├── book ├── .gitignore ├── novice │ ├── git │ │ └── img │ │ │ ├── phd101212s.png │ │ │ ├── git-diff-review.pdf │ │ │ ├── git-file-trees.pdf │ │ │ ├── git-after-merging.pdf │ │ │ ├── git-staging-area.pdf │ │ │ ├── git-commit-add-review.pdf │ │ │ ├── github-create-repo-01.png │ │ │ ├── github-create-repo-02.png │ │ │ ├── github-create-repo-03.png │ │ │ ├── git-after-duplicate-clone.pdf │ │ │ ├── git-after-pushing-merge.pdf │ │ │ ├── github-change-repo-string.png │ │ │ ├── github-find-repo-string.png │ │ │ ├── git-when-revisions-updated.pdf │ │ │ ├── git-freshly-made-github-repo.pdf │ │ │ ├── github-repo-after-first-push.pdf │ │ │ ├── git-after-pulling-to-local-repo.pdf │ │ │ ├── git-after-change-to-duplicate-repo.pdf │ │ │ ├── git-after-first-conflicting-change.pdf │ │ │ └── git-after-second-conflicting-change.pdf │ ├── python │ │ └── img │ │ │ ├── grid5x3.png │ │ │ ├── color_row.png │ │ │ ├── diagonal.png │ │ │ ├── color-cube.png │ │ │ ├── pink_heatmap.png │ │ │ ├── ave-inflammation.png │ │ │ ├── heatmap_improved.png │ │ │ ├── initial-heat-map.png │ │ │ ├── initial-heatmap.png │ │ │ ├── initial_heatmap.png │ │ │ ├── max-inflammation.png │ │ │ ├── min-inflammation.png │ │ │ ├── standard_colors.png │ │ │ ├── combined-inflammation.png │ │ │ ├── inflammation-loop-01.png │ │ │ ├── inflammation-loop-02.png │ │ │ ├── inflammation-loop-03.png │ │ │ ├── loop-inflammation-01.png │ │ │ ├── loop-inflammation-02.png │ │ │ ├── loop-inflammation-03.png │ │ │ ├── python-call-stack-01.pdf │ │ │ ├── python-call-stack-02.pdf │ │ │ ├── python-call-stack-03.pdf │ │ │ ├── python-call-stack-04.pdf │ │ │ ├── python-call-stack-05.pdf │ │ │ ├── python-call-stack-06.pdf │ │ │ ├── python-call-stack-07.pdf │ │ │ ├── combined-inflammation-2.png │ │ │ ├── min-inflammation-per-day.png │ │ │ ├── ave-inflammation-over-time.png │ │ │ ├── max-inflammation-over-time.png │ │ │ ├── python-overlapping-ranges.pdf │ │ │ ├── combined-inflammation-per-day.png │ │ │ ├── python-flowchart-conditional.pdf │ │ │ ├── python-flowchart-nested-loops.pdf │ │ │ ├── python-operations-across-axes.pdf │ │ │ ├── python-sticky-note-variables-01.pdf │ │ │ ├── python-sticky-note-variables-02.pdf │ │ │ └── python-sticky-note-variables-03.pdf │ ├── shell │ │ └── img │ │ │ ├── homedir.pdf │ │ │ ├── filesystem.pdf │ │ │ ├── find-file-tree.pdf │ │ │ ├── nano-screenshot.png │ │ │ ├── home-directories.pdf │ │ │ └── filesystem-challenge.pdf │ ├── sql │ │ └── img │ │ │ ├── sql-filter.pdf │ │ │ └── sql-aggregation.pdf │ └── extras │ │ └── img │ │ ├── madeleine.jpg │ │ ├── git-fork-ui.png │ │ ├── git-forking-01.pdf │ │ ├── git-forking-02.pdf │ │ ├── git-forking-03.pdf │ │ ├── git-branching-01.pdf │ │ ├── git-branching-02.pdf │ │ ├── git-branching-03.pdf │ │ ├── git-branching-04.pdf │ │ ├── git-branching-05.pdf │ │ ├── git-branching-06.pdf │ │ ├── python-alias-01.pdf │ │ ├── python-alias-02.pdf │ │ ├── python-alias-03.pdf │ │ ├── python-alias-04.pdf │ │ ├── python-alias-05.pdf │ │ ├── python-alias-06.pdf │ │ ├── python-alias-07.pdf │ │ └── x-for-directories.pdf └── Makefile ├── novice ├── python │ ├── small-01.csv │ ├── small-03.csv │ ├── small-02.csv │ ├── argv-list.py │ ├── sys-version.py │ ├── starry_night.jpg │ ├── img │ │ ├── color-cube.png │ │ ├── initial-heat-map.png │ │ ├── loop-inflammation-01.png │ │ ├── loop-inflammation-02.png │ │ ├── loop-inflammation-03.png │ │ ├── python-call-stack-01.odg │ │ ├── python-call-stack-01.png │ │ ├── python-call-stack-02.odg │ │ ├── python-call-stack-02.png │ │ ├── python-call-stack-03.odg │ │ ├── python-call-stack-03.png │ │ ├── python-call-stack-04.odg │ │ ├── python-call-stack-04.png │ │ ├── python-call-stack-05.odg │ │ ├── python-call-stack-05.png │ │ ├── python-call-stack-06.odg │ │ ├── python-call-stack-06.png │ │ ├── python-call-stack-07.odg │ │ ├── python-call-stack-07.png │ │ ├── combined-inflammation-2.png │ │ ├── min-inflammation-per-day.png │ │ ├── ave-inflammation-over-time.png │ │ ├── max-inflammation-over-time.png │ │ ├── python-overlapping-ranges.odg │ │ ├── python-overlapping-ranges.png │ │ ├── combined-inflammation-per-day.png │ │ ├── python-flowchart-conditional.odg │ │ ├── python-flowchart-conditional.png │ │ ├── python-flowchart-nested-loops.odg │ │ ├── python-flowchart-nested-loops.png │ │ ├── python-operations-across-axes.odg │ │ ├── python-operations-across-axes.png │ │ ├── python-sticky-note-variables-01.odg │ │ ├── python-sticky-note-variables-01.png │ │ ├── python-sticky-note-variables-02.odg │ │ ├── python-sticky-note-variables-02.png │ │ ├── python-sticky-note-variables-03.odg │ │ └── python-sticky-note-variables-03.png │ ├── rectangle.py │ ├── count-stdin.py │ ├── 03-loop_files │ │ └── novice │ │ │ └── python │ │ │ ├── 03-loop_2_0.png │ │ │ ├── 03-loop_49_1.png │ │ │ ├── 03-loop_49_3.png │ │ │ ├── 03-loop_49_5.png │ │ │ └── 03-loop_4_0.png │ ├── 01-numpy_files │ │ └── novice │ │ │ └── python │ │ │ ├── 01-numpy_74_0.png │ │ │ ├── 01-numpy_76_0.png │ │ │ ├── 01-numpy_78_1.png │ │ │ ├── 01-numpy_78_3.png │ │ │ └── 01-numpy_83_0.png │ ├── errors_01.py │ ├── readings-01.py │ ├── readings-02.py │ └── readings-03.py ├── shell │ ├── filesystem │ │ ├── data │ │ │ ├── backup │ │ │ │ └── backup.log │ │ │ ├── network.cfg │ │ │ ├── access.log │ │ │ └── hardware.cfg │ │ └── users │ │ │ ├── nelle │ │ │ ├── Desktop │ │ │ │ └── .my.log │ │ │ ├── writing │ │ │ │ ├── old │ │ │ │ │ └── .my.log │ │ │ │ ├── tools │ │ │ │ │ ├── old │ │ │ │ │ │ └── oldtool │ │ │ │ │ ├── stats │ │ │ │ │ └── format │ │ │ │ ├── thesis │ │ │ │ │ └── empty-draft.md │ │ │ │ └── haiku.txt │ │ │ ├── pizza.cfg │ │ │ ├── notes.txt │ │ │ ├── solar.pdf │ │ │ ├── north-pacific-gyre │ │ │ │ └── 2012-07-03 │ │ │ │ │ ├── goodiff │ │ │ │ │ └── goostats │ │ │ └── data │ │ │ │ ├── elements │ │ │ │ ├── Cm.xml │ │ │ │ ├── Cf.xml │ │ │ │ ├── Es.xml │ │ │ │ ├── Fm.xml │ │ │ │ ├── Lr.xml │ │ │ │ ├── Md.xml │ │ │ │ ├── Bk.xml │ │ │ │ ├── No.xml │ │ │ │ ├── At.xml │ │ │ │ ├── Ac.xml │ │ │ │ ├── La.xml │ │ │ │ ├── Rn.xml │ │ │ │ ├── W.xml │ │ │ │ ├── Ba.xml │ │ │ │ ├── Cs.xml │ │ │ │ ├── Hf.xml │ │ │ │ ├── Ir.xml │ │ │ │ ├── Os.xml │ │ │ │ ├── Pb.xml │ │ │ │ ├── Pt.xml │ │ │ │ ├── Ta.xml │ │ │ │ ├── Ar.xml │ │ │ │ ├── Au.xml │ │ │ │ ├── B.xml │ │ │ │ ├── Be.xml │ │ │ │ ├── Bi.xml │ │ │ │ ├── Ca.xml │ │ │ │ ├── Cd.xml │ │ │ │ ├── Er.xml │ │ │ │ ├── Fe.xml │ │ │ │ ├── Fr.xml │ │ │ │ ├── Ga.xml │ │ │ │ ├── He.xml │ │ │ │ ├── Hg.xml │ │ │ │ ├── In.xml │ │ │ │ ├── K.xml │ │ │ │ ├── Kr.xml │ │ │ │ ├── Lu.xml │ │ │ │ ├── Mg.xml │ │ │ │ ├── Mo.xml │ │ │ │ ├── Nd.xml │ │ │ │ ├── Ne.xml │ │ │ │ ├── O.xml │ │ │ │ ├── Po.xml │ │ │ │ ├── Ra.xml │ │ │ │ ├── Rb.xml │ │ │ │ ├── Re.xml │ │ │ │ ├── Rh.xml │ │ │ │ ├── Ru.xml │ │ │ │ ├── Sn.xml │ │ │ │ ├── Sr.xml │ │ │ │ ├── Tl.xml │ │ │ │ ├── Xe.xml │ │ │ │ ├── Y.xml │ │ │ │ ├── Zn.xml │ │ │ │ ├── Zr.xml │ │ │ │ ├── Ag.xml │ │ │ │ ├── Al.xml │ │ │ │ └── C.xml │ │ │ │ └── pdb │ │ │ │ └── ammonia.pdb │ │ │ ├── backup │ │ │ ├── original │ │ │ │ └── backup.log │ │ │ ├── pnas_final │ │ │ │ └── backup.log │ │ │ └── pnas_sub │ │ │ │ └── backup.log │ │ │ └── thing │ │ │ └── backup │ │ │ ├── 2012-12-01 │ │ │ └── backup.log │ │ │ ├── 2013-01-08 │ │ │ └── backup.log │ │ │ └── 2013-01-27 │ │ │ └── backup.log │ ├── img │ │ ├── homedir.odg │ │ ├── filesystem.odg │ │ ├── filesystem.png │ │ ├── vlad-homedir.png │ │ ├── find-file-tree.odg │ │ ├── find-file-tree.png │ │ ├── nano-screenshot.png │ │ ├── home-directories.odg │ │ ├── home-directories.png │ │ ├── filesystem-challenge.odg │ │ └── filesystem-challenge.png │ ├── README.txt │ └── gen-sequence.py ├── git │ ├── README.txt │ └── img │ │ ├── conflict.odg │ │ ├── phd101212s.gif │ │ ├── phd101212s.png │ │ ├── git-checkout.odg │ │ ├── git-checkout.png │ │ ├── ssh-keychain.png │ │ ├── git-committing.odg │ │ ├── git-committing.png │ │ ├── git-diff-review.png │ │ ├── git-file-trees.png │ │ ├── github-ssh-keys.png │ │ ├── git-staging-area.odg │ │ ├── git-staging-area.png │ │ ├── github-add-ssh-key.png │ │ ├── github-collaboration.odg │ │ ├── github-ssh-clone-url.png │ │ ├── git-commit-add-review.png │ │ ├── github-create-repo-01.png │ │ ├── github-create-repo-02.png │ │ ├── github-create-repo-03.png │ │ ├── github-account-settings.png │ │ ├── github-add-collaborators.png │ │ ├── github-add-collaborators.xcf │ │ ├── github-change-repo-string.png │ │ ├── github-find-repo-string.png │ │ ├── git-when-revisions-updated.odg │ │ ├── git-when-revisions-updated.png │ │ ├── git-freshly-made-github-repo.odg │ │ ├── git-freshly-made-github-repo.png │ │ ├── github-repo-after-first-push.odg │ │ └── github-repo-after-first-push.png ├── hg │ ├── README.txt │ └── img │ │ ├── phd101212s.gif │ │ ├── hg-after-merging.odg │ │ ├── bitbucket-create-repo-01.png │ │ ├── bitbucket-create-repo-02.png │ │ ├── bitbucket-create-repo-03.png │ │ ├── bitbucket-find-repo-string.png │ │ ├── hg-after-duplicate-clone.odg │ │ ├── hg-kdiff3-conflict-windows.png │ │ ├── bitbucket-repo-after-first-push.odg │ │ ├── hg-after-pulling-to-local-repo.odg │ │ ├── hg-freshly-made-bitbucket-repo.odg │ │ ├── hg-after-change-to-duplicate-repo.odg │ │ ├── hg-after-first-conflicting-change.odg │ │ ├── hg-after-second-conflicting-change.odg │ │ └── hg-kdiff3-conflict-windows-resolved.png ├── r │ ├── ggplot.pdf │ └── figure │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-12.png │ │ ├── unnamed-chunk-13.png │ │ ├── unnamed-chunk-14.png │ │ ├── unnamed-chunk-15.png │ │ ├── unnamed-chunk-21.png │ │ ├── unnamed-chunk-22.png │ │ ├── unnamed-chunk-23.png │ │ ├── unnamed-chunk-26.png │ │ ├── unnamed-chunk-29.