<!--{{{-->
<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]];}

#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]];}

.sparkline {background:[[ColorPalette::PrimaryPale]]; border:0;}
.sparktick {background:[[ColorPalette::PrimaryDark]];}

.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]];}

#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 0em 1em 1em; left:-1px; top:-1px;}
.headerForeground {position:absolute; padding:4.5em 0em 1em 1em; left:0px; top:0px;}

.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:0em 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 .3em 0;}
#sidebarTabs .tabContents {width:15em; overflow:hidden;}

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

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

.tiddlerPopupButton {padding:0.2em 0.2em 0.2em 0.2em;}
.popupTiddler {position: absolute; z-index:300; padding:1em 1em 1em 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 0em;}
.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 0em 0em 0.5em;}
.tab {margin:0em 0em 0em 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 0em 14em;}

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

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

.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:0em 0.25em; padding:0em 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:0px 3px 0px 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 0em; font-size:.9em;}
.editorFooter .button {padding-top:0px; padding-bottom:0px;}

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

.sparkline {line-height:1em;}
.sparktick {outline:0;}

.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 0.3em 0.5em;}
#backstageToolbar {position:relative;}
#backstageArea a {font-weight:bold; margin-left:0.5em; padding:0.3em 0.5em 0.3em 0.5em;}
#backstageButton {display:none; position:absolute; z-index:175; top:0em; right:0em;}
#backstageButton a {padding:0.1em 0.4em 0.1em 0.4em; margin:0.1em 0.1em 0.1em 0.1em;}
#backstage {position:relative; width:100%; z-index:50;}
#backstagePanel {display:none; z-index:100; position:absolute; margin:0em 3em 0em 3em; padding:1em 1em 1em 1em;}
.backstagePanelFooter {padding-top:0.2em; float:right;}
.backstagePanelFooter a {padding:0.2em 0.4em 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 1em;}
/* Fixes a feature in Firefox 1.5.0.2 where print preview displays the noscript content */
noscript {display:none;}
}
/*}}}*/

<!--{{{-->
<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 closeTiddler closeOthers +editTiddler > fields syncing permalink references jump'></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 +saveTiddler -cancelTiddler deleteTiddler'></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'></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>>

[img[P1010105.75percent.JPG]]
I grew up in Chelmsford, MA where I attended Chelmsford High, and I had my first employment experience stuffing bills into envelopes at a [[doctor's office|http://www.allergy-asthma.net]], long before I had heard of biomedical informatics.  At Brown University, I majored in [[Computer Science|http://www.cs.brown.edu]], but only after graduating did I start to find out about bioinformatics.  


To make up for my missing biology background, I took biology classes at Harvard Extension School while I worked a software job.  In 2004 I joined the [[Benoist-Mathis Lab| http://cbdm.joslin.harvard.edu]] at Harvard Medical school, where I had the amazing opportunity of doing a lot of the computational work to help interpret the immunological microarray data the lab was generating.  This experience convinced me to pursue my ~PhD in bioinformatics, and I was happy to join this department in 2007.

[[Here|Courses]] is a listing of courses I've taken which seem the most useful so far

![[Brown | http://www.cs.brown.edu/courses]]
Intro to Object Oriented Programming in Java
Intro to Algorithms and Data Structures
Intro to Discrete Mathematics
Models of Computation
Intro to Software Engineering
Design and Analysis of Algorithms
Linear Algebra

![[Harvard Extension | http://www.extension.harvard.edu]]
Multivariable calculus
Organic Chemistry I
Biochemistry
Immunology I
Principles of Genetics

![[Columbia|http://www.columbia.edu/cu/bulletin/uwb/]]
Molecular Systems Biology I and II
Machine Learning
Computational Biology II

!Someday, I hope
A really good statistics class...

