<!--{{{-->
<link rel='alternate' type='application/rss+xml' title='RSS' href='index.xml' />
<!--}}}-->
Background: #fff
Foreground: #000
PrimaryPale: #8cf
PrimaryLight: #18f
PrimaryMid: #04b
PrimaryDark: #014
SecondaryPale: #ffc
SecondaryLight: #fe8
SecondaryMid: #db4
SecondaryDark: #841
TertiaryPale: #eee
TertiaryLight: #ccc
TertiaryMid: #999
TertiaryDark: #666
Error: #f88
/*{{{*/
body {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];}

a {color:[[ColorPalette::PrimaryMid]];}
a:hover {background-color:[[ColorPalette::PrimaryMid]]; color:[[ColorPalette::Background]];}
a img {border:0;}

h1,h2,h3,h4,h5,h6 {color:[[ColorPalette::SecondaryDark]]; background:transparent;}
h1 {border-bottom:2px solid [[ColorPalette::TertiaryLight]];}
h2,h3 {border-bottom:1px solid [[ColorPalette::TertiaryLight]];}

.button {color:[[ColorPalette::PrimaryDark]]; border:1px solid [[ColorPalette::Background]];}
.button:hover {color:[[ColorPalette::PrimaryDark]]; background:[[ColorPalette::SecondaryLight]]; border-color:[[ColorPalette::SecondaryMid]];}
.button:active {color:[[ColorPalette::Background]]; background:[[ColorPalette::SecondaryMid]]; border:1px solid [[ColorPalette::SecondaryDark]];}

.header {background:[[ColorPalette::PrimaryMid]];}
.headerShadow {color:[[ColorPalette::Foreground]];}
.headerShadow a {font-weight:normal; color:[[ColorPalette::Foreground]];}
.headerForeground {color:[[ColorPalette::Background]];}
.headerForeground a {font-weight:normal; color:[[ColorPalette::PrimaryPale]];}

.tabSelected{color:[[ColorPalette::PrimaryDark]];
	background:[[ColorPalette::TertiaryPale]];
	border-left:1px solid [[ColorPalette::TertiaryLight]];
	border-top:1px solid [[ColorPalette::TertiaryLight]];
	border-right:1px solid [[ColorPalette::TertiaryLight]];
}
.tabUnselected {color:[[ColorPalette::Background]]; background:[[ColorPalette::TertiaryMid]];}
.tabContents {color:[[ColorPalette::PrimaryDark]]; background:[[ColorPalette::TertiaryPale]]; border:1px solid [[ColorPalette::TertiaryLight]];}
.tabContents .button {border:0;}

#sidebar {}
#sidebarOptions input {border:1px solid [[ColorPalette::PrimaryMid]];}
#sidebarOptions .sliderPanel {background:[[ColorPalette::PrimaryPale]];}
#sidebarOptions .sliderPanel a {border:none;color:[[ColorPalette::PrimaryMid]];}
#sidebarOptions .sliderPanel a:hover {color:[[ColorPalette::Background]]; background:[[ColorPalette::PrimaryMid]];}
#sidebarOptions .sliderPanel a:active {color:[[ColorPalette::PrimaryMid]]; background:[[ColorPalette::Background]];}

.wizard {background:[[ColorPalette::PrimaryPale]]; border:1px solid [[ColorPalette::PrimaryMid]];}
.wizard h1 {color:[[ColorPalette::PrimaryDark]]; border:none;}
.wizard h2 {color:[[ColorPalette::Foreground]]; border:none;}
.wizardStep {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];
	border:1px solid [[ColorPalette::PrimaryMid]];}
.wizardStep.wizardStepDone {background:[[ColorPalette::TertiaryLight]];}
.wizardFooter {background:[[ColorPalette::PrimaryPale]];}
.wizardFooter .status {background:[[ColorPalette::PrimaryDark]]; color:[[ColorPalette::Background]];}
.wizard .button {color:[[ColorPalette::Foreground]]; background:[[ColorPalette::SecondaryLight]]; border: 1px solid;
	border-color:[[ColorPalette::SecondaryPale]] [[ColorPalette::SecondaryDark]] [[ColorPalette::SecondaryDark]] [[ColorPalette::SecondaryPale]];}
.wizard .button:hover {color:[[ColorPalette::Foreground]]; background:[[ColorPalette::Background]];}
.wizard .button:active {color:[[ColorPalette::Background]]; background:[[ColorPalette::Foreground]]; border: 1px solid;
	border-color:[[ColorPalette::PrimaryDark]] [[ColorPalette::PrimaryPale]] [[ColorPalette::PrimaryPale]] [[ColorPalette::PrimaryDark]];}

.wizard .notChanged {background:transparent;}
.wizard .changedLocally {background:#80ff80;}
.wizard .changedServer {background:#8080ff;}
.wizard .changedBoth {background:#ff8080;}
.wizard .notFound {background:#ffff80;}
.wizard .putToServer {background:#ff80ff;}
.wizard .gotFromServer {background:#80ffff;}

#messageArea {border:1px solid [[ColorPalette::SecondaryMid]]; background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]];}
#messageArea .button {color:[[ColorPalette::PrimaryMid]]; background:[[ColorPalette::SecondaryPale]]; border:none;}

.popupTiddler {background:[[ColorPalette::TertiaryPale]]; border:2px solid [[ColorPalette::TertiaryMid]];}

.popup {background:[[ColorPalette::TertiaryPale]]; color:[[ColorPalette::TertiaryDark]]; border-left:1px solid [[ColorPalette::TertiaryMid]]; border-top:1px solid [[ColorPalette::TertiaryMid]]; border-right:2px solid [[ColorPalette::TertiaryDark]]; border-bottom:2px solid [[ColorPalette::TertiaryDark]];}
.popup hr {color:[[ColorPalette::PrimaryDark]]; background:[[ColorPalette::PrimaryDark]]; border-bottom:1px;}
.popup li.disabled {color:[[ColorPalette::TertiaryMid]];}
.popup li a, .popup li a:visited {color:[[ColorPalette::Foreground]]; border: none;}
.popup li a:hover {background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]]; border: none;}
.popup li a:active {background:[[ColorPalette::SecondaryPale]]; color:[[ColorPalette::Foreground]]; border: none;}
.popupHighlight {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];}
.listBreak div {border-bottom:1px solid [[ColorPalette::TertiaryDark]];}

.tiddler .defaultCommand {font-weight:bold;}

.shadow .title {color:[[ColorPalette::TertiaryDark]];}

.title {color:[[ColorPalette::SecondaryDark]];}
.subtitle {color:[[ColorPalette::TertiaryDark]];}

.toolbar {color:[[ColorPalette::PrimaryMid]];}
.toolbar a {color:[[ColorPalette::TertiaryLight]];}
.selected .toolbar a {color:[[ColorPalette::TertiaryMid]];}
.selected .toolbar a:hover {color:[[ColorPalette::Foreground]];}

