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Qingpeng Zhang
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fix tutorial and generate html file
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‎html4css1.css

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/*
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:Author: David Goodger ([email protected])
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:Id: $Id$
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:Copyright: This stylesheet has been placed in the public domain.
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Default cascading style sheet for the HTML output of Docutils.
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See http://docutils.sf.net/docs/howto/html-stylesheets.html for how to
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customize this style sheet.
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*/
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/* used to remove borders from tables and images */
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.borderless, table.borderless td, table.borderless th {
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border: 0 }
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table.borderless td, table.borderless th {
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/* Override padding for "table.docutils td" with "! important".
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The right padding separates the table cells. */
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padding: 0 0.5em 0 0 ! important }
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.first {
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/* Override more specific margin styles with "! important". */
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margin-top: 0 ! important }
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.last, .with-subtitle {
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margin-bottom: 0 ! important }
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.hidden {
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display: none }
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a.toc-backref {
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text-decoration: none ;
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color: black }
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blockquote.epigraph {
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margin: 2em 5em ; }
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dl.docutils dd {
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margin-bottom: 0.5em }
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object[type="image/svg+xml"], object[type="application/x-shockwave-flash"] {
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overflow: hidden;
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}
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/* Uncomment (and remove this text!) to get bold-faced definition list terms
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dl.docutils dt {
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font-weight: bold }
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*/
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div.abstract {
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margin: 2em 5em }
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div.abstract p.topic-title {
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font-weight: bold ;
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text-align: center }
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div.admonition, div.attention, div.caution, div.danger, div.error,
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div.hint, div.important, div.note, div.tip, div.warning {
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margin: 2em ;
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border: medium outset ;
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padding: 1em }
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div.admonition p.admonition-title, div.hint p.admonition-title,
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div.important p.admonition-title, div.note p.admonition-title,
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div.tip p.admonition-title {
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font-weight: bold ;
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font-family: sans-serif }
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div.attention p.admonition-title, div.caution p.admonition-title,
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div.danger p.admonition-title, div.error p.admonition-title,
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div.warning p.admonition-title, .code .error {
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color: red ;
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font-weight: bold ;
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font-family: sans-serif }
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/* Uncomment (and remove this text!) to get reduced vertical space in
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compound paragraphs.
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div.compound .compound-first, div.compound .compound-middle {
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margin-bottom: 0.5em }
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div.compound .compound-last, div.compound .compound-middle {
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margin-top: 0.5em }
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*/
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div.dedication {
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margin: 2em 5em ;
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text-align: center ;
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font-style: italic }
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div.dedication p.topic-title {
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font-weight: bold ;
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font-style: normal }
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div.figure {
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margin-left: 2em ;
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margin-right: 2em }
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div.footer, div.header {
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clear: both;
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font-size: smaller }
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div.line-block {
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display: block ;
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margin-top: 1em ;
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margin-bottom: 1em }
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div.line-block div.line-block {
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margin-top: 0 ;
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margin-bottom: 0 ;
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margin-left: 1.5em }
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div.sidebar {
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margin: 0 0 0.5em 1em ;
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border: medium outset ;
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padding: 1em ;
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background-color: #ffffee ;
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width: 40% ;
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float: right ;
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clear: right }
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div.sidebar p.rubric {
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font-family: sans-serif ;
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font-size: medium }
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div.system-messages {
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margin: 5em }
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div.system-messages h1 {
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color: red }
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div.system-message {
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border: medium outset ;
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padding: 1em }
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div.system-message p.system-message-title {
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color: red ;
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font-weight: bold }
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div.topic {
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margin: 2em }
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h1.section-subtitle, h2.section-subtitle, h3.section-subtitle,
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h4.section-subtitle, h5.section-subtitle, h6.section-subtitle {
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margin-top: 0.4em }
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h1.title {
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text-align: center }
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h2.subtitle {
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text-align: center }
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hr.docutils {
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width: 75% }
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img.align-left, .figure.align-left, object.align-left {
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clear: left ;
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float: left ;
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margin-right: 1em }
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img.align-right, .figure.align-right, object.align-right {
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clear: right ;
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float: right ;
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margin-left: 1em }
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img.align-center, .figure.align-center, object.align-center {
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display: block;
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margin-left: auto;
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margin-right: auto;
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}
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.align-left {
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text-align: left }
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.align-center {
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clear: both ;
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text-align: center }
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.align-right {
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text-align: right }
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/* reset inner alignment in figures */
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div.align-right {
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text-align: inherit }
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/* div.align-center * { */
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/* text-align: left } */
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ol.simple, ul.simple {
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margin-bottom: 1em }
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ol.arabic {
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list-style: decimal }
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ol.loweralpha {
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list-style: lower-alpha }
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ol.upperalpha {
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list-style: upper-alpha }
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ol.lowerroman {
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list-style: lower-roman }
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ol.upperroman {
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list-style: upper-roman }
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p.attribution {
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text-align: right ;
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margin-left: 50% }
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p.caption {
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font-style: italic }
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p.credits {
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font-style: italic ;
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font-size: smaller }
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p.label {
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white-space: nowrap }
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p.rubric {
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font-weight: bold ;
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font-size: larger ;
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color: maroon ;
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text-align: center }
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p.sidebar-title {
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font-family: sans-serif ;
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font-weight: bold ;
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font-size: larger }
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p.sidebar-subtitle {
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font-family: sans-serif ;
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font-weight: bold }
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p.topic-title {
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font-weight: bold }
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pre.address {
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margin-bottom: 0 ;
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margin-top: 0 ;
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font: inherit }
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pre.literal-block, pre.doctest-block, pre.math, pre.code {
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margin-left: 2em ;
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margin-right: 2em }
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pre.code .ln { color: grey; } /* line numbers */
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pre.code, code { background-color: #eeeeee }
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pre.code .comment, code .comment { color: #5C6576 }
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pre.code .keyword, code .keyword { color: #3B0D06; font-weight: bold }
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pre.code .literal.string, code .literal.string { color: #0C5404 }
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pre.code .name.builtin, code .name.builtin { color: #352B84 }
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pre.code .deleted, code .deleted { background-color: #DEB0A1}
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pre.code .inserted, code .inserted { background-color: #A3D289}
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span.classifier {
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font-family: sans-serif ;
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font-style: oblique }
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span.classifier-delimiter {
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font-family: sans-serif ;
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font-weight: bold }
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span.interpreted {
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font-family: sans-serif }
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span.option {
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white-space: nowrap }
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span.pre {
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white-space: pre }
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span.problematic {
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color: red }
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span.section-subtitle {
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/* font-size relative to parent (h1..h6 element) */
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font-size: 80% }
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table.citation {
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border-left: solid 1px gray;
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margin-left: 1px }
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table.docinfo {
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margin: 2em 4em }
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table.docutils {
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margin-top: 0.5em ;
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margin-bottom: 0.5em }
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table.footnote {
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border-left: solid 1px black;
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margin-left: 1px }
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table.docutils td, table.docutils th,
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table.docinfo td, table.docinfo th {
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padding-left: 0.5em ;
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padding-right: 0.5em ;
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vertical-align: top }
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table.docutils th.field-name, table.docinfo th.docinfo-name {
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font-weight: bold ;
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text-align: left ;
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white-space: nowrap ;
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padding-left: 0 }
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/* "booktabs" style (no vertical lines) */
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table.docutils.booktabs {
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border: 0px;
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border-top: 2px solid;
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border-bottom: 2px solid;
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border-collapse: collapse;
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}
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table.docutils.booktabs * {
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border: 0px;
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}
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table.docutils.booktabs th {
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border-bottom: thin solid;
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text-align: left;
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}
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h1 tt.docutils, h2 tt.docutils, h3 tt.docutils,
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h4 tt.docutils, h5 tt.docutils, h6 tt.docutils {
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font-size: 100% }
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ul.auto-toc {
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list-style-type: none }