/***
|''Name:''|CryptoFunctionsPlugin|
|''Description:''|Support for cryptographic functions|
***/
//{{{
if(!version.extensions.CryptoFunctionsPlugin) {
version.extensions.CryptoFunctionsPlugin = {installed:true};

//--
//-- Crypto functions and associated conversion routines
//--

// Crypto "namespace"
function Crypto() {}

// Convert a string to an array of big-endian 32-bit words
Crypto.strToBe32s = function(str)
{
	var be = Array();
	var len = Math.floor(str.length/4);
	var i, j;
	for(i=0, j=0; i<len; i++, j+=4) {
		be[i] = ((str.charCodeAt(j)&0xff) << 24)|((str.charCodeAt(j+1)&0xff) << 16)|((str.charCodeAt(j+2)&0xff) << 8)|(str.charCodeAt(j+3)&0xff);
	}
	while (j<str.length) {
		be[j>>2] |= (str.charCodeAt(j)&0xff)<<(24-(j*8)%32);
		j++;
	}
	return be;
};

// Convert an array of big-endian 32-bit words to a string
Crypto.be32sToStr = function(be)
{
	var str = "";
	for(var i=0;i<be.length*32;i+=8)
		str += String.fromCharCode((be[i>>5]>>>(24-i%32)) & 0xff);
	return str;
};

// Convert an array of big-endian 32-bit words to a hex string
Crypto.be32sToHex = function(be)
{
	var hex = "0123456789ABCDEF";
	var str = "";
	for(var i=0;i<be.length*4;i++)
		str += hex.charAt((be[i>>2]>>((3-i%4)*8+4))&0xF) + hex.charAt((be[i>>2]>>((3-i%4)*8))&0xF);
	return str;
};

// Return, in hex, the SHA-1 hash of a string
Crypto.hexSha1Str = function(str)
{
	return Crypto.be32sToHex(Crypto.sha1Str(str));
};

// Return the SHA-1 hash of a string
Crypto.sha1Str = function(str)
{
	return Crypto.sha1(Crypto.strToBe32s(str),str.length);
};

// Calculate the SHA-1 hash of an array of blen bytes of big-endian 32-bit words
Crypto.sha1 = function(x,blen)
{
	// Add 32-bit integers, wrapping at 32 bits
	add32 = function(a,b)
	{
		var lsw = (a&0xFFFF)+(b&0xFFFF);
		var msw = (a>>16)+(b>>16)+(lsw>>16);
		return (msw<<16)|(lsw&0xFFFF);
	};
	// Add five 32-bit integers, wrapping at 32 bits
	add32x5 = function(a,b,c,d,e)
	{
		var lsw = (a&0xFFFF)+(b&0xFFFF)+(c&0xFFFF)+(d&0xFFFF)+(e&0xFFFF);
		var msw = (a>>16)+(b>>16)+(c>>16)+(d>>16)+(e>>16)+(lsw>>16);
		return (msw<<16)|(lsw&0xFFFF);
	};
	// Bitwise rotate left a 32-bit integer by 1 bit
	rol32 = function(n)
	{
		return (n>>>31)|(n<<1);
	};

	var len = blen*8;
	// Append padding so length in bits is 448 mod 512
	x[len>>5] |= 0x80 << (24-len%32);
	// Append length
	x[((len+64>>9)<<4)+15] = len;
	var w = Array(80);

	var k1 = 0x5A827999;
	var k2 = 0x6ED9EBA1;
	var k3 = 0x8F1BBCDC;
	var k4 = 0xCA62C1D6;

	var h0 = 0x67452301;
	var h1 = 0xEFCDAB89;
	var h2 = 0x98BADCFE;
	var h3 = 0x10325476;
	var h4 = 0xC3D2E1F0;

	for(var i=0;i<x.length;i+=16) {
		var j,t;
		var a = h0;
		var b = h1;
		var c = h2;
		var d = h3;
		var e = h4;
		for(j = 0;j<16;j++) {
			w[j] = x[i+j];
			t = add32x5(e,(a>>>27)|(a<<5),d^(b&(c^d)),w[j],k1);
			e=d; d=c; c=(b>>>2)|(b<<30); b=a; a = t;
		}
		for(j=16;j<20;j++) {
			w[j] = rol32(w[j-3]^w[j-8]^w[j-14]^w[j-16]);
			t = add32x5(e,(a>>>27)|(a<<5),d^(b&(c^d)),w[j],k1);
			e=d; d=c; c=(b>>>2)|(b<<30); b=a; a = t;
		}
		for(j=20;j<40;j++) {
			w[j] = rol32(w[j-3]^w[j-8]^w[j-14]^w[j-16]);
			t = add32x5(e,(a>>>27)|(a<<5),b^c^d,w[j],k2);
			e=d; d=c; c=(b>>>2)|(b<<30); b=a; a = t;
		}
		for(j=40;j<60;j++) {
			w[j] = rol32(w[j-3]^w[j-8]^w[j-14]^w[j-16]);
			t = add32x5(e,(a>>>27)|(a<<5),(b&c)|(d&(b|c)),w[j],k3);
			e=d; d=c; c=(b>>>2)|(b<<30); b=a; a = t;
		}
		for(j=60;j<80;j++) {
			w[j] = rol32(w[j-3]^w[j-8]^w[j-14]^w[j-16]);
			t = add32x5(e,(a>>>27)|(a<<5),b^c^d,w[j],k4);
			e=d; d=c; c=(b>>>2)|(b<<30); b=a; a = t;
		}

