showed a great variations between days (and sometimes even on one day between people). So on some days, it was just not enough! The quality was mainly (but not always) okay. I liked the 2 sports events to get out of the dayly routine.  After the day off, it was a bit hard to get started again - for me it would be maybe even better, to have the day off maybe at bit later (nat after half of the course, but after 2/3 of it ...)",Some,None,None,Some
+4/19/2013 16:53:24,Excellent,Just right,"More teaching on programming topics, please",,It was just right for me,Not adequate,Not bad but needed more windows,"Too much lecture, too little time for exercises",Very Good,Good,Poor,Good,Very Good,Good,Very Good,Good,Average,Average,Very Good,Good,Poor,Very relevant 	,Very relevant 	,Very relevant 	,I don't know,I don't know,I don't know,Probably,I don't know,Probably not,Probably,Very relevant 	,Very relevant 	,Very relevant 	,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Too short,Just right,Too long,Just right,Too short,,Yes,Yes,I don't know,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,Very Good,Average,Average,Very Good,I don't know,No,No,Yes,Just right,Too long,Too long,Just right,Very,Yes,Our project found the right balance,We could have used 1-2 more days,0-5 years,Some,,Evoldir website,Need to learn for my current project,Yes,"Perl!! And R.These lectures were probably the most well structured.",Yes,It was very useful not only by the contents of the course but by the experience by itself!,None,None,None,Some
+4/19/2013 16:55:08,Good,Just right,Ratio was just right,maybe statistical analyses,It was just right for me,Adequate,"Too stuffy! with so many people working for so many hours, we need more windows that open......","Too much lecture, too little time for exercises",Good,Good,Poor,Good,Average,Very Good,Very Good,Good,Good,Good,Very Good,Very Good,Poor,Very relevant 	,Very relevant 	,Probably,Probably,Probably not,Probably,Very relevant 	,Not at all,Probably,Probably,Probably,Probably,Probably,Just right,Just right,Too long,Too short,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,I don't know,I don't know,Yes,Yes,Yes,No,Very Good,Very Good,Very Good,Very Good,I don't know,No,No,I don't know,Just right,Just right,Just right,Just right,A little bit,Yes,Our project found the right balance,It was just right,0-5 years,Some,,Evoldir website,all of the above!,Yes,The parties? I found the R and Perl modules very interesting.  ,Yes,"An idea I had, was to introduce the final projects a bit earlier (for example, after a week?) and assign just an hour (or couple of hours?) every other day or so, to start digesting the different steps of the projects. I guess the different bioinformatics tools are not introduced yet at that stage, but on the other hand it also gives people a sort of ""goal"" when they are listening to the lectures. Sometimes you get nicer ideas when you can step away from the project for a day or so. Does that make sense?  Also, it would give people a chance to switch (I guess only in rare cases, like if they see that one project is not appropriate for what they want/need to learn). But you guys might have thought about this and rejected this for good reasons, in which case please disregard this =). I would have liked to spend more time on practising some of the tools, like the mapping (using BWA/Bowtie/samtools that sort of thing!!!!!) But overall I would like to say that I really enjoyed the course, learned a lot, and sad that it's over. I would like to be a TA!",None,None,None,Some
+4/19/2013 16:55:37,Good,Just right,"More teaching on programming topics, please",More practicals on the population genomics programming,It was just right for me,Adequate,"The seats were comfortable despite long hours of sitting at the computer. There was sufficient desk space for each student. There were no problems in viewing the presentations. The temperature was too warm at times and air flow was poor.", Just about right,Very Good,Very Good,Poor,Good,Average,Very Good,Very Good,Very Good,Average,Good,Good,Average,Average,Very relevant 	,Very relevant 	,Probably not,I don't know,Probably not,Probably,Very relevant 	,Probably not,Probably not,Probably not,Very relevant 	,Very relevant 	,Very relevant 	,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Very Good,Good,Average,Very Good,Yes,No,No,Yes,Just right,Just right,Too long,Just right,A little bit,Yes,Our project found the right balance,It was just right,5-10 years,Some,,Through a colleague, Interesting collection of programming languages and tools,Yes,"Unix skills - recently installed ubuntu and now very happy to be using it. Also, I didn't realize how powerful R can potentially be.",Yes,"I enjoyed the final projects but I think that this time might have been better spent by revisiting some of the programming languages with structured exercises.  