‎khmer-counting.bib

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%% http://bibdesk.sourceforge.net/
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%% Created for Qingpeng Zhang at 2013-06-27 01:13:56 -0400
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%% Created for Qingpeng Zhang at 2013-06-27 01:26:17 -0400
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%% Saved with string encoding Unicode (UTF-8)
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@article{Mackelprang2011,
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Abstract = {Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 $\,^{\circ}$C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.},
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Author = {Mackelprang, Rachel and Waldrop, Mark P and DeAngelis, Kristen M and David, Maude M and Chavarria, Krystle L and Blazewicz, Steven J and Rubin, Edward M and Jansson, Janet K},
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Date-Added = {2013-06-27 05:16:27 +0000},
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Date-Modified = {2013-06-27 05:16:27 +0000},
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Doi = {10.1038/nature10576},
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Journal = {Nature},
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Journal-Full = {Nature},
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Mesh = {Alaska; Arctic Regions; Bacteria; Carbon; Carbon Cycle; DNA; Freezing; Genes, rRNA; Metagenome; Metagenomics; Methane; Nitrogen; Nitrogen Cycle; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S; Soil; Soil Microbiology; Temperature; Time Factors},
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Month = {Dec},
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Number = {7377},
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Pages = {368-71},
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Pmid = {22056985},
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Pst = {epublish},
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Title = {Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw},
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Volume = {480},
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Year = {2011},
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Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature10576}}
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@article{Howe2012,
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Abstract = {The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.},
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Author = {Adina Chuang Howe and Janet Jansson and Stephanie A. Malfatti and Susannah G. Tringe and James M. Tiedje and C. Titus Brown},

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