.tagging, .tagged {border:1px solid [[ColorPalette::TertiaryPale]]; background-color:[[ColorPalette::TertiaryPale]];}
.selected .tagging, .selected .tagged {background-color:[[ColorPalette::TertiaryLight]]; border:1px solid [[ColorPalette::TertiaryMid]];}
.tagging .listTitle, .tagged .listTitle {color:[[ColorPalette::PrimaryDark]];}
.tagging .button, .tagged .button {border:none;}

.footer {color:[[ColorPalette::TertiaryLight]];}
.selected .footer {color:[[ColorPalette::TertiaryMid]];}

.error, .errorButton {color:[[ColorPalette::Foreground]]; background:[[ColorPalette::Error]];}
.warning {color:[[ColorPalette::Foreground]]; background:[[ColorPalette::SecondaryPale]];}
.lowlight {background:[[ColorPalette::TertiaryLight]];}

.zoomer {background:none; color:[[ColorPalette::TertiaryMid]]; border:3px solid [[ColorPalette::TertiaryMid]];}

.imageLink, #displayArea .imageLink {background:transparent;}

.annotation {background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]]; border:2px solid [[ColorPalette::SecondaryMid]];}

.viewer .listTitle {list-style-type:none; margin-left:-2em;}
.viewer .button {border:1px solid [[ColorPalette::SecondaryMid]];}
.viewer blockquote {border-left:3px solid [[ColorPalette::TertiaryDark]];}

.viewer table, table.twtable {border:2px solid [[ColorPalette::TertiaryDark]];}
.viewer th, .viewer thead td, .twtable th, .twtable thead td {background:[[ColorPalette::SecondaryMid]]; border:1px solid [[ColorPalette::TertiaryDark]]; color:[[ColorPalette::Background]];}
.viewer td, .viewer tr, .twtable td, .twtable tr {border:1px solid [[ColorPalette::TertiaryDark]];}

.viewer pre {border:1px solid [[ColorPalette::SecondaryLight]]; background:[[ColorPalette::SecondaryPale]];}
.viewer code {color:[[ColorPalette::SecondaryDark]];}
.viewer hr {border:0; border-top:dashed 1px [[ColorPalette::TertiaryDark]]; color:[[ColorPalette::TertiaryDark]];}

.highlight, .marked {background:[[ColorPalette::SecondaryLight]];}

.editor input {border:1px solid [[ColorPalette::PrimaryMid]];}
.editor textarea {border:1px solid [[ColorPalette::PrimaryMid]]; width:100%;}
.editorFooter {color:[[ColorPalette::TertiaryMid]];}
.readOnly {background:[[ColorPalette::TertiaryPale]];}

#backstageArea {background:[[ColorPalette::Foreground]]; color:[[ColorPalette::TertiaryMid]];}
#backstageArea a {background:[[ColorPalette::Foreground]]; color:[[ColorPalette::Background]]; border:none;}
#backstageArea a:hover {background:[[ColorPalette::SecondaryLight]]; color:[[ColorPalette::Foreground]]; }
#backstageArea a.backstageSelTab {background:[[ColorPalette::Background]]; color:[[ColorPalette::Foreground]];}
#backstageButton a {background:none; color:[[ColorPalette::Background]]; border:none;}
#backstageButton a:hover {background:[[ColorPalette::Foreground]]; color:[[ColorPalette::Background]]; border:none;}
#backstagePanel {background:[[ColorPalette::Background]]; border-color: [[ColorPalette::Background]] [[ColorPalette::TertiaryDark]] [[ColorPalette::TertiaryDark]] [[ColorPalette::TertiaryDark]];}
.backstagePanelFooter .button {border:none; color:[[ColorPalette::Background]];}
.backstagePanelFooter .button:hover {color:[[ColorPalette::Foreground]];}
#backstageCloak {background:[[ColorPalette::Foreground]]; opacity:0.6; filter:alpha(opacity=60);}
/*}}}*/
/*{{{*/
* html .tiddler {height:1%;}

body {font-size:.75em; font-family:arial,helvetica; margin:0; padding:0;}

h1,h2,h3,h4,h5,h6 {font-weight:bold; text-decoration:none;}
h1,h2,h3 {padding-bottom:1px; margin-top:1.2em;margin-bottom:0.3em;}
h4,h5,h6 {margin-top:1em;}
h1 {font-size:1.35em;}
h2 {font-size:1.25em;}
h3 {font-size:1.1em;}
h4 {font-size:1em;}
h5 {font-size:.9em;}

hr {height:1px;}

a {text-decoration:none;}

dt {font-weight:bold;}

ol {list-style-type:decimal;}
ol ol {list-style-type:lower-alpha;}
ol ol ol {list-style-type:lower-roman;}
ol ol ol ol {list-style-type:decimal;}
ol ol ol ol ol {list-style-type:lower-alpha;}
ol ol ol ol ol ol {list-style-type:lower-roman;}
ol ol ol ol ol ol ol {list-style-type:decimal;}

.txtOptionInput {width:11em;}

#contentWrapper .chkOptionInput {border:0;}

.externalLink {text-decoration:underline;}

.indent {margin-left:3em;}
.outdent {margin-left:3em; text-indent:-3em;}
code.escaped {white-space:nowrap;}

.tiddlyLinkExisting {font-weight:bold;}
.tiddlyLinkNonExisting {font-style:italic;}

/* the 'a' is required for IE, otherwise it renders the whole tiddler in bold */
a.tiddlyLinkNonExisting.shadow {font-weight:bold;}

#mainMenu .tiddlyLinkExisting,
	#mainMenu .tiddlyLinkNonExisting,
	#sidebarTabs .tiddlyLinkNonExisting {font-weight:normal; font-style:normal;}
#sidebarTabs .tiddlyLinkExisting {font-weight:bold; font-style:normal;}

.header {position:relative;}
.header a:hover {background:transparent;}
.headerShadow {position:relative; padding:4.5em 0 1em 1em; left:-1px; top:-1px;}
.headerForeground {position:absolute; padding:4.5em 0 1em 1em; left:0; top:0;}

.siteTitle {font-size:3em;}
.siteSubtitle {font-size:1.2em;}

#mainMenu {position:absolute; left:0; width:10em; text-align:right; line-height:1.6em; padding:1.5em 0.5em 0.5em 0.5em; font-size:1.1em;}

#sidebar {position:absolute; right:3px; width:16em; font-size:.9em;}
#sidebarOptions {padding-top:0.3em;}
#sidebarOptions a {margin:0 0.2em; padding:0.2em 0.3em; display:block;}
#sidebarOptions input {margin:0.4em 0.5em;}
#sidebarOptions .sliderPanel {margin-left:1em; padding:0.5em; font-size:.85em;}
#sidebarOptions .sliderPanel a {font-weight:bold; display:inline; padding:0;}
#sidebarOptions .sliderPanel input {margin:0 0 0.3em 0;}
#sidebarTabs .tabContents {width:15em; overflow:hidden;}