The food portions at dinner were a little small. Katja and Rui were great hosts! The TAs were a great help, and added bonus that they were also all very friendly! I learnt a lot from going through problems with the TAs one to one.",Some,None,None,None
+4/19/2013 16:56:36,Good,Too Long,"More teaching on programming topics, please",BioPerl felt rushed and we ran out of time to practice both SNP calling with David and using Deseq and differential expression.,It was just right for me,Adequate,Other than a lack of oxygen it was great., Just about right,Good,Very Good,Very Poor,Very Good,Good,Good,Good,Good,Average,Average,Very Good,Good,Poor,Very relevant 	,Very relevant 	,Very relevant 	,Probably,Probably not,Probably not,Very relevant 	,Very relevant 	,I don't know,Probably not,Probably,Probably,Probably not,Just right,Too short,Just right,Just right,Just right,Just right,Just right,Too short,Just right,Just right,Just right,Too short,Just right,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,No,No,Yes,Yes,No,Average,Good,Poor,Good,No,Yes,No,Yes,Just right,Just right,Too long,Just right,Very,Yes,Our project found the right balance,It was just right,5-10 years,None,,Through a colleague, Interesting collection of programming languages and tools,Yes,"The course was very intensive and I honestly have forgot what happened for the first week at the moment - but it got me up to speed on a wide range of topics and I am now not intimidated by the type of data challenges I will face in the future. Sophia and perl was excellent, the Unix intro well paced and beneficial for me as a PC user, as was databases. Alignment and gene expression were great but brief. I learnt a lot about during the group projects and met a great bunch of people overall. TA's were awesome.",Yes,"Coming to this workshop  I was most interested in how to deal with the volumes of data generated by NGS and develop my own pipelines. I now know a lot more than before and the course has been beneficial - but also at times frustrating. Below are some suggestions: 1) A lot of time was spent on peoples research - but not always in a way that reinforced what we could get out of the approaches we were learning. Networks was a great example for this - I am still unsure how best to implement what we learnt. Population genomics is another example where what we were taught was only relevant for humans and I did not really learn anything that would help me with my own non-model system. 2) Most infuriating was Sonjas talk about replication - which is not really what I, as a biologist, came to the workshop for. Two days were spent on this  - when more time could have been devoted to David's topics about alignment and snp calling - something that groups struggled with during the project time. 3) One more sport night would be awesome as well - I really enjoyed football. 4) Visiting lecturers, Katja and Rui were all underused - Sarah new a lot about the ins and outs of gene expression but we did not get into that in here talk. I have no idea what Katja works on  - even though the networks and enrichment topics seem to be what she does. ",A lot,None,None,Some
+4/19/2013 16:59:06,Good,Just right,Ratio was just right,"I think that the Comparative Genomics should have had more time. It was a little bit too rushed. And more time with hands on exercise and comparing methods/pipelines. ",It was just right for me,Adequate,The room should have more windows or a better ventilation!,"Too much lecture, too little time for exercises",Very Good,Good,Very Poor,Good,Very Good,Good,Very Good,Very Good,Very Poor,Poor,Very Good,Very Good,Poor,Very relevant 	,Very relevant 	,I don't know,Probably,Very relevant 	,Probably,Very relevant 	,Very relevant 	,I don't know,Probably not,Probably,Probably,Probably not,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Too short,Too long,Too long,Just right,Just