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-30.png │ │ ├── unnamed-chunk-31.png │ │ ├── unnamed-chunk-32.png │ │ ├── unnamed-chunk-33.png │ │ ├── unnamed-chunk-35.png │ │ ├── unnamed-chunk-36.png │ │ ├── unnamed-chunk-38.png │ │ ├── unnamed-chunk-40.png │ │ ├── unnamed-chunk-5.png │ │ ├── unnamed-chunk-6.png │ │ ├── unnamed-chunk-7.png │ │ ├── unnamed-chunk-81.png │ │ ├── unnamed-chunk-82.png │ │ ├── unnamed-chunk-191.png │ │ ├── unnamed-chunk-192.png │ │ ├── unnamed-chunk-193.png │ │ ├── unnamed-chunk-194.png │ │ ├── unnamed-chunk-195.png │ │ ├── unnamed-chunk-196.png │ │ ├── unnamed-chunk-197.png │ │ ├── unnamed-chunk-198.png │ │ ├── unnamed-chunk-199.png │ │ ├── unnamed-chunk-241.png │ │ ├── unnamed-chunk-242.png │ │ ├── unnamed-chunk-243.png │ │ ├── unnamed-chunk-244.png │ │ ├── unnamed-chunk-245.png │ │ ├── unnamed-chunk-246.png │ │ ├── unnamed-chunk-247.png │ │ ├── unnamed-chunk-248.png │ │ ├── unnamed-chunk-249.png │ │ ├── unnamed-chunk-281.png │ │ ├── unnamed-chunk-282.png │ │ ├── unnamed-chunk-283.png │ │ ├── unnamed-chunk-284.png │ │ ├── unnamed-chunk-285.png │ │ ├── unnamed-chunk-286.png │ │ ├── unnamed-chunk-287.png │ │ ├── unnamed-chunk-288.png │ │ ├── unnamed-chunk-289.png │ │ ├── unnamed-chunk-361.png │ │ ├── unnamed-chunk-362.png │ │ ├── unnamed-chunk-371.png │ │ ├── unnamed-chunk-372.png │ │ ├── unnamed-chunk-391.png │ │ ├── unnamed-chunk-392.png │ │ ├── 01-starting-with-data-plot-avg-inflammation.png │ │ ├── 01-starting-with-data-plot-max-inflammation.png │ │ └── 01-starting-with-data-plot-min-inflammation.png ├── ref │ └── img │ │ ├── r.png │ │ ├── bash.png │ │ ├── emacs.png │ │ ├── less.png │ │ ├── man.png │ │ ├── more.png │ │ ├── nano.png │ │ ├── vim.png │ │ ├── ipython.png │ │ ├── python.png │ │ ├── emacs-gui.png │ │ ├── r-unclosed.png │ │ ├── bash-unclosed.png │ │ ├── python-unclosed.png │ │ └── ipython-unclosed.png ├── sql │ ├── img │ │ ├── sql-filter.odg │ │ ├── sql-filter.png │ │ ├── sql-aggregation.odg │ │ └── sql-aggregation.png │ └── README.txt ├── extras │ └── img │ │ ├── madeleine.jpg │ │ ├── git-fork-ui.png │ │ ├── git-forking-01.odg │ │ ├── git-forking-01.png │ │ ├── git-forking-02.odg │ │ ├── git-forking-02.png │ │ ├── git-forking-03.odg │ │ ├── git-forking-03.png │ │ ├── git-branching-01.odg │ │ ├── git-branching-01.png │ │ ├── git-branching-02.odg │ │ ├── git-branching-02.png │ │ ├── git-branching-03.odg │ │ ├── git-branching-03.png │ │ ├── git-branching-04.odg │ │ ├── git-branching-04.png │ │ ├── git-branching-05.odg │ │ ├── git-branching-05.png │ │ ├── git-branching-06.odg │ │ ├── git-branching-06.png │ │ ├── github-pr-changes.png │ │ ├── github-pr-compare.png │ │ ├── github-pr-create.png │ │ ├── github-pr-initial.png │ │ ├── python-alias-01.odg │ │ ├── python-alias-01.png │ │ ├── python-alias-02.odg │ │ ├── python-alias-02.png │ │ ├── python-alias-03.odg │ │ ├── python-alias-03.png │ │ ├── python-alias-04.odg │ │ ├── python-alias-04.png │ │ ├── python-alias-05.odg │ │ ├── python-alias-05.png │ │ ├── python-alias-06.odg │ │ ├── python-alias-06.png │ │ ├── python-alias-07.odg │ │ ├── python-alias-07.png │ │ ├── x-for-directories.odg │ │ ├── x-for-directories.png │ │ ├── debugger-screenshot.png │ │ ├── github-pr-comment-box.png │ │ ├── github-pr-comment-icon.png │ │ ├── github-pr-files-changed.png │ │ └── github-pr-comment-submitted.png └── matlab │ ├── kelvin_to_celsius.m │ ├── img │ ├── 01-intro_1.png │ ├── 01-intro_2.png │ ├── 01-intro_3.png │ ├── 01-intro_4.png │ ├── 01-intro_5.png │ ├── matrix-base.odg │ ├── matrix-row.odg │ ├── matrix-multi-cols.odg │ ├── matrix-multi-rows.odg │ ├── matrix-submatrix.odg │ ├── matrix-strided-rows.odg │ ├── matrix-single-element.odg │ ├── matrix-strided-rowncols.odg │ ├── matlab-operations-across-axes.odg │ ├── matlab-sticky-note-variables-01.odg │ ├── matlab-sticky-note-variables-02.odg │ └── matlab-sticky-note-variables-03.odg │ ├── fahr_to_kelvin.m │ ├── fahr_to_celsius.m │ └── center.m ├── extras ├── r-ggplot2 │ ├── .gitignore │ └── figure │ │ ├── qplot1.png │ │ ├── facetcol.png │ │ ├── ggfacet.png │ │ ├── gghexbin.png │ │ ├── irisbase.png │ │ ├── basediamond.png │ │ ├── clarcolor.png │ │ ├── facetclar.png │ │ ├── ggboxplots.png │ │ ├── ggclarcol.png │ │ ├── ggdiamonds.png │ │ ├── ggfillhisto.png │ │ ├── gghexbin2.png │ │ ├── smoothgam.png │ │ ├── facetclarcol.png │ │ ├── smoothlinear.png │ │ ├── ggdepthdensity.png │ │ └── facetclarcol_colcut.png └── python-climate-data │ ├── cstringio-demo.py │ ├── csv-demo.py │ ├── csv-demo-2.py │ ├── get-data.py │ └── parse-manually.py ├── intermediate ├── make │ ├── config.mk │ ├── paper.tex │ ├── wildcard.mk │ ├── hello.mk │ ├── img │ │ └── example-dependencies.png │ ├── variables.mk │ ├── multiple.mk │ ├── target-variable.mk │ ├── reference.md │ ├── double.mk │ ├── phony.mk │ ├── pattern-rule.mk │ ├── all-patterns.mk │ ├── false-dependencies.mk │ ├── with-variables.mk │ └── use-pattern.mk ├── r │ ├── chunk_options.R │ ├── reproducible-research │ │ ├── exercise.md │ │ └── README.md │ ├── R-basics │ │ ├── data-types.png │ │ ├── stackoverflow.png │ │ └── rdocumentation.png │ ├── data-manipulation │ │ ├── mutate.png │ │ ├── sac_full.png │ │ ├── data │ │ │ ├── mammals.csv │ │ │ └── baby-names2.csv.bz2 │ │ ├── split-apply1.png │ │ ├── splitapply.png │ │ ├── full_apply_suite.png │ │ └── sample_workflow.png │ ├── data-visualization │ │ ├── ggplot.pdf │ │ ├── slides.png │ │ ├── data │ │ │ └── Grazing.pdf │ │ └── images │ │ │ ├── hadley.png │ │ │ ├── git_repo.png │ │ │ ├── chang_book.png │ │ │ ├── color_palette.png │ │ │ └── color_schemes.png │ ├── testing-documentation │ │ ├── inline_documentation.png │ │ ├── rendered_documentation.png │ │ └── what_roxygen_generates.png │ └── functions │ │ └── README.md ├── regex │ ├── 06-more-tools.md │ └── img │ │ ├── 01-intro-notebook-1.png │ │ ├── 01-intro-notebook-2.png │ │ ├── Keyboard-left_keys.jpg │ │ └── 01-intro-notebook-1-metachars.png ├── python │ ├── speedup.png │ ├── decision_tree_example.png │ ├── decision_tree_example.url │ ├── 01-intro-python_files │ │ └── intermediate │ │ │ └── python │ │ │ ├── 01-intro-python_66_1.png │ │ │ └── 01-intro-python_68_0.png │ ├── 02-modularization-documentation_files │ │ └── intermediate │ │ │ └── python │ │ │ ├── 02-modularization-documentation_19_1.png │ │ │ ├── 02-modularization-documentation_21_1.png │ │ │ └── 02-modularization-documentation_64_1.png │ └── A1_mosquito_data.csv ├── shell │ ├── 01-perm.md │ ├── img │ │ ├── shell-on-shell.png │ │ ├── direct-shell-usage.png │ │ ├── public-private-keys.png │ │ └── remote-shell-usage.png │ ├── guide.md │ └── README.md ├── doit │ ├── clean_directory.sh │ └── .gitignore ├── git │ └── README.md └── sql │ └── README.md ├── img ├── readme │ ├── step1.png │ ├── step2.png │ └── step3.png ├── rss-icon-blue.png ├── site │ └── main_shadow.png ├── slides │ ├── enrolment.png │ └── workshops.png ├── bootcamps │ ├── 2012-12-uta.png │ ├── 2012-11-scripps.png │ ├── 2013-01-mcgill.png │ └── 2013-01-mckellar.png ├── mozilla-science-lab.png ├── osi-approved-license.png ├── books │ └── ray-ray-unix-linux.png ├── software-carpentry-banner.png ├── software-carpentry-large.png └── creative-commons-attribution-license.png ├── css ├── bootstrap │ └── img │ │ ├── glyphicons-halflings.png │ │ └── glyphicons-halflings-white.png └── book.css ├── .gitignore ├── setup └── windows-installer │ ├── software-carpentry-logo.ico │ └── setup.py ├── data ├── evil │ ├── notebook-3.txt │ ├── notebook-1.txt │ └── notebook-2.txt ├── chem │ ├── elements │ │ ├── Cm.xml │ │ ├── Cf.xml │ │ ├── Es.xml │ │ ├── Fm.xml │ │ ├── Lr.xml │ │ ├── Md.xml │ │ ├── Bk.xml │ │ ├── No.xml │ │ ├── At.xml │ │ ├── Ac.xml │ │ ├── La.xml │ │ ├── Ba.xml │ │ ├── Hf.xml │ │ ├── Rn.xml │ │ ├── W.xml │ │ ├── Ar.xml │ │ ├── Cs.xml │ │ ├── Ir.xml │ │ ├── Os.xml │ │ ├── Pb.xml │ │ ├── Po.xml │ │ ├── Pt.xml │ │ ├── Ta.xml │ │ ├── Zn.xml │ │ ├── Ag.xml │ │ ├── Au.xml │ │ ├── B.xml │ │ ├── Be.xml │ │ ├── Bi.xml │ │ ├── Ca.xml │ │ ├── Cd.xml │ │ ├── Co.xml │ │ ├── Dy.xml │ │ ├── Er.xml │ │ ├── Fe.xml │ │ ├── Fr.xml │ │ ├── Ga.xml │ │ ├── Gd.xml │ │ ├── He.xml │ │ ├── Hg.xml │ │ ├── Ho.xml │ │ ├── In.xml │ │ ├── K.xml │ │ ├── Kr.xml │ │ ├── Li.xml │ │ ├── Lu.xml │ │ ├── Mg.xml │ │ ├── Mo.xml │ │ ├── Nd.xml │ │ ├── Ne.xml │ │ ├── Ni.xml │ │ ├── O.xml │ │ ├── Ra.xml │ │ ├── Rb.xml │ │ ├── Re.xml │ │ ├── Rh.xml │ │ ├── Ru.xml │ │ ├── Sc.xml │ │ ├── Sn.xml │ │ ├── Sr.xml │ │ ├── Tb.xml │ │ ├── Tl.xml │ │ ├── Tm.xml │ │ ├── Xe.xml │ │ ├── Y.xml │ │ ├── Zr.xml │ │ ├── Al.xml │ │ ├── C.xml │ │ ├── Ce.xml │ │ ├── Cr.xml │ │ ├── Cu.xml │ │ ├── Eu.xml │ │ ├── F.xml │ │ ├── H.xml │ │ ├── Na.xml │ │ ├── Nb.xml │ │ ├── Pd.xml │ │ ├── Pm.xml │ │ ├── Pr.xml │ │ ├── S.xml │ │ ├── Sm.xml │ │ ├── Th.xml │ │ ├── Ti.xml │ │ ├── Yb.xml │ │ ├── Br.xml │ │ ├── Ge.xml │ │ ├── Mn.xml │ │ ├── Pa.xml │ │ ├── Sb.xml │ │ ├── Se.xml │ │ ├── Si.xml │ │ ├── Tc.xml │ │ ├── Te.xml │ │ ├── V.xml │ │ ├── Am.xml │ │ ├── As.xml │ │ ├── Cl.xml │ │ ├── I.xml │ │ ├── Np.xml │ │ ├── P.xml │ │ ├── Pu.xml │ │ ├── U.xml │ │ └── N.xml │ └── pdb │ │ └── ammonia.pdb └── bio │ └── amino_acids.txt ├── bin └── unwarn.py └── _includes ├── javascript.html └── banner.html /book/.gitignore: 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-------------------------------------------------------------------------------- 1 | import sys 2 | print 'sys.argv is', sys.argv 3 | -------------------------------------------------------------------------------- /novice/git/README.txt: -------------------------------------------------------------------------------- 1 | # Resources 2 | 3 | * `img`: images used in lessons 4 | -------------------------------------------------------------------------------- /novice/hg/README.txt: -------------------------------------------------------------------------------- 1 | # Resources 2 | 3 | * `img`: images used in lessons 4 | -------------------------------------------------------------------------------- /novice/python/sys-version.py: -------------------------------------------------------------------------------- 1 | import sys 2 | print 'version is', sys.version 3 | -------------------------------------------------------------------------------- /intermediate/make/paper.tex: 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fahr_to_celsius(ftemp) 3 | ktemp = fahr_to_kelvin(ftemp); 4 | ctemp = kelvin_to_celsius(ktemp); 5 | -------------------------------------------------------------------------------- /book/novice/git/img/git-after-change-to-duplicate-repo.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/book/novice/git/img/git-after-change-to-duplicate-repo.pdf -------------------------------------------------------------------------------- /book/novice/git/img/git-after-first-conflicting-change.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/book/novice/git/img/git-after-first-conflicting-change.pdf -------------------------------------------------------------------------------- /book/novice/git/img/git-after-second-conflicting-change.pdf: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | # multiple.mk 2 | 3 | summary-1.dat : data-1-1.dat data-1-2.dat data-1-3.dat 4 | python stats.py summary-1.dat data-1-1.dat data-1-2.dat data-1-3.dat 5 | -------------------------------------------------------------------------------- /setup/windows-installer/setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | import py2exe 3 | 4 | setup(name='swc-windows-installer', 5 | console=['swc-windows-installer.py'] 6 | ) 7 | -------------------------------------------------------------------------------- /intermediate/make/target-variable.mk: -------------------------------------------------------------------------------- 1 | # target-variable.mk 2 | 3 | summary-1.dat : data-1-1.dat data-1-2.dat data-1-3.dat 4 | python stats.py $@ $^ #data-1-1.dat data-1-2.dat data-1-3.dat 5 | -------------------------------------------------------------------------------- /novice/python/errors_01.py: -------------------------------------------------------------------------------- 1 | def favorite_ice_cream(): 2 | ice_creams = [ 3 | "chocolate", 4 | "vanilla", 5 | "strawberry" 6 | ] 7 | print ice_creams[3] 8 | -------------------------------------------------------------------------------- /intermediate/doit/.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore doit's database file 2 | .doit.db 3 | 4 | # Ignore the data files, if the lesson works they should be automatically 5 | # downloaded anyway... 6 | *.txt 7 | -------------------------------------------------------------------------------- /intermediate/make/reference.md: -------------------------------------------------------------------------------- 1 | --- 2 | layout: lesson 3 | root: ../.. 4 | title: Make Reference 5 | level: Intermediate 6 | --- 7 | * [Gnu Make Manual](https://www.gnu.org/software/make/manual/) 8 | -------------------------------------------------------------------------------- /intermediate/python/01-intro-python_files/intermediate/python/01-intro-python_66_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/intermediate/python/01-intro-python_files/intermediate/python/01-intro-python_66_1.png -------------------------------------------------------------------------------- /intermediate/python/01-intro-python_files/intermediate/python/01-intro-python_68_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/intermediate/python/01-intro-python_files/intermediate/python/01-intro-python_68_0.png -------------------------------------------------------------------------------- /intermediate/make/double.mk: -------------------------------------------------------------------------------- 1 | # double.mk 2 | 3 | figure-1.svg : summary-1.dat 4 | python create_figure.py figure-1.svg summary-1.dat 5 | 6 | figure-2.svg : summary-2.dat 7 | python create_figure.py figure-2.svg summary-2.dat 8 | -------------------------------------------------------------------------------- /book/Makefile: -------------------------------------------------------------------------------- 1 | LATEX = pdflatex 2 | 3 | ALL_TEX = $(wildcard *.tex) 4 | 5 | all : book.pdf 6 | 7 | book.pdf : $(ALL_TEX) 8 | $(LATEX) book 9 | $(LATEX) book 10 | 11 | clean : 12 | rm -f book.pdf *.aux *.log *.toc *~ 13 | -------------------------------------------------------------------------------- /extras/python-climate-data/csv-demo.py: -------------------------------------------------------------------------------- 1 | import cStringIO 2 | import csv 3 | 4 | data = 'first\nsecond\nthird\n' 5 | reader = cStringIO.StringIO(data) 6 | wrapper = csv.reader(reader) 7 | for record in wrapper: 8 | print record 9 | -------------------------------------------------------------------------------- /extras/python-climate-data/csv-demo-2.py: -------------------------------------------------------------------------------- 1 | import cStringIO 2 | import csv 3 | 4 | data = '1901,12.3\n1902,45.6\n1903,78.9\n' 5 | reader = cStringIO.StringIO(data) 6 | wrapper = csv.reader(reader) 7 | for record in wrapper: 8 | print record 9 | -------------------------------------------------------------------------------- /data/evil/notebook-3.txt: -------------------------------------------------------------------------------- 1 | Date Site Evil(mvad) 2 | May 29 2010 (Hartnell) 1029.3 3 | May 30 2010 (Hartnell) 1119.2 4 | June 1 2010 (Hartnell) 1319.4 5 | May 29 2010 (Troughton) 1419.3 6 | May 30 2010 (Troughton) 1420.0 7 | June 1 2010 (Troughton) 1419.8 8 | 9 | -------------------------------------------------------------------------------- /novice/python/readings-01.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import numpy as np 3 | 4 | def main(): 5 | script = sys.argv[0] 6 | filename = sys.argv[1] 7 | data = np.loadtxt(filename, delimiter=',') 8 | for m in data.mean(axis=1): 9 | print m 10 | -------------------------------------------------------------------------------- /css/book.css: -------------------------------------------------------------------------------- 1 | span.subtitle { 2 | color: #030303; 3 | display: block; 4 | font-family: inherit; 5 | font-size: 31.5px; 6 | font-weight: bold; 7 | line-height: 40px; 8 | margin: 40px 0px 10px 0px; 9 | text-rendering: optimizelegibility; 10 | } 11 | -------------------------------------------------------------------------------- /intermediate/make/phony.mk: -------------------------------------------------------------------------------- 1 | # phony.mk 2 | 3 | all : figure-1.svg figure-2.svg 4 | 5 | figure-1.svg : summary-1.dat 6 | python create_figure.py figure-1.svg summary-1.dat 7 | 8 | figure-2.svg : summary-2.dat 9 | python create_figure.py figure-2.svg summary-2.dat 10 | -------------------------------------------------------------------------------- /novice/python/readings-02.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import numpy as np 3 | 4 | def main(): 5 | script = sys.argv[0] 6 | filename = sys.argv[1] 7 | data = np.loadtxt(filename, delimiter=',') 8 | for m in data.mean(axis=1): 9 | print m 10 | 11 | main() 12 | -------------------------------------------------------------------------------- /data/chem/elements/Cm.xml: -------------------------------------------------------------------------------- 1 | 2 | Cm 3 | 96 4 | 247.0703 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /intermediate/python/02-modularization-documentation_files/intermediate/python/02-modularization-documentation_19_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/intermediate/python/02-modularization-documentation_files/intermediate/python/02-modularization-documentation_19_1.png -------------------------------------------------------------------------------- /intermediate/python/02-modularization-documentation_files/intermediate/python/02-modularization-documentation_21_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/intermediate/python/02-modularization-documentation_files/intermediate/python/02-modularization-documentation_21_1.png -------------------------------------------------------------------------------- /intermediate/python/02-modularization-documentation_files/intermediate/python/02-modularization-documentation_64_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dpsanders/bc/master/intermediate/python/02-modularization-documentation_files/intermediate/python/02-modularization-documentation_64_1.png -------------------------------------------------------------------------------- /data/chem/elements/Cf.xml: -------------------------------------------------------------------------------- 1 | 2 | Cf 3 | 98 4 | 251.0796 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /data/chem/elements/Es.xml: -------------------------------------------------------------------------------- 1 | 2 | Es 3 | 99 4 | 252.083 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /data/chem/elements/Fm.xml: -------------------------------------------------------------------------------- 1 | 2 | Fm 3 | 100 4 | 257.0951 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /data/chem/elements/Lr.xml: -------------------------------------------------------------------------------- 1 | 2 | Lr 3 | 103 4 | 262.11 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /data/chem/elements/Md.xml: -------------------------------------------------------------------------------- 1 | 2 | Md 3 | 101 4 | 258.1 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /intermediate/python/A1_mosquito_data.csv: -------------------------------------------------------------------------------- 1 | year,temperature,rainfall,mosquitos 2 | 2001,80,157,150 3 | 2002,85,252,217 4 | 2003,86,154,153 5 | 2004,87,159,158 6 | 2005,74,292,243 7 | 2006,75,283,237 8 | 2007,80,214,190 9 | 2008,85,197,181 10 | 2009,74,231,200 11 | 2010,74,207,184 12 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/north-pacific-gyre/2012-07-03/goodiff: -------------------------------------------------------------------------------- 1 | # difference of two input files 2 | # demo version, just return a random number or "files are identical" 3 | if [ "$1" == "$2" ] 4 | then 5 | echo "files are identical" 6 | else 7 | echo 0.$RANDOM 8 | fi 9 | -------------------------------------------------------------------------------- /data/chem/elements/Bk.xml: -------------------------------------------------------------------------------- 1 | 2 | Bk 3 | 97 4 | 247.0703 5 | +3, +4 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /data/chem/elements/No.xml: -------------------------------------------------------------------------------- 1 | 2 | No 3 | 102 4 | 259.1009 5 | +2, +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/python/readings-03.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import numpy as np 3 | 4 | def main(): 5 | script = sys.argv[0] 6 | for filename in sys.argv[1:]: 7 | data = np.loadtxt(filename, delimiter=',') 8 | for m in data.mean(axis=1): 9 | print m 10 | 11 | main() 12 | -------------------------------------------------------------------------------- /bin/unwarn.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys 4 | while True: 5 | line = sys.stdin.readline() 6 | if not line: 7 | break 8 | if ('Entity' in line): 9 | sys.stdin.readline() 10 | sys.stdin.readline() 11 | else: 12 | sys.stdout.write(line) 13 | -------------------------------------------------------------------------------- /_includes/javascript.html: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /data/chem/elements/At.xml: -------------------------------------------------------------------------------- 1 | 2 | At 3 | 85 4 | 209.9871 5 | solid 6 | 575 7 | 610 8 | 9 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Cm.xml: -------------------------------------------------------------------------------- 1 | 2 | Cm 3 | 96 4 | 247.0703 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Cf.xml: -------------------------------------------------------------------------------- 1 | 2 | Cf 3 | 98 4 | 251.0796 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Es.xml: -------------------------------------------------------------------------------- 1 | 2 | Es 3 | 99 4 | 252.083 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Fm.xml: -------------------------------------------------------------------------------- 1 | 2 | Fm 3 | 100 4 | 257.0951 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Lr.xml: -------------------------------------------------------------------------------- 1 | 2 | Lr 3 | 103 4 | 262.11 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Md.xml: -------------------------------------------------------------------------------- 1 | 2 | Md 3 | 101 4 | 258.1 5 | +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /data/chem/elements/Ac.xml: -------------------------------------------------------------------------------- 1 | 2 | Ac 3 | 89 4 | 227.0278 5 | solid, metal 6 | 1320 7 | 3470 8 | 9 | -------------------------------------------------------------------------------- /data/chem/elements/La.xml: -------------------------------------------------------------------------------- 1 | 2 | La 3 | 57 4 | 138.9055 5 | solid, metal 6 | 1194 7 | 3730 8 | 9 | -------------------------------------------------------------------------------- /extras/python-climate-data/get-data.py: -------------------------------------------------------------------------------- 1 | import requests 2 | 3 | url = 'http://climatedataapi.worldbank.org/climateweb/rest/v1/country/cru/tas/year/CAN.csv' 4 | response = requests.get(url) 5 | if response.status_code != 200: 6 | print 'Failed to get data:', response.status_code 7 | else: 8 | print response.text 9 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Bk.xml: -------------------------------------------------------------------------------- 1 | 2 | Bk 3 | 97 4 | 247.0703 5 | +3, +4 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/No.xml: -------------------------------------------------------------------------------- 1 | 2 | No 3 | 102 4 | 259.1009 5 | +2, +3 6 | solid, metal 7 | 8 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/north-pacific-gyre/2012-07-03/goostats: -------------------------------------------------------------------------------- 1 | while getopts J:r: option 2 | do 3 | case "$option" in 4 | J) Jarg="$OPTARG" 5 | shift $((OPTIND));; 6 | r) shift $((OPTIND-1));; 7 | esac 8 | done 9 | 10 | sleep 2 11 | head -3 $1 | cut -d , -f 1 | sort | uniq > $2 12 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/writing/haiku.txt: -------------------------------------------------------------------------------- 1 | The Tao that is seen 2 | Is not the true Tao, until 3 | You bring fresh toner. 4 | 5 | With searching comes loss 6 | and the presence of absence: 7 | "My Thesis" not found. 8 | 9 | Yesterday it worked 10 | Today it is not working 11 | Software is like that. 12 | -------------------------------------------------------------------------------- /intermediate/r/functions/README.md: -------------------------------------------------------------------------------- 1 | 2 | # Functions and control structures 3 | 4 | In this section we'll learn how to write functions and deal with various types of control flows. 5 | 6 | * Control structures 7 | * Introduction to writing functions 8 | * Basics of writing functions in R 9 | * Scoping rules 10 | 11 | -------------------------------------------------------------------------------- /novice/shell/README.txt: -------------------------------------------------------------------------------- 1 | # Resources 2 | 3 | * `filesystem`: filesystem used in "Files and Directories" 4 | * `creatures`: DNA data used in "Loops" 5 | * `finding`: data using in "Finding Things" 6 | * `molecules`: PDB files used in "Pipes and Filters" 7 | * `scripting`: files and directories used in "Shell Scripts" 8 | -------------------------------------------------------------------------------- /intermediate/make/pattern-rule.mk: -------------------------------------------------------------------------------- 1 | # pattern-rule.mk 2 | 3 | figure-%.svg : summary-%.dat 4 | python create_figure.py $@ $^ 5 | 6 | summary-1.dat : data-1-*.dat 7 | python stats.py $@ $^ 8 | 9 | summary-2.dat : data-2-*.dat 10 | python stats.py $@ $^ 11 | 12 | summary-1.dat : stats.py 13 | summary-2.dat : stats.py 14 | -------------------------------------------------------------------------------- /novice/matlab/center.m: -------------------------------------------------------------------------------- 1 | 2 | function out = center(data, desired) 3 | % Center data around a desired value. 4 | % 5 | % center(DATA, DESIRED) 6 | % 7 | % Returns a new array containing the values in 8 | % DATA centered around the value. 9 | 10 | out = (data - mean(data)) + desired; 11 | -------------------------------------------------------------------------------- /novice/sql/README.txt: -------------------------------------------------------------------------------- 1 | # Resources 2 | 3 | * `gen-survey-database.sql`: re-generate survey database used in examples. 4 | * `sqlitemagic.py`: IPython Notebook plugin to support SQLite interaction. 5 | 6 | # Notes 7 | 8 | * Run 'sqlite3 survey.db < gen-survey-database.sql' to re-create survey database before loading notebooks. 