.wizard {padding:0.1em 1em 0 2em;}
.wizard h1 {font-size:2em; font-weight:bold; background:none; padding:0; margin:0.4em 0 0.2em;}
.wizard h2 {font-size:1.2em; font-weight:bold; background:none; padding:0; margin:0.4em 0 0.2em;}
.wizardStep {padding:1em 1em 1em 1em;}
.wizard .button {margin:0.5em 0 0; font-size:1.2em;}
.wizardFooter {padding:0.8em 0.4em 0.8em 0;}
.wizardFooter .status {padding:0 0.4em; margin-left:1em;}
.wizard .button {padding:0.1em 0.2em;}

#messageArea {position:fixed; top:2em; right:0; margin:0.5em; padding:0.5em; z-index:2000; _position:absolute;}
.messageToolbar {display:block; text-align:right; padding:0.2em;}
#messageArea a {text-decoration:underline;}

.tiddlerPopupButton {padding:0.2em;}
.popupTiddler {position: absolute; z-index:300; padding:1em; margin:0;}

.popup {position:absolute; z-index:300; font-size:.9em; padding:0; list-style:none; margin:0;}
.popup .popupMessage {padding:0.4em;}
.popup hr {display:block; height:1px; width:auto; padding:0; margin:0.2em 0;}
.popup li.disabled {padding:0.4em;}
.popup li a {display:block; padding:0.4em; font-weight:normal; cursor:pointer;}
.listBreak {font-size:1px; line-height:1px;}
.listBreak div {margin:2px 0;}

.tabset {padding:1em 0 0 0.5em;}
.tab {margin:0 0 0 0.25em; padding:2px;}
.tabContents {padding:0.5em;}
.tabContents ul, .tabContents ol {margin:0; padding:0;}
.txtMainTab .tabContents li {list-style:none;}
.tabContents li.listLink { margin-left:.75em;}

#contentWrapper {display:block;}
#splashScreen {display:none;}

#displayArea {margin:1em 17em 0 14em;}

.toolbar {text-align:right; font-size:.9em;}

.tiddler {padding:1em 1em 0;}

.missing .viewer,.missing .title {font-style:italic;}

.title {font-size:1.6em; font-weight:bold;}

.missing .subtitle {display:none;}
.subtitle {font-size:1.1em;}

.tiddler .button {padding:0.2em 0.4em;}

.tagging {margin:0.5em 0.5em 0.5em 0; float:left; display:none;}
.isTag .tagging {display:block;}
.tagged {margin:0.5em; float:right;}
.tagging, .tagged {font-size:0.9em; padding:0.25em;}
.tagging ul, .tagged ul {list-style:none; margin:0.25em; padding:0;}
.tagClear {clear:both;}

.footer {font-size:.9em;}
.footer li {display:inline;}

.annotation {padding:0.5em; margin:0.5em;}

* html .viewer pre {width:99%; padding:0 0 1em 0;}
.viewer {line-height:1.4em; padding-top:0.5em;}
.viewer .button {margin:0 0.25em; padding:0 0.25em;}
.viewer blockquote {line-height:1.5em; padding-left:0.8em;margin-left:2.5em;}
.viewer ul, .viewer ol {margin-left:0.5em; padding-left:1.5em;}

.viewer table, table.twtable {border-collapse:collapse; margin:0.8em 1.0em;}
.viewer th, .viewer td, .viewer tr,.viewer caption,.twtable th, .twtable td, .twtable tr,.twtable caption {padding:3px;}
table.listView {font-size:0.85em; margin:0.8em 1.0em;}
table.listView th, table.listView td, table.listView tr {padding:0 3px 0 3px;}

.viewer pre {padding:0.5em; margin-left:0.5em; font-size:1.2em; line-height:1.4em; overflow:auto;}
.viewer code {font-size:1.2em; line-height:1.4em;}

.editor {font-size:1.1em;}
.editor input, .editor textarea {display:block; width:100%; font:inherit;}
.editorFooter {padding:0.25em 0; font-size:.9em;}
.editorFooter .button {padding-top:0; padding-bottom:0;}

.fieldsetFix {border:0; padding:0; margin:1px 0px;}

.zoomer {font-size:1.1em; position:absolute; overflow:hidden;}
.zoomer div {padding:1em;}

* html #backstage {width:99%;}
* html #backstageArea {width:99%;}
#backstageArea {display:none; position:relative; overflow: hidden; z-index:150; padding:0.3em 0.5em;}
#backstageToolbar {position:relative;}
#backstageArea a {font-weight:bold; margin-left:0.5em; padding:0.3em 0.5em;}
#backstageButton {display:none; position:absolute; z-index:175; top:0; right:0;}
#backstageButton a {padding:0.1em 0.4em; margin:0.1em;}
#backstage {position:relative; width:100%; z-index:50;}
#backstagePanel {display:none; z-index:100; position:absolute; width:90%; margin-left:3em; padding:1em;}
.backstagePanelFooter {padding-top:0.2em; float:right;}
.backstagePanelFooter a {padding:0.2em 0.4em;}
#backstageCloak {display:none; z-index:20; position:absolute; width:100%; height:100px;}