right,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,No,No,Yes,Yes,No,Very Good,Very Good,Good,Very Good,No,No,Yes,Yes,Just right,Just right,Too long,Just right,Very,Yes,Our project found the right balance,We could have used 1-2 more days,>10 years,Some,,Evoldir website,Need to learn for my current project,Barely,I think I got more comfortable with using R and the command line. ,Yes,"I do! :-) For the modules NGS non-model organisms and  Phylogenomics we had almost no time for exercises and the lectures were basic introductions to the topic. In the end, I still don't know very well how to do a phylogenomics analysis and how to deal with genomes from non model organisms. It was a bit of a waste of time. Similarly, the module of Population Genomics was too human centered  and we got almost no practice on how to analyze SNP data and what to do with the vcf files. Given that this is a topic that interests many people it would be good to try to design exercises around a very small project and go through the pipeline.  In the modules I think that worked very well, the structure was always the same - a little intro, exercises, intro to another tool, exercise with that - and with hints on how to solve the problem. I believe that structure helps the learning process and has the advantage of not transforming the classroom in a complete chaos (as it happened in the Phylogenomics and Networks module). As I said before most of expected to have some hints on how to deal with the pragmatic question of ""now that I have the data, what should/can I do?"". It would be good to design the modules and the exercises around this idea. The module of Comparative Transcriptomics was very good, but too short in time. It would be nice to have it extended for one more day/morning and to try to compare using different tools to compare gene expression.  Overall, I think that most of us come here to learn how to better handle the programming tools (and get the scare away), it would be better to make sure that we do learn the tools of each module. I would also think that adding python could be a good idea.  P.S. The TAs were very helpful and did a good job! Most of the days I had Lydia's help and she is a great teacher. You should congratulate her! :-)",Enough,None,None,None
+4/19/2013 17:00:33,Good,Too Long,"More teaching on programming topics, please","programming (R, perl) next-gen sequence data",It was just right for me,Not adequate,more air please!  :-),"Too much lecture, too little time for exercises",Good,Good,Very Poor,Good,Very Good,Good,Very Good,Good,Average,Good,Very Good,Average,Average,Probably,I don't know,Not at all,Probably,Probably,I don't know,Very relevant 	,I don't know,I don't know,I don't know,Very relevant 	,I don't know,I don't know,Just right,Too short,Too long,Just right,Just right,Just right,Too short,Just right,Just right,Just right,Too short,Too short,Just right,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Very Good,Good,Very Poor,Very Good,I don't know,No,No,Yes,Just right,Just right,Too long,Just right,Very,Yes,Our project found the right balance,We could have used 1-2 more days,5-10 years,Some,,Through a colleague, Interesting collection of programming languages and tools,Yes,"the football tournament was fun. I really enjoyed the project. Even though it was tiring, it was good to apply some things we had learned and to combat challenges as a team.",Yes,"Although the programming courses were excellent and very helpful, I would have liked to have spent more time on them. Some of the lectures could have been omitted entirely or at least just offered on an optional basis. I did not enjoy being forced to sit through long, tedious and completely irrelevent talks (e.g. ""non-model organisms"" and ""Genomics of speciation""). This time could have been spent on programming which was the reason I attended. So, all in all, I believe the course could be shorter and concentrate more on programming, as these parts were the most relevant and most useful.The help from most TAs was excellent (esp. Tiago and Jan), the atmosphere was great and most parts were very helpful. Thank you",Some,Some,None,None