		h0 = add32(h0,a);
		h1 = add32(h1,b);
		h2 = add32(h2,c);
		h3 = add32(h3,d);
		h4 = add32(h4,e);
	}
	return Array(h0,h1,h2,h3,h4);
};


}
//}}}

[[Welcome]]

/***
|''Name:''|DeprecatedFunctionsPlugin|
|''Description:''|Support for deprecated functions removed from core|
***/
//{{{
if(!version.extensions.DeprecatedFunctionsPlugin) {
version.extensions.DeprecatedFunctionsPlugin = {installed:true};

//--
//-- Deprecated code
//--

// @Deprecated: Use createElementAndWikify and this.termRegExp instead
config.formatterHelpers.charFormatHelper = function(w)
{
	w.subWikify(createTiddlyElement(w.output,this.element),this.terminator);
};

// @Deprecated: Use enclosedTextHelper and this.lookaheadRegExp instead
config.formatterHelpers.monospacedByLineHelper = function(w)
{
	var lookaheadRegExp = new RegExp(this.lookahead,"mg");
	lookaheadRegExp.lastIndex = w.matchStart;
	var lookaheadMatch = lookaheadRegExp.exec(w.source);
	if(lookaheadMatch && lookaheadMatch.index == w.matchStart) {
		var text = lookaheadMatch[1];
		if(config.browser.isIE)
			text = text.replace(/\n/g,"\r");
		createTiddlyElement(w.output,"pre",null,null,text);
		w.nextMatch = lookaheadRegExp.lastIndex;
	}
};

// @Deprecated: Use <br> or <br /> instead of <<br>>
config.macros.br = {};
config.macros.br.handler = function(place)
{
	createTiddlyElement(place,"br");
};

// Find an entry in an array. Returns the array index or null
// @Deprecated: Use indexOf instead
Array.prototype.find = function(item)
{
	var i = this.indexOf(item);
	return i == -1 ? null : i;
};

// Load a tiddler from an HTML DIV. The caller should make sure to later call Tiddler.changed()
// @Deprecated: Use store.getLoader().internalizeTiddler instead
Tiddler.prototype.loadFromDiv = function(divRef,title)
{
	return store.getLoader().internalizeTiddler(store,this,title,divRef);
};

// Format the text for storage in an HTML DIV
// @Deprecated Use store.getSaver().externalizeTiddler instead.
Tiddler.prototype.saveToDiv = function()
{
	return store.getSaver().externalizeTiddler(store,this);
};

// @Deprecated: Use store.allTiddlersAsHtml() instead
function allTiddlersAsHtml()
{
	return store.allTiddlersAsHtml();
}

// @Deprecated: Use refreshPageTemplate instead
function applyPageTemplate(title)
{
	refreshPageTemplate(title);
}

// @Deprecated: Use story.displayTiddlers instead
function displayTiddlers(srcElement,titles,template,unused1,unused2,animate,unused3)
{
	story.displayTiddlers(srcElement,titles,template,animate);
}

// @Deprecated: Use story.displayTiddler instead
function displayTiddler(srcElement,title,template,unused1,unused2,animate,unused3)
{
	story.displayTiddler(srcElement,title,template,animate);
}

// @Deprecated: Use functions on right hand side directly instead
var createTiddlerPopup = Popup.create;
var scrollToTiddlerPopup = Popup.show;
var hideTiddlerPopup = Popup.remove;