.whenBackstage {display:none;}
.backstageVisible .whenBackstage {display:block;}
/*}}}*/
/***
StyleSheet for use when a translation requires any css style changes.
This StyleSheet can be used directly by languages such as Chinese, Japanese and Korean which need larger font sizes.
***/
/*{{{*/
body {font-size:0.8em;}
#sidebarOptions {font-size:1.05em;}
#sidebarOptions a {font-style:normal;}
#sidebarOptions .sliderPanel {font-size:0.95em;}
.subtitle {font-size:0.8em;}
.viewer table.listView {font-size:0.95em;}
/*}}}*/
/*{{{*/
@media print {
#mainMenu, #sidebar, #messageArea, .toolbar, #backstageButton, #backstageArea {display: none !important;}
#displayArea {margin: 1em 1em 0em;}
noscript {display:none;} /* Fixes a feature in Firefox 1.5.0.2 where print preview displays the noscript content */
}
/*}}}*/
<!--{{{-->
<div class='header' macro='gradient vert [[ColorPalette::PrimaryLight]] [[ColorPalette::PrimaryMid]]'>
<div class='headerShadow'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>&nbsp;
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
</div>
<div class='headerForeground'>
<span class='siteTitle' refresh='content' tiddler='SiteTitle'></span>&nbsp;
<span class='siteSubtitle' refresh='content' tiddler='SiteSubtitle'></span>
</div>
</div>
<div id='mainMenu' refresh='content' tiddler='MainMenu'></div>
<div id='sidebar'>
<div id='sidebarOptions' refresh='content' tiddler='SideBarOptions'></div>
<div id='sidebarTabs' refresh='content' force='true' tiddler='SideBarTabs'></div>
</div>
<div id='displayArea'>
<div id='messageArea'></div>
<div id='tiddlerDisplay'></div>
</div>
<!--}}}-->
<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::ViewToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='subtitle'><span macro='view modifier link'></span>, <span macro='view modified date'></span> (<span macro='message views.wikified.createdPrompt'></span> <span macro='view created date'></span>)</div>
<div class='tagging' macro='tagging'></div>
<div class='tagged' macro='tags'></div>
<div class='viewer' macro='view text wikified'></div>
<div class='tagClear'></div>
<!--}}}-->
<!--{{{-->
<div class='toolbar' macro='toolbar [[ToolbarCommands::EditToolbar]]'></div>
<div class='title' macro='view title'></div>
<div class='editor' macro='edit title'></div>
<div macro='annotations'></div>
<div class='editor' macro='edit text'></div>
<div class='editor' macro='edit tags'></div><div class='editorFooter'><span macro='message views.editor.tagPrompt'></span><span macro='tagChooser excludeLists'></span></div>
<!--}}}-->
To get started with this blank [[TiddlyWiki]], you'll need to modify the following tiddlers:
* [[SiteTitle]] & [[SiteSubtitle]]: The title and subtitle of the site, as shown above (after saving, they will also appear in the browser title bar)
* [[MainMenu]]: The menu (usually on the left)
* [[DefaultTiddlers]]: Contains the names of the tiddlers that you want to appear when the TiddlyWiki is opened
You'll also need to enter your username for signing your edits: <<option txtUserName>>
These [[InterfaceOptions]] for customising [[TiddlyWiki]] are saved in your browser

Your username for signing your edits. Write it as a [[WikiWord]] (eg [[JoeBloggs]])

<<option txtUserName>>
<<option chkSaveBackups>> [[SaveBackups]]
<<option chkAutoSave>> [[AutoSave]]
<<option chkRegExpSearch>> [[RegExpSearch]]
<<option chkCaseSensitiveSearch>> [[CaseSensitiveSearch]]
<<option chkAnimate>> [[EnableAnimations]]

----
Also see [[AdvancedOptions]]
<<importTiddlers>>
Students are encouraged to work in groups on homework and lab assignments, however, ''all work turned in must be your own''. In contrast, exams ''may not be discussed with anyone and must represent individual work''.  

All students of the University of Colorado at Boulder are responsible for knowing and adhering to the academic integrity policy of this institution.  Violations of this policy may include: cheating, plagiarism, aid of academic dishonesty, fabrication, lying, bribery, and threatening behavior.  All incidents of academic misconduct shall be reported to the Honor Code Council (honor@colorado.edu; 5-2273). 

Students who are found to be in violation of the academic integrity policy will be subject to both academic sanctions (a final grade of F in this course) and non-academic sanctions (including but not limited to university probation, suspension, or expulsion).  See  policies [[here|http://www.colorado.edu/academics/honorcode]].
<<option chkGenerateAnRssFeed>> GenerateAnRssFeed
<<option chkOpenInNewWindow>> OpenLinksInNewWindow
<<option chkSaveEmptyTemplate>> SaveEmptyTemplate
<<option chkToggleLinks>> Clicking on links to tiddlers that are already open causes them to close
^^(override with Control or other modifier key)^^
<<option chkHttpReadOnly>> HideEditingFeatures when viewed over HTTP
<<option chkForceMinorUpdate>> Treat edits as MinorChanges by preserving date and time
^^(override with Shift key when clicking 'done' or by pressing Ctrl-Shift-Enter^^
<<option chkConfirmDelete>> ConfirmBeforeDeleting
Maximum number of lines in a tiddler edit box: <<option txtMaxEditRows>>
Folder name for backup files: <<option txtBackupFolder>>
<<option chkInsertTabs>> Use tab key to insert tab characters instead of jumping to next field
Welcome to the home page for Physics 7810, Foundations of Quantitative Biology, Fall 2012.

9/13/12:  I posted HW 4, sorry for the delay.

9/17/12: Lab this week will be held in JSCBB  B115.  We will end a half an hour early (3:30).

9/24/12: Here are some [[guidelines|StudentPresentations.pdf]] for student presentations.
/***
|Name|BetterTimelineMacro|
|Created by|SaqImtiaz|
|Location|http://lewcid.googlepages.com/lewcid.html#BetterTimelineMacro|
|Version|0.5 beta|
|Requires|~TW2.x|
!!!Description:
A replacement for the core timeline macro that offers more features:
*list tiddlers with only specfic tag
*exclude tiddlers with a particular tag
*limit entries to any number of days, for example one week
*specify a start date for the timeline, only tiddlers after that date will be listed.

!!!Installation:
Copy the contents of this tiddler to your TW, tag with systemConfig, save and reload your TW.
Edit the ViewTemplate to add the fullscreen command to the toolbar.

!!!Syntax:
{{{<<timeline better:true>>}}}
''the param better:true enables the advanced features, without it you will get the old timeline behaviour.''

additonal params:
(use only the ones you want)
{{{<<timeline better:true  onlyTag:Tag1 excludeTag:Tag2 sortBy:modified/created firstDay:YYYYMMDD maxDays:7 maxEntries:30>>}}}

''explanation of syntax:''
onlyTag: only tiddlers with this tag will be listed. Default is to list all tiddlers.
excludeTag: tiddlers with this tag will not be listed.
sortBy: sort tiddlers by date modified or date created. Possible values are modified or created.
firstDay: useful for starting timeline from a specific date. Example: 20060701 for 1st of July, 2006
maxDays: limits timeline to include only tiddlers from the specified number of days. If you use a value of 7 for example, only tiddlers from the last 7 days will be listed.
maxEntries: limit the total number of entries in the timeline.


!!!History:
*28-07-06: ver 0.5 beta, first release

!!!Code
***/
//{{{
// Return the tiddlers as a sorted array
TiddlyWiki.prototype.getTiddlers = function(field,excludeTag,includeTag)
{
          var results = [];
          this.forEachTiddler(function(title,tiddler)
          {
          if(excludeTag == undefined || tiddler.tags.find(excludeTag) == null)
                        if(includeTag == undefined || tiddler.tags.find(includeTag)!=null)
                                      results.push(tiddler);
          });
          if(field)
                   results.sort(function (a,b) {if(a[field] == b[field]) return(0); else return (a[field] < b[field]) ? -1 : +1; });
          return results;
}



//this function by Udo
function getParam(params, name, defaultValue)
{
          if (!params)
          return defaultValue;
          var p = params[0][name];
          return p ? p[0] : defaultValue;
}

window.old_timeline_handler= config.macros.timeline.handler;
config.macros.timeline.handler = function(place,macroName,params,wikifier,paramString,tiddler)
{
          var args = paramString.parseParams("list",null,true);
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Students and faculty each have responsibility for maintaining an appropriate learning environment. As part of this responsibility, you are expected to
* turn off cell phone ringers during class,
* not use laptop computers, cell phones, pagers, or other electronic devices in class, except as necessary for class work and
* not read newspapers or magazines in class.  
Students who fail to adhere to behavioral standards may be subject to discipline. 