+4/19/2013 17:01:10,Good,Too Long,Ratio was just right,The problem is spending time on too many different topics.,It was just right for me,Adequate,"Too hot. It really has a massive detrimental impact on learning ability, stress levels, motivation etc.","Too much lecture, too little time for exercises",Poor,Poor,Poor,Poor,Good,Poor,Good,Average,Average,Average,Very Good,Good,Very Poor,Very relevant 	,Very relevant 	,Very relevant 	,Probably not,Probably,Probably,Very relevant 	,Probably not,Probably not,I don't know,Probably,Probably,Very relevant 	,Too long,Too long,Too long,Too long,Just right,Too long,Just right,Just right,Too long,Too long,Just right,Just right,Too long,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,No,Yes,Yes,No,Good,Good,Average,Very Good,Yes,No,No,Yes,Too long,Too long,Too long,Too long,Very,Yes,Our project was too ambitious,We could have used 1-2 more days,5-10 years,None,,Through a colleague,Need to learn for my current project,Barely,The group of people.,No,"There is too much information to take in, the work schedule is too intense and there isn't enough time to take any of the information in - to the point where it feels like a waste of time. If you throw more information at people, that doesn't mean they will learn more - quite the opposite. I would have liked 'open' sessions, maybe every three days or so. In these sessions, you are free to go over the topics/exercises that you didn't understand from the past three days, in your own time, with TAs and lecturers around to help you.  That way, you can consolidate your understanding and learn at your own pace, in your own way.  The problem with the work schedule is that there is absolutely no free time to go over any of the lecture notes or practicals, if you want (need) too. Also, some of the TA's didn't have a good teaching style.  Often, they would walk past, watch over your shoulder and laugh at you.  When you're struggling to keep up, this is very hurtful and stressful - they should just be nice to you and have proper manners! the teaching format of having the lecturer or TA type things on a screen while everyone follows along is stupid.  I can see the logic of why it's a good idea, but it is impossible to look at the projection, listen to what the lecturers says and make notes and look at your computer screen at the same time.  The result is utter confusion, everyone falls behind and more importantly, loses motivation. Many of the instructors were not engaging and incredibly boring. It was clear they were good in their fields, but that doesn't mean they are skilled teachers - that's a completely different skill set which many of them clearly lacked. The evening sessions were counter productive too.  This might have been a good opportunity to have optional open sessions. ",Some,None,None,None
+4/19/2013 17:02:40,Excellent,Too Long,"More teaching on programming topics, please","More exercises, and less time for lectures.",It was just right for me,Adequate,"The infrastructure was enough during the course, but maybe it will be useful to have faster computers during the development of the projects. ","Too much lecture, too little time for exercises",Average,Good,Poor,Average,Poor,Good,Good,Good,Very Poor,Poor,Good,Average,Poor,Probably,Very relevant 	,Probably,Probably,Probably not,Probably,Very relevant 	,Probably not,Probably,Very relevant 	,Probably,Probably,Very relevant 	,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Too long,Too long,Just right,Just right,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,No,Yes,Yes,No,Good,Good,Average,Very Good,I don't know,I don't know,No,Yes,Just right,Just right,Just right,Just right,Very,Yes,Our project found the right balance,We could have used 1-2 more days,5-10 years,None,,Evoldir website, Interesting collection of programming languages and tools,Barely,"The exercises with R, because it is useful to me. Some unix tools and Perl scripts, because they were well explored during the course.  ",Maybe,"It would be useful to receive some references/papers to read before the beginning of the course. Most of the lectures can be reduced in time, and more hands on would be useful. You have to think about change the teachers of the topics: popgen, phylogenomics, and networks. Most of the students in this course doesn't work with humans, it is important to think about that before choose teachers and speakers. ",Some,None,None,Some