// @Deprecated: Use right hand side directly instead
var regexpBackSlashEn = new RegExp("\\\\n","mg");
var regexpBackSlash = new RegExp("\\\\","mg");
var regexpBackSlashEss = new RegExp("\\\\s","mg");
var regexpNewLine = new RegExp("\n","mg");
var regexpCarriageReturn = new RegExp("\r","mg");

}
//}}}

/***
|''Name:''|LegacyStrikeThroughPlugin|
|''Description:''|Support for legacy (pre 2.1) strike through formatting|
|''Version:''|1.0.2|
|''Date:''|Jul 21, 2006|
|''Source:''|http://www.tiddlywiki.com/#LegacyStrikeThroughPlugin|
|''Author:''|MartinBudden (mjbudden (at) gmail (dot) com)|
|''License:''|[[BSD open source license]]|
|''CoreVersion:''|2.1.0|
***/

//{{{
// Ensure that the LegacyStrikeThrough Plugin is only installed once.
if(!version.extensions.LegacyStrikeThroughPlugin) {
version.extensions.LegacyStrikeThroughPlugin = {installed:true};

config.formatters.push(
{
	name: "legacyStrikeByChar",
	match: "==",
	termRegExp: /(==)/mg,
	element: "strike",
	handler: config.formatterHelpers.createElementAndWikify
});

} //# end of "install only once"
//}}}

[[AllMusic | www.allmusic.com]] -- I am intermittently obsessed with this
[[LifeHacker | www.lifehacker.com]]  -- dorkily lovable
[[The Village Voice | www.villagevoice.com]]

!more professional links
[[DBMI|www.dbmi.columbia.edu]]
[[C2B2|www.c2b2.columbia.edu]]

[[About me]]
[[Research]]
[[Links]]
TiddlyWiki

<<toggleSideBar " " "show sidebar" "hide">>

<div id='header'>
<div id='titleLine'>
<span id='siteTitle' refresh='content' tiddler='SiteTitle'></span>
<span id='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>

I did my first rotation at the Califano lab, and now I'm working with Dennis Vitkup.

Hopefully I'll put more here later, but for now here are a few papers I really like:
[[Evolution of alternative transcriptional circuits with identical logic|http://www.ncbi.nlm.nih.gov/pubmed/17006507?dopt=AbstractPlus]]
[[Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data | http://www.sciencemag.org/cgi/content/full/308/5721/523]]
[[Identifying metabolic enzymes with multiple types of association evidence | http://vitkuplab.cu-genome.org/html/papers/Kharchenko_bmc_06.pdf]]

Dept of Biomedical Informatics / Center for Computational Biology & Bioinformatics

Rachel Melamed

/***
|''Name:''|SparklinePlugin|
|''Description:''|Sparklines macro|
***/
//{{{
if(!version.extensions.SparklinePlugin) {
version.extensions.SparklinePlugin = {installed:true};

//--
//-- Sparklines
//--

config.macros.sparkline = {};
config.macros.sparkline.handler = function(place,macroName,params)
{
	var data = [];
	var min = 0;
	var max = 0;
	var v;
	for(var t=0; t<params.length; t++) {
		v = parseInt(params[t]);
		if(v < min)
			min = v;
		if(v > max)
			max = v;
		data.push(v);
	}
	if(data.length < 1)
		return;
	var box = createTiddlyElement(place,"span",null,"sparkline",String.fromCharCode(160));
	box.title = data.join(",");
	var w = box.offsetWidth;
	var h = box.offsetHeight;
	box.style.paddingRight = (data.length * 2 - w) + "px";
	box.style.position = "relative";
	for(var d=0; d<data.length; d++) {
		var tick = document.createElement("img");
		tick.border = 0;
		tick.className = "sparktick";
		tick.style.position = "absolute";
		tick.src = "data:image/gif,GIF89a%01%00%01%00%91%FF%00%FF%FF%FF%00%00%00%C0%C0%C0%00%00%00!%F9%04%01%00%00%02%00%2C%00%00%00%00%01%00%01%00%40%02%02T%01%00%3B";
		tick.style.left = d*2 + "px";
		tick.style.width = "2px";
		v = Math.floor(((data[d] - min)/(max-min)) * h);
		tick.style.top = (h-v) + "px";
		tick.style.height = v + "px";
		box.appendChild(tick);
	}
};