Faculty have the professional responsibility to treat students with understanding, dignity and respect, to guide classroom discussion and to set reasonable limits on the manner in which students express opinions.  For more information, see the [[University|http://www.colorado.edu/policies/classbehavior.html]] and [[student affairs|http://www.colorado.edu/studentaffairs/judicialaffairs/code.html#student_code]] policies on classroom behavior.

Professional courtesy and sensitivity are especially important with respect to individuals and topics dealing with differences of race, culture, religion, politics, sexual orientation, gender variance, and nationalities.  Class rosters are provided to me with the student's legal name. I will gladly honor your request to address you by an alternate name or gender pronoun. Please advise me of this preference early in the semester so that I may make appropriate changes to my records.
*This course covers the foundations of quantitative biology. 
*Note that although there are two separate course numbers, this course is run as an integrated 6-credit course including the lectures on Tuesdays/Thursdays and the lab on Wednesdays. 
*Topics covered include review of basic thermodynamics, kinetics, and chemistry; review of essential math including calculus, differential equations, linear algebra, probability, and statistics; using and programming matlab; cellular structure and components; essentials of imaging; macromolecular structure and function; molecular biophysics; modeling biochemical network dynamics; modeling in ecology and evolutionary biology; and chemical biology.
* For more details, see the [[Detailed Schedule]].
!!!Prerequisites
*Instructor permission
!General information
* [[Instructor]]''s''
* [[Textbooks]]
* [[Resources]]
* [[Course Goals]]
* [[Detailed Schedule]]
!Course components
* [[Lectures]]
* [[Lab]]
* [[Homework]]
* [[Exams]]
* [[Presentations]]
* [[Participation]]
!Grading
* [[Grading Policy]]
!Policies and requirements
* [[Dropping the course]]
* [[Extra help]]
* [[Exams]]
* [[Academic honesty]]
* [[Classroom behavior]]
* [[Disabilities]]
* [[Religious observances]]
* [[Equity and discrimination]]
/% PDF file of the [[syllabus|syllabus.pdf]] distributed on the first day of class. %/
[[Announcements]]
[[Course Information]]
This is the course schedule, reading assignments, and links to homework, lab and exam information. [[Textbooks]] The topics listed for each day are preliminary and may change (some material may be covered more quickly or slowly than listed in the schedule). 



| Week | Dates | Lecture topics | Lab topics  | Reading | Assignments | Taught By, Comments |
| - | 8/20-8/24 | Boot Camp  | Matlab ([[slides|MatlabBootcamp.pdf]], [[exercise 1|matlabbootcampday1.pdf]], [[exercise 2|matlabbootcampday2.pdf]]), Probability and Statistics, Differential Equations, Biology building blocks ([[outline|BiochemistryBootcampOutline.pdf]],[[slides|IQBioBootcampSlides.pdf]]) | | | Loren, David, Manuel and Tom  |
| 1 | 8/28-8/30 | [[Tour of the Cell|Foundations_TourofCell.pdf]] | [[Enzyme Kinetics|lab1.pdf]]  (LH) | ~MBoC | [[HW 1|hw0.pdf]], [[HW2|hw2.pdf]] |  Tom |
| 2 | 9/4-9/6 | [[Protein Structure and Function|ProteinStrucFolding.pdf]] | [[PyMol|pymol-tutorial-2012.pdf]] (DM) | | [[paper|59full.pdf]],[[HW3|Foundations2012PS3.pdf]] | Tom |
| 3 | 9/11 -9/13 | Experimental Methods [[part1|ExperimentalDesign.pptx]], [[part 2 |ExperimentalDesign2.pptx]] | Ramachandran Plots (LH) | ~MBoC chapter 8 | [[paper|Tischer.pdf]]  [[HW4|hw4.pdf]] | Loren (Tom out of town) |
| 4 | 9/18-9/20 | Chemical Kinetics [[notes|Sept18LectureNotes.pdf]] and [[slides|IQ_Enzymes_Sept18.pdf]] |  [[Single molecule fluorescent techniques|lab5.pdf]](LH) | | [[HW5|Foundations_PS5_2012.pdf]]  | Tom |
| 5 | 9/25-9/27 | Confronting biological models with data [[(part1|Wk5_class1_upload.ppt]], [[part2|Wk5_class2_upload.ppt]], [[part3|wk5_class3_upload.ppt]], [[derivation|Keeling_derivation.pdf]], [[more|SIRhomogeneous.csv]]) | Likelihood methods (BM) | | | Brett Melbourne, (Tom out tuesday) |
| 6 | 10/2-10/4 | Confronting biological models with data [[Part1|Wk6class1.ppt]], [[Part2|Wk6class2.ppt]], [[Part3|Wk6class3.ppt]], [[Data|wk6lineardata.pdf]], [[Data|wk6SIRhomogeneous2.pdf]], [[FurtherReading|Further_reading.ppt]] | Bayesian methods (BM) | | |  Brett Melbourne (Tom out) |
| 7 | 10/9-10/11 | Infectious disease modeling and stochastic modeling [[Part1|Wk7class1.pdf]], [[Part 2|Wk7class2.pdf]] | Sim Biology and stochastic modeling (DB) | | | David Bortz |
| 8 | 10/16-10/18 | Waves and fourier transforms [[Part1|Wk8EMLecture_Small.pdf]] (X-ray crystallography) | Fourier transforms [[Lab|Wk8lab_xray.pdf]] (LH) | | | Loren |
| 9 | 10/23-10/25 | Electron microscopy (Loren) Molecular docking/more EM (Dylan) [[Slides|Wk9class.pdf]] | Student Presentations, [[guidelines|StudentPresentations.pdf]] | | | Loren/Dylan |
| 10 | 10/30-11/1 | Diffusion and random walks [[Slides|Wk10class.pdf]] | Ramachandran cont. |  | [[HW|Wk10homework.pdf]] | Loren, (Tom out tuesday, wed) |
| 11 | 11/6-11/8 | RNA structure [[Slides|Wk11Slides.pdf]], [[Notes|Wk11LectureNotes1.pdf]] | Student Presentations | | | Tom |
| 12 | 11/13-11/15 | End of diffusion/ Molecular evolution and sequence alignment [[Slides|Wk12Slides.pdf]] | RNA folding/M fold (TC) |[[Article|Article.pdf]], [[Supplemental|Article_Supp.pdf]] |[[Practicum|Wk12Practicum.pdf]], [[Midterm1|Midterm1.pdf]], [[Midterm2|Midterm2.pdf]]  | Loren |
| - | 11/20-11/22 | Thanksgiving break ||||
| 13 | 11/27-11/29 | Biological networks and mathematical models of synthetic and signaling networks [[Slides1|Wk13SlidesLH.pdf]], [[Slides2|Wk13Slides.pdf]] | Nonlinear dynamics of a synthetic genetic toggle switch. (LH) | | | Loren (tuesday), Tom (thursday) |
| 14 | 12/4-12/6 | Genome-wide analysis and “precision medicine” [[Slides|Wk14Slides.pdf]]  | New Lab (TC) | | | Tom |
| 15 | 12/11-1213 | Genome-wide analysis concluded, including genome-browsers (tuesday) and Course wrap-up (thursday) | Using databases in biological research (Jacob Schwartz) [[Lab|Wk15Lab.pdf]], [[Publication1|Wk15Article1.pdf]], [[Publication2|Wk15Article2.pdf]] | | | Tom (tuesday) |
If you qualify for accommodations because of a disability, please submit a letter to us from Disability Services in a timely manner (during the first two weeks of class) so that your needs may be addressed. Disability Services determines accommodations based on documented disabilities.  Contact: 2-8671, Center for Community N200, or [[this site|http://www.Colorado.EDU/disabilityservices]].  If you have a temporary medical condition or injury, see guidelines at [[this site|http://www.colorado.edu/disabilityservices/go.cgi?select=temporary.html]]. Disability Services' letters for students with disabilities indicate legally mandated reasonable accommodations. The syllabus statements and answers to Frequently Asked Questions can be found at [[this site|http://www.colorado.edu/disabilityservices]].
Advice from the Dean's office is recommended before dropping any course.  After the drop date, the course is possible only with a petition approved by the Dean's office.
* The University of Colorado at Boulder policy on Discrimination and Harassment (available at [[this site|http://www.colorado.edu/policies/discrimination.html]]), the University of Colorado policy on Sexual Harassment and the University of Colorado policy on Amorous Relationships applies to all students, staff and faculty.  
* Any student, staff or faculty member who believes s/he has been the subject of discrimination or harassment based upon race, color, national origin, sex, age, disability, religion, sexual orientation, or veteran status should contact the Office of Discrimination and Harassment (ODH) at 303-492-2127 or the Office of Judicial Affairs at 303-492-5550.  
* Information about the ODH and the campus resources available to assist individuals regarding discrimination or harassment can be obtained [[here|http://www.colorado.edu/odh]].
There will be two take-home exams: 
/%
* [[Midterm Exam]], Tuesday 10/4 - Tuesday 10/11
* [[Final Exam]], Tuesday 12/6 - Tuesday 12/13
%/
!Exam policies
* There will be ''no'' make-up exams or early exams.  If you are sick during an exam, please bring a note from your doctor verifying your illness.  Your course grade will then be determined by the rest of your course work.  
You are encouraged to get extra help whenever you need it. Work with other students in the course. Come to office hours and ask questions.
* Please review the general information about the [[Exams]]. 
!Point breakdown 
|!Category|!Percentage |!Points|
|Homework | 30% |60 points, based on 12 assignments of 5 points each |
|Lab | 30% |60 points, based on 15 assignments of 4 points each |
|Midterm exam  | 15% |30 points |
|Final exam | 15% |30 points |
|Presentations | 5% |10 points |
|Participation | 5% |10 points |
|>|Total |200 points |
!Grade determination
|!Points|!Grade|
|>180|A|
|>160, <180|B|
|>140, <160|C|
|>120, <140|D|
|<120|F|
These are the strictest possible grading standards. In other words, if you receive more than 180 points, you are guaranteed an A for the course. However, the grading standards may be relaxed (curved): the cutoff for an A may be lower than 180 points, but it will never be higher than 180 points.