+4/19/2013 17:02:41,Good,Too Long,"More teaching on programming topics, please","- Less on lectures (background), more on where, what kind of problems one does encounter and how to deal with them/where to find solution - NGS on non-model organism was not helpful at all, it was nothing what I expected it to be. Nothing on how to deal with the problem of having fewer tools developed for your species and how to deal with this. - More overviews on what kind of tools are available, how to get familar with them, where to find help etc - I would prefer to start on time, but go home earlier - After basic introduction into a programming language I would find it interesting to know more and get examples on how to develop pipe lines, and on how to combine the different languages.. - Use smaller and illustative datasets ",It was just right for me,Adequate,"Unfamiliar to handle (keybord..), a bit slow, but ok","Too much lecture, too little time for exercises",Very Good,Good,Very Poor,Good,Very Good,Average,Very Good,Very Good,Average,Average,Very Good,Very Good,Good,Very relevant 	,Very relevant 	,Probably,I don't know,I don't know,Probably,Very relevant 	,Very relevant 	,Probably,Probably,Probably,Probably,Probably,Just right,Too short,Too long,Just right,Just right,Too long,Just right,Too short,Too long,Just right,Just right,Too short,Just right,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,I don't know,Yes,Yes,Yes,Yes,Very Good,Very Good,Poor,Very Good,I don't know,I don't know,I don't know,I don't know,Just right,Just right,Too long,Just right,A little bit,Yes,Our project found the right balance,It was just right,0-5 years,None,,Through a colleague,Need to learn for my current project,Yes,"Looking at your skript and trying to find where I made the mistake and finally finding it in a missing comma :)",Maybe,,Enough,None,None,None
+4/19/2013 17:03:21,Good,Just right,Ratio was just right,"Mapping non model organisms note to previous: Talks were great, but more time for programming and practice should have been obtained in some lectures.",It was just right for me,Adequate,"Room was good. Chairs a bit uncomfortable, actually.. Note to previous: Computers were fine, but sometimes there might have been sample data sets or better work-grouping organization in order to speed-up computationally intensive excercises..","Too much lecture, too little time for exercises",Very Good,Average,Poor,Good,Average,Average,Good,Good,Good,Average,Very Good,Average,Poor,Very relevant 	,Probably,I don't know,I don't know,Probably not,I don't know,Probably,I don't know,I don't know,I don't know,Very relevant 	,Probably,I don't know,Just right,Just right,Too short,Just right,Too long,Just right,Just right,Just right,Just right,Too short,Just right,Too short,Just right,Yes,Yes,No,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,No,Very Good,Very Good,Very Good,Very Good,Yes,I don't know,I don't know,Yes,Just right,Just right,Too long,Just right,Very,Yes,Our project was too ambitious,We could have used 1-2 more days,5-10 years,None,,Through one of the organizers,Need to learn for my current project,Yes,"Perl scripting (I hope)
+Great people, working on very high quality projects!",Maybe,"I think next courses should be a bit more focused.. I would leave short scientific talks but reduce the number of arguments (e.g. data visualization, networks.. may be left out?).",Some,None,None,None
+4/23/2013 10:40:48,Excellent,Just right,Ratio was just right,"There should be spend one day longer on the Perl Lessons and Bioperl. Therefore it could be spend less time on the non-model organisms lecture. ",It was just right for me,Adequate,ok, Just about right,Very Good,Very Good,Average,Very Good,Very Good,Very Good,Very Good,Good,Average,Very Good,Very Good,Very Good,Good,Very relevant 	,Very relevant 	,I don't know,Probably,I don't know,Probably,Very relevant 	,Very relevant 	,I don't know,Very relevant 	,Very relevant 	,Very relevant 	,I don't know,Just right,Just right,Too long,Just right,Just right,Just right,Just right,Just right,Just right,Just right,Too short,Too short,Just right,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Yes,Very Good,Very Good,Very Good,Very Good,I don't know,I don't know,I don't know,I don't know,Just right,Just right,Just right,Just right,Very,Yes,Our project found the right balance,It was just right,0-5 years,None,,Through a colleague, Interesting collection of programming languages and tools,Yes,Everything was good!,Yes,,None,Some,None,None

File feedback2013/results/plots/feedback_charts.pdf

Binary file added.