9 | -------------------------------------------------------------------------------- /_includes/banner.html: -------------------------------------------------------------------------------- 1 | Fork me on GitHub 2 | 7 | -------------------------------------------------------------------------------- /intermediate/make/all-patterns.mk: -------------------------------------------------------------------------------- 1 | # all-patterns.mk 2 | 3 | paper.pdf : paper.tex figure-1.svg figure-2.svg 4 | cat $^ > $@ 5 | 6 | figure-%.svg : summary-%.dat 7 | python create_figure.py $@ $^ 8 | 9 | summary-%.dat : data-%-*.dat 10 | python stats.py $@ $^ 11 | 12 | summary-1.dat : stats.py 13 | summary-2.dat : stats.py 14 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/At.xml: -------------------------------------------------------------------------------- 1 | 2 | At 3 | 85 4 | 209.9871 5 | solid 6 | 575 7 | 610 8 | 9 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ac.xml: -------------------------------------------------------------------------------- 1 | 2 | Ac 3 | 89 4 | 227.0278 5 | solid, metal 6 | 1320 7 | 3470 8 | 9 | -------------------------------------------------------------------------------- /data/chem/pdb/ammonia.pdb: -------------------------------------------------------------------------------- 1 | COMPND Ammonia 2 | AUTHOR DAVE WOODCOCK 97 10 31 3 | ATOM 1 N 1 0.257 -0.363 0.000 4 | ATOM 2 H 1 0.257 0.727 0.000 5 | ATOM 3 H 1 0.771 -0.727 0.890 6 | ATOM 4 H 1 0.771 -0.727 -0.890 7 | TER 5 1 8 | END -------------------------------------------------------------------------------- /intermediate/r/reproducible-research/README.md: -------------------------------------------------------------------------------- 1 | # Reproducible research and make 2 | 3 | **Installing** 4 | 5 | *knitr* 6 | ```coffee 7 | install.packages("knitr", dependencies = TRUE) 8 | install.packages("pander") 9 | ``` 10 | 11 | For Make and Pandoc installation instructions please see the [additional-software](../additional_software.md) file. -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/La.xml: -------------------------------------------------------------------------------- 1 | 2 | La 3 | 57 4 | 138.9055 5 | solid, metal 6 | 1194 7 | 3730 8 | 9 | -------------------------------------------------------------------------------- /intermediate/make/false-dependencies.mk: -------------------------------------------------------------------------------- 1 | # false-dependencies.mk 2 | 3 | paper.pdf : paper.tex figure-1.svg figure-2.svg 4 | cat $^ > $@ 5 | 6 | figure-%.svg : summary-%.dat 7 | python create_figure.py $@ $^ 8 | 9 | summary-%.dat : data-%-*.dat 10 | python stats.py $@ $^ 11 | 12 | data-*-*.dat : stats.py 13 | touch $@ 14 | 15 | .SECONDARY : 16 | -------------------------------------------------------------------------------- /data/chem/elements/Ba.xml: -------------------------------------------------------------------------------- 1 | 2 | Ba 3 | 56 4 | 137.327 5 | +2 6 | solid 7 | 1002 8 | 1910 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Hf.xml: -------------------------------------------------------------------------------- 1 | 2 | Hf 3 | 72 4 | 178.49 5 | +4 6 | solid 7 | 2503 8 | 5470 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Rn.xml: -------------------------------------------------------------------------------- 1 | 2 | Rn 3 | 86 4 | 222.0176 5 | 0 6 | gas 7 | 202 8 | 211.4 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/W.xml: -------------------------------------------------------------------------------- 1 | 2 | W 3 | 74 4 | 183.84 5 | +6 6 | solid 7 | 3680 8 | 5930 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ar.xml: -------------------------------------------------------------------------------- 1 | 2 | Ar 3 | 18 4 | 39.948 5 | 0 6 | gas, nonmetal 7 | 83.8 8 | 87.3 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Cs.xml: -------------------------------------------------------------------------------- 1 | 2 | Cs 3 | 55 4 | 132.90543 5 | +1 6 | solid 7 | 301.6 8 | 951.6 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ir.xml: -------------------------------------------------------------------------------- 1 | 2 | Ir 3 | 77 4 | 192.22 5 | +3,+4 6 | solid 7 | 2683 8 | 4403 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Os.xml: -------------------------------------------------------------------------------- 1 | 2 | Os 3 | 76 4 | 190.23 5 | +3,+4 6 | solid 7 | 3327 8 | 5300 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pb.xml: -------------------------------------------------------------------------------- 1 | 2 | Pb 3 | 82 4 | 207.2 5 | +2,+4 6 | solid 7 | 600.65 8 | 2013 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Po.xml: -------------------------------------------------------------------------------- 1 | 2 | Po 3 | 84 4 | 208.9824 5 | +2,+4 6 | solid 7 | 527 8 | 1235 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pt.xml: -------------------------------------------------------------------------------- 1 | 2 | Pt 3 | 78 4 | 195.08 5 | +2,+4 6 | solid 7 | 2045 8 | 4100 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ta.xml: -------------------------------------------------------------------------------- 1 | 2 | Ta 3 | 73 4 | 180.9479 5 | +5 6 | solid 7 | 3269 8 | 5698 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Zn.xml: -------------------------------------------------------------------------------- 1 | 2 | Zn 3 | 30 4 | 65.39 5 | +2 6 | solid, metal 7 | 692.73 8 | 1180 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ag.xml: -------------------------------------------------------------------------------- 1 | 2 | Ag 3 | 47 4 | 107.8682 5 | +1 6 | solid, metal 7 | 1235.1 8 | 2485 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Au.xml: -------------------------------------------------------------------------------- 1 | 2 | Au 3 | 79 4 | 196.96654 5 | +1,+3 6 | solid 7 | 1337.58 8 | 3080 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/B.xml: -------------------------------------------------------------------------------- 1 | 2 | B 3 | 5 4 | 10.811 5 | +3 6 | solid, metalloid 7 | 2573 8 | 3931 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Be.xml: -------------------------------------------------------------------------------- 1 | 2 | Be 3 | 4 4 | 9.01218 5 | +2 6 | solid, metal 7 | 1551 8 | 3243 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Bi.xml: -------------------------------------------------------------------------------- 1 | 2 | Bi 3 | 83 4 | 208.98037 5 | +3,+5 6 | solid 7 | 544.5 8 | 1883 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ca.xml: -------------------------------------------------------------------------------- 1 | 2 | Ca 3 | 20 4 | 40.078 5 | +2 6 | solid, metal 7 | 1112 8 | 1757 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Cd.xml: -------------------------------------------------------------------------------- 1 | 2 | Cd 3 | 48 4 | 112.411 5 | +2 6 | solid, metal 7 | 594.1 8 | 1038 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Co.xml: -------------------------------------------------------------------------------- 1 | 2 | Co 3 | 27 4 | 58.9332 5 | +2,+3 6 | solid, metal 7 | 1768 8 | 3143 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Dy.xml: -------------------------------------------------------------------------------- 1 | 2 | Dy 3 | 66 4 | 162.50 5 | +3 6 | solid, metal 7 | 1685 8 | 2835 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Er.xml: -------------------------------------------------------------------------------- 1 | 2 | Er 3 | 68 4 | 167.26 5 | +3 6 | solid, metal 7 | 1802 8 | 3136 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Fe.xml: -------------------------------------------------------------------------------- 1 | 2 | Fe 3 | 26 4 | 55.847 5 | +2,+3 6 | solid, metal 7 | 1808 8 | 3023 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Fr.xml: -------------------------------------------------------------------------------- 1 | 2 | Fr 3 | 87 4 | 223.0197 5 | +1 6 | liquid, metal 7 | 300 8 | 950 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ga.xml: -------------------------------------------------------------------------------- 1 | 2 | Ga 3 | 31 4 | 69.723 5 | +3 6 | solid, metal 7 | 302.93 8 | 2676 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Gd.xml: -------------------------------------------------------------------------------- 1 | 2 | Gd 3 | 64 4 | 157.25 5 | +3 6 | solid, metal 7 | 1586 8 | 3539 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/He.xml: -------------------------------------------------------------------------------- 1 | 2 | He 3 | 2 4 | 4.002602 5 | 0 6 | gas, non-metal 7 | 0.95 8 | 4.216 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Hg.xml: -------------------------------------------------------------------------------- 1 | 2 | Hg 3 | 80 4 | 200.59 5 | +1,+2 6 | liquid 7 | 234.28 8 | 629.73 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ho.xml: -------------------------------------------------------------------------------- 1 | 2 | Ho 3 | 67 4 | 164.93032 5 | +3 6 | solid, metal 7 | 1747 8 | 2968 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/In.xml: -------------------------------------------------------------------------------- 1 | 2 | In 3 | 49 4 | 114.818 5 | +3 6 | solid, metal 7 | 429.32 8 | 2353 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/K.xml: -------------------------------------------------------------------------------- 1 | 2 | K 3 | 19 4 | 39.0983 5 | +1 6 | solid, metal 