For help on the homework problems, you are encouraged to work with other students in the course and ask questions of the instructors.

The homeworks are listed in the assignments section of the detailed schedule.

/%|!HW |!Due Date|!Problems|!Hints|!Solutions (PDF)|
| 0 | 8/29 |[[Homework 0|hw0.pdf]]  | | |
| 1 | 8/30 |[[Homework 1|hw1.pdf]]  | | |
| 2 | 9/6 |[[Homework 2|hw2.pdf]]  | | |
| 3 | 9/15 |[[Homework 3|hw3.pdf]] | | |
| 4 | 9/22 |[[Homework 4|hw4.pdf]] |||
| 5 | 9/29 |[[Homework 5|hw5.pdf]] |||
| 6 | 10/20 |[[Homework 6|hw6.pdf]] |||
| 7 | 10/27 |[[Homework 7|hw7.pdf]] |[[Tsankov et al 2010|tsankov10.pdf]]||
| 8 | ''Wednesday 11/2'' |[[Homework 8|hw8.pdf]] |[[Barski et al 2007|Barski07.pdf]]||
| 9 | |[[Homework 9|hw9.pdf]] ||| %/
To do well in this course, you should do (and understand) the homework.  Ask questions.  Homework  is due Tuesday in class.  Late homework will ''not be accepted or graded''. To receive full credit for a homework problem you must ''show all your work.'' 
| Instructor | Loren Hough | Tom Cech |
| Office | JSCBB D214 or Duane 5th floor | JSCBB B421 |
| Office Hours |  JSCBB Room A226 Tuesday 10-12 | JSCBB Room A226 Tuesday 10-12  |
| Phone |  | 2-8606 |
| Email | hough at colorado dot edu | thomas dot cech at colorado dot edu |

Email availability: We will typically respond to email sent during office hours by the end of office hours. At other times, we make every effort to respond to email within 24-48 hours. We typically do not reply to email at night or on weekends.

| TA | Robert Blackwell |
| Office |  Duane F511  |
| Office Hours |    |
| Phone | 706-296-8658  |
| Email | robert dot blackwell at colorado dot edu |
The Lab portion of the course is on Wed 1:30-4pm in Duane G116 or D142.
The 9/19/12 Lab will be held in JSCBB B115.

Here are some [[guidelines|lab_guidelines.pdf]] for lab writeups. 