File feedback2013/src/plot_evaluations.R

+#!/usr/bin/env Rscript
+# 
+# Generate Plots to visualize students' evaluations on the Leipzig workshop
+
+library(ggplot2)
+library(reshape)
+library(stringr)
+
+feedback <- read.delim("evaluations2013.csv", sep=',', quote='"', header=T, na.strings="")
+orig.names = names(feedback)
+names(feedback)[10:22] <- str_match(names(feedback)[10:22], "How.*lectures\\.\\.\\.\\.(.*)\\.\\..*?")[,2]       # Rate of lectures
+names(feedback)[62:65] <- str_match(names(feedback)[62:65], "How.*talks\\.\\.\\.\\.(.*)\\.\\..*?")[,2]             # Rate of talks
+names(feedback)[23:35] <- str_match(names(feedback)[23:35], "Do.*work\\.\\.\\.\\.(.*)\\.\\..*?")[,2]            # Relevance of lectures
+names(feedback)[66:69] <- str_match(names(feedback)[66:69], "Do.*work.\\.\\.\\.\\.(.*)\\.\\..*?")[,2]              # Relevance of talks
+names(feedback)[36:48] <- str_match(names(feedback)[36:48], "How.*lectures\\.\\.\\.\\.(.*)\\.\\..*?")[,2]       # Length of lectures
+names(feedback)[70:73] <- str_match(names(feedback)[70:73], "How.*talks\\.\\.\\.\\.(.*)\\.\\..*?")[,2]             # Length of talks
+
+pdf("results/plots/feedback_charts.pdf", paper="a4r", width=1280, height=1024, title="Leipzig workshop feedback 2012")
+
+
+generic_questions_plot = list (theme_bw(),
+        geom_bar(aes(x=answer)),
+        facet_wrap(~question, scales='free', nrow=3), 
+        opts(axis.text.x=theme_text(angle=0, hjust=0.5, vjust=1 ))
+        )
+
+barchart_plot = list (theme_bw(),
+        geom_bar(width=1),
+        opts(legend.position='bottom'),
+        facet_wrap(~variable, nrow=3),
+        opts(axis.text.x=theme_text(angle=45, hjust=1, vjust=1 )),
+#        opts(axis.text.x=theme_text(angle=90, hjust=0.4 )),
+#        coord_polar(theta='y'),
+        scale_x_discrete("answer")
+        )
+
+violin_plot = list (theme_bw(),
+        geom_violin(aes(x=variable, y=as.numeric(answer), fill=1)),
+        opts(legend.position='none'),
+#        facet_wrap(~variable, nrow=3),
+        opts(axis.text.x=theme_text(angle=45, hjust=1, vjust=1 )),
+        scale_x_discrete("Lecture")
+#        scale_y_continuous(breaks=plot_labels)
+        )    
+student_barchart_plot = list(theme_bw(),
+        geom_bar(aes(x=answer, fill=answer)),
+        facet_wrap(~Timestamp, nrow=3),
+        opts(legend.position='none'),
+        opts(axis.text.x=theme_text(angle=45, hjust=1, vjust=1 )),
+        scale_x_discrete("Student (Timestamp of when the feedback form was filled)")
+        )
+
+student_violin_plot = list(theme_bw(),
+        geom_violin(aes(x=Timestamp, y=as.numeric(answer), fill='#0072B2')),
+        opts(legend.position='none'),
+        opts(axis.text.x=theme_text(angle=45, hjust=1, vjust=1 )),
+        scale_x_discrete("Student (Timestamp of when the feedback form was filled)")
+        )
+
+
+# Generic questions
+plot_title = "Generic questions"
+print(plot_title)
+#print(summary(feedback))
+#feedback.overall <- subset(feedback, select=c(1, 4:6, 8, 9, 86:90, 94, 98, 102))
+feedback.overall <- subset(feedback, select=c(1:4, 6, 7, 9, 74:78, 79, 83, 85, 87:90))
+feedback.overall.long <- melt(feedback.overall, id.vars="Timestamp")
+feedback.overall.long <- feedback.overall.long[complete.cases(feedback.overall.long),]
+feedback.overall.long$question <- factor(feedback.overall.long$variable)
+feedback.overall.long$question <- gsub("(\\w*\\.\\w*\\.\\w*\\.\\w*\\.\\w*)\\.", "\\1\n", feedback.overall.long$question, perl=T)
+feedback.overall.long$question <- gsub("\n$", "", feedback.overall.long$question, perl=T)