7 | 336.8 8 | 1047 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Kr.xml: -------------------------------------------------------------------------------- 1 | 2 | Kr 3 | 36 4 | 83.8 5 | 0 6 | gas, nonmetal 7 | 116.6 8 | 120.85 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Li.xml: -------------------------------------------------------------------------------- 1 | 2 | Li 3 | 3 4 | 6.941 5 | +1 6 | solid, metal 7 | 553.69 8 | 1118.15 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Lu.xml: -------------------------------------------------------------------------------- 1 | 2 | Lu 3 | 71 4 | 174.967 5 | +3 6 | solid, metal 7 | 1936 8 | 3668 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Mg.xml: -------------------------------------------------------------------------------- 1 | 2 | Mg 3 | 12 4 | 24.305 5 | +2 6 | solid, metal 7 | 922 8 | 1363 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Mo.xml: -------------------------------------------------------------------------------- 1 | 2 | Mo 3 | 42 4 | 95.94 5 | +6 6 | solid, metal 7 | 2890 8 | 4885 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Nd.xml: -------------------------------------------------------------------------------- 1 | 2 | Nd 3 | 60 4 | 144.24 5 | +3 6 | solid, metal 7 | 1294 8 | 3341 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ne.xml: -------------------------------------------------------------------------------- 1 | 2 | Ne 3 | 10 4 | 20.1797 5 | 0 6 | gas, nonmetal 7 | 24,48 8 | 27.1 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ni.xml: -------------------------------------------------------------------------------- 1 | 2 | Ni 3 | 28 4 | 58.6934 5 | +2,+3 6 | solid, metal 7 | 1726 8 | 3005 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/O.xml: -------------------------------------------------------------------------------- 1 | 2 | O 3 | 8 4 | 15.9994 5 | -2 6 | gas, nonmetal 7 | 54.8 8 | 90.19 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ra.xml: -------------------------------------------------------------------------------- 1 | 2 | Ra 3 | 88 4 | 226.0254 5 | +2 6 | solid, metal 7 | 973 8 | 1413 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Rb.xml: -------------------------------------------------------------------------------- 1 | 2 | Rb 3 | 37 4 | 85.4678 5 | +1 6 | solid, metal 7 | 312.2 8 | 961 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Re.xml: -------------------------------------------------------------------------------- 1 | 2 | Re 3 | 75 4 | 186.207 5 | +4,+6,+7 6 | solid 7 | 3453 8 | 5900 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Rh.xml: -------------------------------------------------------------------------------- 1 | 2 | Rh 3 | 45 4 | 102.9055 5 | +3 6 | solid, metal 7 | 2239 8 | 4000 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ru.xml: -------------------------------------------------------------------------------- 1 | 2 | Ru 3 | 44 4 | 101.07 5 | +3 6 | solid, metal 7 | 2583 8 | 4173 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Sc.xml: -------------------------------------------------------------------------------- 1 | 2 | Sc 3 | 21 4 | 44.95591 5 | +3 6 | solid, metal 7 | 1814 8 | 3104 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Sn.xml: -------------------------------------------------------------------------------- 1 | 2 | Sn 3 | 50 4 | 118.71 5 | +2,+4 6 | solid, metal 7 | 505.1 8 | 2543 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Sr.xml: -------------------------------------------------------------------------------- 1 | 2 | Sr 3 | 38 4 | 87.62 5 | +2 6 | solid, metal 7 | 1042 8 | 1657 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Tb.xml: -------------------------------------------------------------------------------- 1 | 2 | Tb 3 | 65 4 | 158.92534 5 | +3 6 | solid, metal 7 | 1629 8 | 3296 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Tl.xml: -------------------------------------------------------------------------------- 1 | 2 | Tl 3 | 81 4 | 204.3833 5 | +1,+3 6 | solid 7 | 576.6 8 | 1730 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Tm.xml: -------------------------------------------------------------------------------- 1 | 2 | Tm 3 | 69 4 | 168.93421 5 | +3 6 | solid, metal 7 | 1818 8 | 2220 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Xe.xml: -------------------------------------------------------------------------------- 1 | 2 | Xe 3 | 54 4 | 131.29 5 | 0 6 | gas, nonmetal 7 | 161.3 8 | 166.1 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Y.xml: -------------------------------------------------------------------------------- 1 | 2 | Y 3 | 39 4 | 88.90585 5 | +3 6 | solid, metal 7 | 1795 8 | 3611 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Zr.xml: -------------------------------------------------------------------------------- 1 | 2 | Zr 3 | 40 4 | 91.224 5 | +4 6 | solid, metal 7 | 2125 8 | 4650 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Al.xml: -------------------------------------------------------------------------------- 1 | 2 | Al 3 | 13 4 | 26.981539 5 | +3 6 | solid, metal 7 | 933.5 8 | 2740 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/C.xml: -------------------------------------------------------------------------------- 1 | 2 | C 3 | 6 4 | 12.011 5 | +2, +4, -4 6 | solid, nonmetal 7 | 3820 8 | 5100 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ce.xml: -------------------------------------------------------------------------------- 1 | 2 | Ce 3 | 58 4 | 140.115 5 | +3, +4 6 | solid, metal 7 | 1072 8 | 3699 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Cr.xml: -------------------------------------------------------------------------------- 1 | 2 | Cr 3 | 24 4 | 51.9961 5 | +2,+3,+6 6 | solid, metal 7 | 2130 8 | 2945 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Cu.xml: -------------------------------------------------------------------------------- 1 | 2 | Cu 3 | 29 4 | 63.546 5 | +1,+2 6 | solid, metal 7 | 1356.6 8 | 2840 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Eu.xml: -------------------------------------------------------------------------------- 1 | 2 | Eu 3 | 63 4 | 151.965 5 | +2, +3 6 | solid, metal 7 | 1095 8 | 1870 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/F.xml: -------------------------------------------------------------------------------- 1 | 2 | F 3 | 9 4 | 18.998403 5 | -1 6 | gas, nonmetal 7 | 53.53 8 | 85.01 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/H.xml: -------------------------------------------------------------------------------- 1 | 2 | H 3 | 1 4 | 1.00794 5 | +1, -1 6 | gas, non-metal 7 | 14.01 8 | 20.28 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Na.xml: -------------------------------------------------------------------------------- 1 | 2 | Na 3 | 11 4 | 22.989768 5 | +1 6 | solid, metal 7 | 370.96 8 | 1156.1 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Nb.xml: -------------------------------------------------------------------------------- 1 | 2 | Nb 3 | 41 4 | 92.90638 5 | +3,+5 6 | solid, metal 7 | 2741 8 | 5015 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pd.xml: -------------------------------------------------------------------------------- 1 | 2 | Pd 3 | 46 4 | 106.42 5 | +2,+3 6 | solid, metal 7 | 1825 8 | 3413 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pm.xml: -------------------------------------------------------------------------------- 1 | 2 | Pm 3 | 61 4 | 144.9127 5 | +3 6 | solid, metal 7 | 1441 8 | 3000 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pr.xml: -------------------------------------------------------------------------------- 1 | 2 | Pr 3 | 59 4 | 140.90765 5 | +3 6 | solid, metal 7 | 1204 8 | 3785 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/S.xml: -------------------------------------------------------------------------------- 1 | 2 | S 3 | 16 4 | 32.068 5 | +4,+6,-2 6 | solid, nonmetal 7 | 386 8 | 717.824 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Sm.xml: -------------------------------------------------------------------------------- 1 | 2 | Sm 3 | 62 4 | 150.36 5 | +2, +3 6 | solid, metal 7 | 1350 8 | 2064 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Th.xml: -------------------------------------------------------------------------------- 1 | 2 | Th 3 | 90 4 | 232.0381 5 | +3, +4 6 | solid, metal 7 | 1842 8 | --- 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ti.xml: -------------------------------------------------------------------------------- 1 | 2 | Ti 3 | 22 4 | 47.88 5 | +2,+3,+4 6 | solid, metal 7 | 1933 8 | 3560 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Yb.xml: -------------------------------------------------------------------------------- 1 | 2 | Yb 3 | 70 4 | 173.04 5 | +2, +3 6 | solid, metal 7 | 1097 8 | 1466 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Br.xml: -------------------------------------------------------------------------------- 1 | 2 | Br 3 | 35 4 | 79.904 5 | +1,+5,-1 6 | liquid, nonmetal 7 | 265.9 8 | 331.9 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Ge.xml: -------------------------------------------------------------------------------- 1 | 2 | Ge 3 | 32 4 | 72.61 5 | +2,+4 6 | solid, metalloid 7 | 1210.6 8 | 3103 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Mn.xml: -------------------------------------------------------------------------------- 1 | 2 | Mn 3 | 25 4 | 54.93805 5 | +2,+3,+4,+7 6 | solid, metal 7 | 1517 8 | 2235 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pa.xml: -------------------------------------------------------------------------------- 1 | 2 | Pa 3 | 91 4 | 231.03588 5 | +4, +5 6 | solid, metal 7 | 2113 8 | 4300 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Sb.xml: -------------------------------------------------------------------------------- 1 | 2 | Sb 3 | 51 4 | 121.757 5 | +3,+5,-3 6 | solid, metalloid 7 | 903.9 8 | 1908 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Se.xml: -------------------------------------------------------------------------------- 1 | 2 | Se 3 | 34 4 | 78.96 5 | +4,+6,-2 6 | solid, nonmetal 7 | 490 8 | 958.1 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Si.xml: -------------------------------------------------------------------------------- 1 | 2 | Si 3 | 14 4 | 28.0855 5 | +2,+4,-4 6 | solid, metalloid 7 | 1683 8 | 2628 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Tc.xml: -------------------------------------------------------------------------------- 1 | 2 | Tc 3 | 43 4 | 97.9072 5 | +4,+6,+7 6 | solid, metal 7 | 2445 8 | 5150 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Te.xml: -------------------------------------------------------------------------------- 1 | 2 | Te 3 | 52 4 | 127.6 5 | +4,+6,-2 6 | solid, metalloid 7 | 722.7 8 | 1263 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/V.xml: -------------------------------------------------------------------------------- 1 | 2 | V 3 | 23 4 | 50.9415 5 | +2,+3,+4.+5 6 | solid, metal 7 | 2160 8 | 3650 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/pdb/ammonia.pdb: -------------------------------------------------------------------------------- 1 | COMPND Ammonia 2 | AUTHOR DAVE WOODCOCK 97 10 31 3 | ATOM 1 N 1 0.257 -0.363 0.000 4 | ATOM 2 H 1 0.257 0.727 0.000 5 | ATOM 3 H 1 0.771 -0.727 0.890 6 | ATOM 4 H 1 0.771 -0.727 -0.890 7 | TER 5 1 8 | END -------------------------------------------------------------------------------- /data/chem/elements/Am.xml: -------------------------------------------------------------------------------- 1 | 2 | Am 3 | 95 4 | 243.0614 5 | +3, +4, +5, +6 6 | solid, metal 7 | 1267 8 | 2880 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/As.xml: -------------------------------------------------------------------------------- 1 | 2 | As 3 | 33 4 | 74.92159 5 | +3,+5,-3 6 | solid, metalloid 7 | 1090 8 | 889 (sub) 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Cl.xml: -------------------------------------------------------------------------------- 1 | 2 | Cl 3 | 17 4 | 35.4527 5 | +1,+5,+7,-1 6 | gas, nonmetal 7 | 172.2 8 | 238.6 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/I.xml: -------------------------------------------------------------------------------- 1 | 2 | I 3 | 53 4 | 126.90447 5 | +1,+5,+7,-1 6 | solid, nonmetal 7 | 386.7 8 | 457.5 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Np.xml: -------------------------------------------------------------------------------- 1 | 2 | Np 3 | 93 4 | 237.048 5 | +3, +4, +5, +6 6 | solid, metal 7 | 913 8 | 4175 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/P.xml: -------------------------------------------------------------------------------- 1 | 2 | P 3 | 15 4 | 30.973762 5 | +3, +5, -3 6 | solid, nonmetal 7 | 317.3 8 | 553 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/Pu.xml: -------------------------------------------------------------------------------- 1 | 2 | Pu 3 | 94 4 | 244.0642 5 | +3, +4, +5, +6 6 | solid, metal 7 | 914 8 | 3505 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/U.xml: -------------------------------------------------------------------------------- 1 | 2 | U 3 | 92 4 | 238.0289 5 | +3, +4, +5, +6 6 | solid, metal 7 | 1405.5 8 | 4018 9 | 10 | -------------------------------------------------------------------------------- /data/chem/elements/N.xml: -------------------------------------------------------------------------------- 1 | 2 | N 3 | 7 4 | 14.00674 5 | +1,+2,+3,+4,+5,-1,-2,-3 6 | gas, nonmetal 7 | 63.29 8 | 77.4 9 | 10 | -------------------------------------------------------------------------------- /data/evil/notebook-1.txt: -------------------------------------------------------------------------------- 1 | Site Date Evil (milliVaders) 2 | Baker 1 2009-11-17 1223.0 3 | Baker 1 2010-06-24 1122.7 4 | Baker 2 2009-07-24 2819.0 5 | Baker 2 2010-08-25 2971.6 6 | Baker 1 2011-01-05 1410.0 7 | Baker 2 2010-09-04 4671.6 8 | Baker 2 2012-02-25 1099.0 9 | Baker 1 2013-01-01 950.9 10 | Baker 1 2012-07-23 2000.0 11 | Baker 2 2013-08-22 3500.4 12 | Baker 2 2014-01-02 4510.1 13 | -------------------------------------------------------------------------------- /extras/python-climate-data/parse-manually.py: -------------------------------------------------------------------------------- 1 | input_data = '1901,12.3\n1902,45.6\n1903,78.9\n' 2 | print 'input data is:' 3 | print input_data 4 | 5 | as_lines = input_data.split('\n') 6 | print 'as lines:' 7 | print as_lines 8 | 9 | for line in as_lines: 10 | fields = line.split(',') 11 | year = int(fields[0]) 12 | value = float(fields[1]) 13 | print year, ':', value 14 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Rn.xml: -------------------------------------------------------------------------------- 1 | 2 | Rn 3 | 86 4 | 222.0176 5 | 0 6 | gas 7 | 202 8 | 211.4 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/W.xml: -------------------------------------------------------------------------------- 1 | 2 | W 3 | 74 4 | 183.84 5 | +6 6 | solid 7 | 3680 8 | 5930 9 | 10 | -------------------------------------------------------------------------------- /data/bio/amino_acids.txt: -------------------------------------------------------------------------------- 1 | Alanine Ala 2 | Arginine Arg 3 | Asparagine Asn 4 | Aspartic acid Asp 5 | Cysteine Cys 6 | Glutamic acid Glu 7 | Glutamine Gln 8 | Glycine Gly 9 | Histidine His 10 | Isoleucine Ile 11 | Leucine Leu 12 | Lysine Lys 13 | Methionine Met 14 | Phenylalanine Phe 15 | Proline Pro 16 | Serine Ser 17 | Threonine Thr 18 | Tryptophan Trp 19 | Tyrosine Tyr 20 | Valine Val 21 | -------------------------------------------------------------------------------- /data/evil/notebook-2.txt: -------------------------------------------------------------------------------- 1 | Site/Date/Evil 2 | Davison/May 23, 2010/1724.7 3 | Pertwee/May 24, 2010/2103.8 4 | Davison/June 19, 2010/1731.9 5 | Davison/July 6, 2010/2010.7 6 | Pertwee/Aug 4, 2010/1731.3 7 | Pertwee/Sept 3, 2010/4981.0 8 | Pertwee/June 20, 2011/2103.8 9 | Davison/June 5, 2011/1731.9 10 | Davison/Dec 14, 2011/2200.4 11 | Pertwee/Nov 2, 2011/930.1 12 | Pertwee/Sept 5, 2011/5000.9 13 | -------------------------------------------------------------------------------- /intermediate/make/with-variables.mk: -------------------------------------------------------------------------------- 1 | # with-variables.mk 2 | 3 | STYLE_DIR=c:/papers/ 4 | 5 | paper.pdf : paper.wdp figure-1.svg figure-2.svg 6 | wdp2pdf --style ${STYLE_DIR}/euphoric.wps $< 7 | 8 | figure-%.svg : summary-%.dat 9 | sgr -N -r -s ${STYLE_DIR}/euphoric.fig $@ $^ 10 | 11 | summary-%.dat : data-%-*.dat 12 | stats.py $@ $^ 13 | 14 | data-*-*.dat : stats.py 15 | touch $@ 16 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ba.xml: -------------------------------------------------------------------------------- 1 | 2 | Ba 3 | 56 4 | 137.327 5 | +2 6 | solid 7 | 1002 8 | 1910 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Cs.xml: -------------------------------------------------------------------------------- 1 | 2 | Cs 3 | 55 4 | 132.90543 5 | +1 6 | solid 7 | 301.6 8 | 951.6 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Hf.xml: -------------------------------------------------------------------------------- 1 | 2 | Hf 3 | 72 4 | 178.49 5 | +4 6 | solid 7 | 2503 8 | 5470 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ir.xml: -------------------------------------------------------------------------------- 1 | 2 | Ir 3 | 77 4 | 192.22 5 | +3,+4 6 | solid 7 | 2683 8 | 4403 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Os.xml: -------------------------------------------------------------------------------- 1 | 2 | Os 3 | 76 4 | 190.23 5 | +3,+4 6 | solid 7 | 3327 8 | 5300 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Pb.xml: -------------------------------------------------------------------------------- 1 | 2 | Pb 3 | 82 4 | 207.2 5 | +2,+4 6 | solid 7 | 600.65 8 | 2013 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Pt.xml: -------------------------------------------------------------------------------- 1 | 2 | Pt 3 | 78 4 | 195.08 5 | +2,+4 6 | solid 7 | 2045 8 | 4100 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ta.xml: -------------------------------------------------------------------------------- 1 | 2 | Ta 3 | 73 4 | 180.9479 5 | +5 6 | solid 7 | 3269 8 | 5698 9 | 10 | -------------------------------------------------------------------------------- /intermediate/make/use-pattern.mk: -------------------------------------------------------------------------------- 1 | # use-pattern.mk 2 | 3 | paper.pdf : paper.tex figure-1.svg figure-2.svg 4 | cat $^ > $@ 5 | 6 | figure-%.svg : summary-%.dat 7 | python create_figure.py $@ $^ 8 | 9 | summary-1.dat : data-1-*.dat 10 | python stats.py $@ $^ 11 | 12 | summary-2.dat : data-2-*.dat 13 | python stats.py $@ $^ 14 | 15 | summary-1.dat : stats.py 16 | summary-2.dat : stats.py 17 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ar.xml: -------------------------------------------------------------------------------- 1 | 2 | Ar 3 | 18 4 | 39.948 5 | 0 6 | gas, nonmetal 7 | 83.8 8 | 87.3 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Au.xml: -------------------------------------------------------------------------------- 1 | 2 | Au 3 | 79 4 | 196.96654 5 | +1,+3 6 | solid 7 | 1337.58 8 | 3080 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/B.xml: -------------------------------------------------------------------------------- 1 | 2 | B 3 | 5 4 | 10.811 5 | +3 6 | solid, metalloid 7 | 2573 8 | 3931 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Be.xml: -------------------------------------------------------------------------------- 1 | 2 | Be 3 | 4 4 | 9.01218 5 | +2 6 | solid, metal 7 | 1551 8 | 3243 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Bi.xml: -------------------------------------------------------------------------------- 1 | 2 | Bi 3 | 83 4 | 208.98037 5 | +3,+5 6 | solid 7 | 544.5 8 | 1883 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ca.xml: -------------------------------------------------------------------------------- 1 | 2 | Ca 3 | 20 4 | 40.078 5 | +2 6 | solid, metal 7 | 1112 8 | 1757 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Cd.xml: -------------------------------------------------------------------------------- 1 | 2 | Cd 3 | 48 4 | 112.411 5 | +2 6 | solid, metal 7 | 594.1 8 | 1038 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Er.xml: -------------------------------------------------------------------------------- 1 | 2 | Er 3 | 68 4 | 167.26 5 | +3 6 | solid, metal 7 | 1802 8 | 3136 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Fe.xml: -------------------------------------------------------------------------------- 1 | 2 | Fe 3 | 26 4 | 55.847 5 | +2,+3 6 | solid, metal 7 | 1808 8 | 3023 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Fr.xml: -------------------------------------------------------------------------------- 1 | 2 | Fr 3 | 87 4 | 223.0197 5 | +1 6 | liquid, metal 7 | 300 8 | 950 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ga.xml: -------------------------------------------------------------------------------- 1 | 2 | Ga 3 | 31 4 | 69.723 5 | +3 6 | solid, metal 7 | 302.93 8 | 2676 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/He.xml: -------------------------------------------------------------------------------- 1 | 2 | He 3 | 2 4 | 4.002602 5 | 0 6 | gas, non-metal 7 | 0.95 8 | 4.216 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Hg.xml: -------------------------------------------------------------------------------- 1 | 2 | Hg 3 | 80 4 | 200.59 5 | +1,+2 6 | liquid 7 | 234.28 8 | 629.73 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/In.xml: -------------------------------------------------------------------------------- 1 | 2 | In 3 | 49 4 | 114.818 5 | +3 6 | solid, metal 7 | 429.32 8 | 2353 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/K.xml: -------------------------------------------------------------------------------- 1 | 2 | K 3 | 19 4 | 39.0983 5 | +1 6 | solid, metal 7 | 336.8 8 | 1047 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Kr.xml: -------------------------------------------------------------------------------- 1 | 2 | Kr 3 | 36 4 | 83.8 5 | 0 6 | gas, nonmetal 7 | 116.6 8 | 120.85 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Lu.xml: -------------------------------------------------------------------------------- 1 | 2 | Lu 3 | 71 4 | 174.967 5 | +3 6 | solid, metal 7 | 1936 8 | 3668 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Mg.xml: -------------------------------------------------------------------------------- 1 | 2 | Mg 3 | 12 4 | 24.305 5 | +2 6 | solid, metal 7 | 922 8 | 1363 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Mo.xml: -------------------------------------------------------------------------------- 1 | 2 | Mo 3 | 42 4 | 95.94 5 | +6 6 | solid, metal 7 | 2890 8 | 4885 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Nd.xml: -------------------------------------------------------------------------------- 1 | 2 | Nd 3 | 60 4 | 144.24 5 | +3 6 | solid, metal 7 | 1294 8 | 3341 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ne.xml: -------------------------------------------------------------------------------- 1 | 2 | Ne 3 | 10 4 | 20.1797 5 | 0 6 | gas, nonmetal 7 | 24,48 8 | 27.1 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/O.xml: -------------------------------------------------------------------------------- 1 | 2 | O 3 | 8 4 | 15.9994 5 | -2 6 | gas, nonmetal 7 | 54.8 8 | 90.19 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Po.xml: -------------------------------------------------------------------------------- 1 | 2 | Po 3 | 84 4 | 208.9824 5 | +2,+4 6 | solid 7 | 527 8 | 1235 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ra.xml: -------------------------------------------------------------------------------- 1 | 2 | Ra 3 | 88 4 | 226.0254 5 | +2 6 | solid, metal 7 | 973 8 | 1413 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Rb.xml: -------------------------------------------------------------------------------- 1 | 2 | Rb 3 | 37 4 | 85.4678 5 | +1 6 | solid, metal 7 | 312.2 8 | 961 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Re.xml: -------------------------------------------------------------------------------- 1 | 2 | Re 3 | 75 4 | 186.207 5 | +4,+6,+7 6 | solid 7 | 3453 8 | 5900 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Rh.xml: -------------------------------------------------------------------------------- 1 | 2 | Rh 3 | 45 4 | 102.9055 5 | +3 6 | solid, metal 7 | 2239 8 | 4000 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ru.xml: -------------------------------------------------------------------------------- 1 | 2 | Ru 3 | 44 4 | 101.07 5 | +3 6 | solid, metal 7 | 2583 8 | 4173 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Sn.xml: -------------------------------------------------------------------------------- 1 | 2 | Sn 3 | 50 4 | 118.71 5 | +2,+4 6 | solid, metal 7 | 505.1 8 | 2543 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Sr.xml: -------------------------------------------------------------------------------- 1 | 2 | Sr 3 | 38 4 | 87.62 5 | +2 6 | solid, metal 7 | 1042 8 | 1657 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Tl.xml: -------------------------------------------------------------------------------- 1 | 2 | Tl 3 | 81 4 | 204.3833 5 | +1,+3 6 | solid 7 | 576.6 8 | 1730 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Xe.xml: -------------------------------------------------------------------------------- 1 | 2 | Xe 3 | 54 4 | 131.29 5 | 0 6 | gas, nonmetal 7 | 161.3 8 | 166.1 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Y.xml: -------------------------------------------------------------------------------- 1 | 2 | Y 3 | 39 4 | 88.90585 5 | +3 6 | solid, metal 7 | 1795 8 | 3611 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Zn.xml: -------------------------------------------------------------------------------- 1 | 2 | Zn 3 | 30 4 | 65.39 5 | +2 6 | solid, metal 7 | 692.73 8 | 1180 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Zr.xml: -------------------------------------------------------------------------------- 1 | 2 | Zr 3 | 40 4 | 91.224 5 | +4 6 | solid, metal 7 | 2125 8 | 4650 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/gen-sequence.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | '''Generate random seuqence data for files in `creatures` directory.''' 4 | 5 | import sys 6 | import random 7 | 8 | assert len(sys.argv) == 3, 'Usage: gen-sequence lines seed' 9 | num_lines = int(sys.argv[1]) 10 | random.seed(sys.argv[2]) 11 | for i in range(num_lines): 12 | print ''.join(random.choice('ACGT') for j in range(10)) 13 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Ag.xml: -------------------------------------------------------------------------------- 1 | 2 | Ag 3 | 47 4 | 107.8682 5 | +1 6 | solid, metal 7 | 1235.1 8 | 2485 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/Al.xml: -------------------------------------------------------------------------------- 1 | 2 | Al 3 | 13 4 | 26.981539 5 | +3 6 | solid, metal 7 | 933.5 8 | 2740 9 | 10 | -------------------------------------------------------------------------------- /novice/shell/filesystem/users/nelle/data/elements/C.xml: -------------------------------------------------------------------------------- 1 | 2 | C 3 | 6 4 | 12.011 5 | +2, +4, -4 6 | solid, nonmetal 7 | 3820 8 | 5100 9 | 10 | --------------------------------------------------------------------------------