For most of the labs, all information is in the [[Detailed Schedule]], otherwise, see below:

# Imaging 
** Reading:
*** If you're not familiar with fluorescence microscopy, look at the wikipedia pages on [[fluorescence|http://en.wikipedia.org/wiki/Fluorescence]], [[fluorescence microscope|http://en.wikipedia.org/wiki/Fluorescence_microscope]], and [[green fluorescent protein|http://en.wikipedia.org/wiki/Green_fluorescent_protein]], as well as the Microscopy U page on [[fluorescence microscopy|http://www.microscopyu.com/articles/fluorescence/fluorescenceintro.html]]. 
***If you're not familiar with the physics of diffraction, look at the wikipedia pages on [[diffraction|http://en.wikipedia.org/wiki/Diffraction]], [[Airy disk|http://en.wikipedia.org/wiki/Airy_disk]], and [[diffraction-limited system|http://en.wikipedia.org/wiki/Diffraction_limit]], as well as the [[Phet simulation of diffraction|http://phet.colorado.edu/en/simulation/wave-interference]] and the Microscopy U articles on [[resolution|http://www.microscopyu.com/articles/formulas/formulasresolution.html]] and [[tutorial on numerical aperture and image resolution|http://www.microscopyu.com/tutorials/java/imageformation/airyna/index.html]]. 
*** Yildiz et al., //Science// ''300'', 2061 (2003) [[(PDF)|yildiz2003.pdf]]
*** Betzig et al., //Science// ''313'', 1642 (2006) [[(PDF)|betzig2006.pdf]]
**Assignment: [[Lab 5|lab5.pdf]]

/%
# Math bootcamp: differential equations 
**Reading: [[Differential equations tutorials|Resources]] 
**Assignment: [[Lab 1|lab1.pdf]] 
# Math bootcamp: probability and statistics 
** Assignment: [[Lab 2|lab2.pdf]] 
# Math bootcamp: probability and statistics 
** Assignment: [[Lab 3|lab3.pdf]] 

*** If you're not familiar with fluorescence microscopy, look at the wikipedia pages on [[fluorescence|http://en.wikipedia.org/wiki/Fluorescence]], [[fluorescence microscope|http://en.wikipedia.org/wiki/Fluorescence_microscope]], and [[green fluorescent protein|http://en.wikipedia.org/wiki/Green_fluorescent_protein]], as well as the Microscopy U page on [[fluorescence microscopy|http://www.microscopyu.com/articles/fluorescence/fluorescenceintro.html]]. 
***If you're not familiar with the physics of diffraction, look at the wikipedia pages on [[diffraction|http://en.wikipedia.org/wiki/Diffraction]], [[Airy disk|http://en.wikipedia.org/wiki/Airy_disk]], and [[diffraction-limited system|http://en.wikipedia.org/wiki/Diffraction_limit]], as well as the [[Phet simulation of diffraction|http://phet.colorado.edu/en/simulation/wave-interference]] and the Microscopy U articles on [[resolution|http://www.microscopyu.com/articles/formulas/formulasresolution.html]] and [[tutorial on numerical aperture and image resolution|http://www.microscopyu.com/tutorials/java/imageformation/airyna/index.html]]. 
*** Yildiz et al., //Science// ''300'', 2061 (2003) [[(PDF)|yildiz2003.pdf]]
*** Betzig et al., //Science// ''313'', 1642 (2006) [[(PDF)|betzig2006.pdf]]
**Assignment: [[Lab 4|lab4.pdf]]
# Quantitative image analysis
** Reading:
*** Information on image processing in matlab: [[documentation|http://www.mathworks.com/help/toolbox/images/index.html]], [[tutorial|http://amath.colorado.edu/computing/Matlab/Tutorial/ImageProcess.html]].
*** ~Sakaue-Sawano et al., //Cell// ''132'', 487 (2008) [[(PDF)|sakauesawano2008.pdf]]
*** [[Movie|liu_cellcycle.avi]] of cell cycle changes in ~HeLa cells from the Liu lab. [[Frame 1|frame_1.jpg]] of the movie. [[Slide|liu_slide.pdf]] explaining the movie.
** Assignment: [[Lab 5|lab5.pdf]]
# RNA structure
# Molecular structure analysis in ~PyMol.
** Assignment: [[Lab 7|lab7.pdf]]
# Sequence and structure conservation.
** Assignment (zipped folder containing all the files): [[Lab 8|lab8.zip]]
# 
# Databases in biological research.
** Assignment: [[Lab 10|lab10.pdf]]
# Nonlinear dynamics of a synthetic genetic toggle switch.
** Gardner et al //Nature// ''403'', 339 (2000) [[(PDF)|gardner00.pdf]]
** Assignment: [[Lab 11|lab11.pdf]]



The computer lab meets Wednesday 1:30 - 4 pm in Duane G116. ''Note the time change.''

%/

Computer lab assignments will be given each Wednesday to be completed with a partner in class. While the lab assignments should be completed in class, if extra time is needed the written assignment may be turned in by Friday (two days later) at 5 pm.  Late lab assignments will  ''not'' be accepted or graded.
*Lectures meet Tuesday/Thursday from 2pm-3:15 in room B231 of JSCBB. 
/%!!Lecture notes
* This is a list of PDF files of the slides, from lectures that used them. Note that these files are fairly large: the approximate size is listed for each files.
| Week | Date | Topic | Slides |
| 2 | 9/1 |Biology background: what's inside cells. |[[Lecture 2-1 notes|lecture2-1.pdf]] (2.9 MB)|
| 2 | 9/3 |Biology background: biomolecules. |[[Lecture 2-2 notes|lecture2-2.pdf]] (2.5 MB)|
| 3 | 9/8 |Biology background: macromolecules. |[[Lecture 3-1 notes|lecture3-1.pdf]] (2.4 MB)|
| 3 | 9/10 |Biology background: time. |[[Lecture 3-2 notes|lecture3-2.pdf]] (1 MB)| %/
[[Course Goals]]
[[Detailed Schedule]]
[[Homework]] 
[[Lab]]
[[Course Information]]
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* [[Midterm exam|midterm.pdf]] and [[associated paper|partikian1998.pdf]].
* The take-home midterm exam will take place Tuesday 10/4 - Tuesday 10/11.
* The exam is open book, open notes, you can look up anything you'd like.
* The exam must be individual work, no discussion with others in the class is allowed.
* Please review the general information about the [[Exams]]. 
/%[>img[exam_1.png]]
* The exam had a median score of 66, standard deviation 23.
* Exam 1 [[solutions|exam_1_solns.pdf]].
* The first exam will take place Wednesday 2/7 in class.%/
* Lab 7 posted to [[Lab]].
* Outlines for weeks 6-7 posted to [[Detailed Schedule]].
* Outline and slides from RNA structure lecture posted to [[Detailed Schedule]].
* Homework 5 posted to [[Homework]]. 
* Lab 5 posted to [[Lab]].
* Slides from cell cycle control lecture posted to [[Detailed Schedule]].
* Outline of cell cycle control lecture posted to [[Detailed Schedule]].
* Homework 4 posted to [[Homework]].
* Reading for Lab 5 posted to [[Lab]].
* Homework 3 posted to [[Homework]]. Note: problem 1 was revised from the original version handed out in class.
* Slides from Dick ~McIntosh's lecture and additional reading on electron microscopy posted to [[Detailed Schedule]] and [[Resources]].
* Lab 4 posted to [[Lab]].
* ''Even more'' suggested reading for Lab 4 posted to [[Lab]].
* Slides on cellular structure and processes used class on Thursday 9/8 posted to [[Detailed Schedule]].
* Slides on protein folding and structure used class on Thursday 9/1 posted to [[Detailed Schedule]].
* Correction to the correction: the reading typo wasn't actually a typo.
* References and further reading on differential equations added to [[Resources]].
* --There was a typo in the reading assignment for week 1: it should have been chapter 15, not chapter 5. Fixed in [[Detailed Schedule]].--* Reading for weeks 2 and 3 updated in [[Detailed Schedule]].
* Week 3 outline posted to [[Detailed Schedule]].
* Note that the time of the [[Lab]] has been changed to 1:30-4 pm on Wednesdays to avoid conflict with seminars that start at 4 pm.
* Assignments 0-2 posted [[Homework]].
* Week 1 and 2 outlines posted to [[Detailed Schedule]].
* Syllabus posted to [[Course Information]].
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This course is structured to include discussion in lecture and work in teams in the labs. Attendance at class sessions and participation in discussions and lab work will contribute to the overall course grade.
Once during the semester each pair of students will be asked to present a 20-30 minute presentation discussing a recent research publication related to a topic covered in class. These may be presented during the Tuesday noon idea exchange sessions, outside of regular classroom hours. 
Campus policy regarding religious observances requires that faculty make every effort to reasonably and fairly deal with all students who, because of religious obligations, have conflicts with scheduled exams, assignments or required attendance.  