+feedback.overall.long$question <- gsub("\\.", " ", feedback.overall.long$question, perl=T)
+# FIX: manually fixing some labels
+feedback.overall.long$question <- gsub("What did .*ratio of teaching versus scientific lectures\n", "What did you think\nof the ratio of teaching versus\nscientific lectures", feedback.overall.long$question, perl=T)
+feedback.overall.long$question <- gsub("In general.*\n.*\n.*", "In general what did\nyou think about the length\nof the course", feedback.overall.long$question, perl=T)
+# FIX: merging "Department bullettin", "mailing list" and "Internal Institute mail" answers together
+feedback.overall.long$answer <- factor(feedback.overall.long$value)
+feedback.overall.long$answer <- gsub("^mailing.*", "Mailing list\n(Institute/\nDepartment/\nother)", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("^internal.*", "Mailing list\n(Institute/\nDepartment/\nother)", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("^Department.*", "Mailing list\n(Institute/\nDepartment/\nother)", feedback.overall.long$answer, perl=T)
+# FIX: manually fixing some answer labels
+feedback.overall.long$answer <- gsub("^Evoldir.*", "Evoldir\nwebsite", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("^More scientific.*", "More\nscientific\nlectures,\nplease", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("^More teaching.*", "More\nteaching\non\nprogramming", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("10 years", "10\nyears", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("([\\w()']*\\s[\\w()']*)\\s", "\\1\n", feedback.overall.long$answer, perl=T)
+feedback.overall.long$answer <- gsub("\\.", " ", feedback.overall.long$answer, perl=T)
+ggplot(data=feedback.overall.long) + generic_questions_plot + ggtitle(plot_title)
+
+# Quality of the lecture
+#png("feedback_quality_piechart.png")
+#dev.new()
+plot_title = "How would you rate the quality of the following lectures?"
+print(plot_title)
+feedback.quality <- subset(feedback, select=c(1, 10:22, 62:65))
+print(summary(feedback.quality))
+feedback.quality.long <- melt(feedback.quality, id.vars="Timestamp")
+feedback.quality.long <- feedback.quality.long[complete.cases(feedback.quality.long),]
+plot_labels = rev(c("Very Good", "Good", "Average", "Poor", "Very Poor"))
+feedback.quality.long$answer <- factor(feedback.quality.long$value, levels=plot_labels)
+qplot(answer, data=feedback.quality.long, fill=answer, main=paste(plot_title, "(Bar charts)")) + barchart_plot
+ggplot(data=feedback.quality.long) + violin_plot + scale_y_continuous("answer", breaks=1:length(plot_labels), labels=plot_labels) + ggtitle(paste(plot_title, "(Violin plots)"))
+ggplot(data=feedback.quality.long) + student_barchart_plot + ggtitle("Distribution of answers by student (Quality of Lectures and Talks)")
+ggplot(data=feedback.quality.long) + student_violin_plot + scale_y_continuous("answer", breaks=1:length(plot_labels), labels=plot_labels) + ggtitle("Distribution of answers by student (Quality of Lectures and Talks)")
+#ggplot(data=feedback.quality.long) + violin_plot
+#dev.off()
+
+# Relevance of the lecture
+#png("feedback_relevance_piechart.png")
+#dev.new()
+plot_title = "Do you think the lecture is or will be relevant to your work?"
+print(plot_title)
+feedback.relevance <- subset(feedback, select=c(1, 23:35, 66:69))
+feedback.relevance.long <- melt(feedback.relevance, id.vars="Timestamp")
+# FIX: the questions on the talks had Yes/No answer options, while the questions on the lectures had "Very Relevant/Probably/Probably not" options. 