In this class, you should speak with the instructors at least two weeks before any anticipated class absences.  See policy details at [[this site|http://www.colorado.edu/policies/fac_relig.html]].
Here are some useful resources for the course and for learning about quantitative biology.
* Electron microscopy
** [[Slides from Dick McIntosh's lecture|mcintoshslides.pdf]] on electron microscopy.
** "Probing the macromolecular organization of cells by electron tomography", Hoenger and McIntosh, //Current Opinion in Cell Biology// ''21'', 1 (2009). [[PDF|hoenger2009.pdf]]. 
** "Cryo-electron tomography of microtubule-kinesin motor complexes", Cope et al., //Journal of Structural Biology// ''170'', 257 (2010). [[PDF|cope2010.pdf]].
** "Electron crystallography for structural and functional studies of membrane proteins", Fujiyoshi, //Journal of Electron Microscopy// ''60'', S149 (2011). [[PDF|fujiyoshi2011.pdf]].
* Differential equations
** Pawl Dawkins has an [[excellent set of notes|http://tutorial.math.lamar.edu/Classes/DE/DE.aspx]] from a differential equations course. This is essentially an online textbook, covering the core topics in differential equations with examples. If you want to really learn differential equations, read this.
** The [[interactive math page on differential equations|http://www.intmath.com/differential-equations/des-intro.php]] starts very basic and focuses on techniques for solving 1st and 2nd order ~ODEs, with lots of examples and exercises.
** I often use the [[differential equation reference|http://eqworld.ipmnet.ru/en/solutions/ode.htm]] pages at equation world. For example, the [[first-order ODE|http://eqworld.ipmnet.ru/en/solutions/ode/ode-toc1.htm]] page has a list of a huge number of classes of first-order ~ODEs and how to solve them.
** The [[Wikipedia page on differential equations|http://en.wikipedia.org/wiki/Differential_equation]] has a good overview of the importance of differential equations, terminology used in classifying differential equations, and a table of exact solutions. For example, note that the first homework's DE problem was type #4 from this table.
** SOS Math has a differential equations [[reference page|http://www.sosmath.com/diffeq/diffeq.html]], with sections that include
*** [[First-order linear DEs|http://www.sosmath.com/diffeq/first/lineareq/lineareq.html]]
*** [[Separable ODEs|http://www.sosmath.com/diffeq/first/separable/separable.html]]
*** [[Second-order linear equations|http://www.sosmath.com/diffeq/second/linear/secondlinear.html]]
* Animations
**[[Molecular animations|http://wehi.edu.au/education/wehi-tv/]] by Drew Barry of the Walter and Eliza Hall Institute. See in particular these animations (direct links to quicktime .mov files)
*** [[Transcription|http://wehi.edu.au/uploads/wehi-tv/CentralDogma_Part1.mov]]
*** [[Translation|http://wehi.edu.au/uploads/wehi-tv/CentralDogma_Part2.mov]]
* Images
**[[Morphbank|http://www.morphbank.net/]] database of biological images of plants and animals.
* Biological imaging information
** [[Web educational resources|http://swehsc.pharmacy.arizona.edu/exppath/micro/index.php]] from the University of Arizona imaging center. Includes links to information on optical, electron, and scanning probe microscopy.
** [[Primer on optical microscopy|http://micro.magnet.fsu.edu/primer/]] from Molecular Expressions.
** [[Optical microscopy information|http://www.microscopyu.com/articles/stereomicroscopy/]] from Nikon.
* Molecular viewing programs
** [[Rasmol|http://www.umass.edu/microbio/rasmol/]]
** [[VMD|http://www.ks.uiuc.edu/Research/vmd/]]
** [[DeepView|http://spdbv.vital-it.ch/]]
* Molecular structure databases
** [[Protein Data Bank|http://www.rcsb.org/pdb/home/home.do]] (PDB)
** [[Molecules to go|http://helixweb.nih.gov/cgi-bin/pdb]] PDB search page
** [[Nucleic Acid Database|http://ndbserver.rutgers.edu/]]
** [[Cambridge Structural Database|http://www.ccdc.cam.ac.uk/products/csd/]] of small molecules
** [[Lipid bilayer for RasMol|http://www.umass.edu/microbio/rasmol/bilayers.htm]] page
* [[Bionumbers|http://bionumbers.hms.harvard.edu/default.aspx]]: web site with quantitative information about organisms, with references. A treasure trove of useful data.
* The [[Online biology book|http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html]] by Michael Farabee has a good introduction to many biology topics.
* [[Select topics in biophysics|http://www.biophysics.org/ProfessionalDevelopment/SelectedTopicsInBiophysics/tabid/2311/Default.aspx]] from the Biophysical Society.
<<search>><<closeAll>><<permaview>><<newTiddler>><<newJournal 'DD MMM YYYY'>><<saveChanges>><<slider chkSliderOptionsPanel OptionsPanel 'options »' 'Change TiddlyWiki advanced options'>>
Phys 7810/Chem 6711/MCDB 6400
Foundations of Quantitative Biology
http://www.colorado.edu/physics/phys8810/phys8810_fa11/
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<<timeline better:true firstDay:20090815 maxDays:30 maxEntries:30>>
This course will use one primary textbook: 
Alberts, Molcular Biology of the Cell

See also the information on [[Resources]].
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<div class='subtitle' align='right'>modified <span macro='view modified date [[DD MMM YYYY]]'></span> </div>