+# Solution: merging "Yes" with "Very Relevant" answers, and "No" with "Probably not".
+feedback.relevance.long <- feedback.relevance.long[complete.cases(feedback.relevance.long),]
+feedback.relevance.long$answer <- feedback.relevance.long$value
+feedback.relevance.long$answer <- gsub("Probably not", "Probably not/No", feedback.relevance.long$answer)
+feedback.relevance.long$answer <- gsub("Very relevant", "Very relevant/Yes", feedback.relevance.long$answer)
+feedback.relevance.long$answer <- gsub("^Yes$", "Very relevant/Yes", feedback.relevance.long$answer)
+feedback.relevance.long$answer <- gsub("^No$", "Probably not/No", feedback.relevance.long$answer)
+#plot_labels = rev(c("Very relevant/Yes", "Relevant", "Probably", "Probably not/No", "I don't know"))
+plot_labels = rev(c("Very relevant/Yes", "Probably", "Probably not/No", "I don't know"))
+feedback.relevance.long$answer <- factor(feedback.relevance.long$answer, levels=plot_labels)
+# FIX: "I don't know" answers should not be included in the violin plots, or at least they should be colored differently. Otherwise, it seems that a "I don't know" answer is better or worst than the other answers. 
+feedback.relevance.long.noIdontknow = subset(feedback.relevance.long, answer != "I don't know")
+qplot(answer, data=feedback.relevance.long.noIdontknow, fill=answer, main=paste(plot_title, "(Bar charts)")) + barchart_plot
+ggplot(data=feedback.relevance.long.noIdontknow) + violin_plot + scale_y_continuous("answer", breaks=1:length(plot_labels), labels=plot_labels)+ ggtitle(paste(plot_title, "(Violin plots)"))
+ggplot(data=feedback.relevance.long.noIdontknow) + student_barchart_plot + ggtitle("Distribution of answers by student (Relevancy of Lectures and Talks)")
+ggplot(data=feedback.relevance.long.noIdontknow) + student_violin_plot + scale_y_continuous("answer", breaks=1:length(plot_labels), labels=plot_labels) + ggtitle("Distribution of answers by student (Relevancy of Lectures and Talks)")
+#dev.off()
+
+#dev.off()
+
+# Length
+#png("feedback_length_piechart.png")
+#dev.new()
+plot_title = "How would you rate the length of the following lectures?"
+print(plot_title)
+feedback.length <- subset(feedback, select=c(1, 36:48, 70:73))
+feedback.length.long <- melt(feedback.length, id.vars="Timestamp")
+feedback.length.long <- feedback.length.long[complete.cases(feedback.length.long),]
+plot_labels = rev(c("Too long", "Just right", "Too short"))
+feedback.length.long$answer <- factor(feedback.length.long$value, levels=plot_labels)
+qplot(answer, data=feedback.length.long, fill=answer, main=paste(plot_title, "(Bar charts)")) + barchart_plot
+ggplot(data=feedback.length.long) + violin_plot + scale_y_continuous("answer", breaks=1:length(plot_labels), labels=plot_labels) + ggtitle(paste(plot_title, "(Violin plots)"))
+ggplot(data=feedback.length.long) + student_barchart_plot + ggtitle("Distribution of answers by student (Length of Lectures and Talks)")
+ggplot(data=feedback.length.long) + student_violin_plot + scale_y_continuous("answer", breaks=1:length(plot_labels), labels=plot_labels) + ggtitle("Distribution of answers by student (Length of Lectures and Talks)")
+#dev.off()
+
+dev.off()
+.. Programming for Evolutionary Biology - Leipzig 2012 documentation master file, created by
+   sphinx-quickstart on Fri Feb 17 16:41:56 2012.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Programming for Evolutionary Biology - Leipzig 2012's documentation!
+===============================================================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\ProgrammingforEvolutionaryBiology-Leipzig2012.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\ProgrammingforEvolutionaryBiology-Leipzig2012.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+:end