}
//}}}

/***
Included Styles
***/
/*{{{*/
[[Styles TagglyTagging]]
[[Styles HorizontalMainMenu]]
[[Styles MessageArea]]
[[Styles SideBarOptions]]
[[Styles Calendar]]
[[Styles Editor]]
[[Styles Breadcrumbs]]
/*}}}*/

/***
Cosmetic fixes
***/
/*{{{*/
h1,h2,h3,h4,h5 { color: #000; background: #f6f6ff;  padding-top: 2px; padding-bottom:0px;}

body { 
  background: #333366; }
.selected .tagging, .selected .tagged {
  padding: 0.5em;
  background-color: #eee;
  border-top:    1px solid #ccc; 
  border-left:   1px solid #ccc; 
  border-bottom: 3px solid #ccc; 
  border-right:  3px solid #ccc; 
  -moz-border-radius: 1em; }


.shadow .title {
  color: #999; }

.siteTitle {
  font-size: 2.5em; }

.siteSubtitle {
  font-size: 1.0em; }

.tabSelected{
  padding-top: 0.0em;
  padding-left: 1em;
  padding-right: 1em;
  -moz-border-radius-topleft: 0.5em; 
  -moz-border-radius-topright: 0.5em;}

.tabUnselected {
  padding-top: 0.0em;
  padding-left: 1em;
  padding-right: 1em;
  -moz-border-radius-topleft: 0.5em; 
  -moz-border-radius-topright: 0.5em;}

.tabContents {
  margin: 0px;
  padding-top: 0px;
  padding-bottom: 0px;
  padding-left: 2px;
  padding-right: 2px;
  -moz-border-radius: 1em; }

.tagging, .tagged {
  padding: 0.5em;
  background-color: #eee;
  border-top:    1px solid #ccc; 
  border-left:   1px solid #ccc; 
  border-bottom: 3px solid #ccc; 
  border-right:  3px solid #ccc; 
  -moz-border-radius: 1em; }

.tiddler {
  border-top:    1px solid #ccc; 
  border-left:   1px solid #ccc; 
  border-bottom: 3px solid #ccc; 
  border-right:  3px solid #ccc; 
  margin: 0.5em; 
  background:#fff; 
  color: #000;
  padding: 0.5em; 
  -moz-border-radius: 1em; }

.title {
  color:black; 
  font-size: 2em; }

.viewer .listTitle { 
  list-style-type: none; 
  margin-left: -2em; }

.viewer pre { 
  background-color: #f8f8ff; 
  border-color: #ddf;}

/** Width of tiddlers */
#displayArea {
	width: 55.75em;
 margin: 0 0 0 17em;
}
/** Shadow effect maybe? */
.tiddler {
	margin: 0 0 .9em 0;
        margin-bottom:2em;
}
#mainMenu{
 width: 19;
 text-align: left;
 color: #ccff99;
}

#mainMenu .tiddlyLinkExisting, 
#mainMenu .tiddlyLinkNonExisting { 
  color: #ccff99; 
  font-weight: bold;
}

.headerShadow {
  padding: 1.0em; }

.headerForeground {
  padding: 1.0em; }

.siteTitle {
  font-size: 2.5em;
}
.siteSubtitle {
  font-size: 1.0em; }
#header
{
	color: #ccff99;
	padding: 1.5em 1em .6em 0;
}
#siteTitle {

	font-size: 2.3em;
 margin: 0;
padding-left: .2em;
}

#siteSubtitle {
	font-size: 1.4em;
	padding-left: .8em;;
}

#titleLine{
 background: transparent;
 padding: 0;
}

#titleLine a {
    color: #cf6;
 background: #333366;
}
/*}}}*/

/***
Styles Editor
***/
/*{{{*/
.editor textarea {height:200px;background-color:#F2F2F2;}

.editorFooter .button { 
  padding-top: 0px; 
  padding-bottom:0px; 
  background: #fff;
  color: #000; 
  border-top:    1px solid #ccc; 
  border-left:   1px solid #ccc; 
  border-bottom: 2px solid #ccc; 
  border-right:  2px solid #ccc; 
  margin-left: 3px;
  padding-top: 1px;
  padding-bottom: 1px;
  padding-left: 5px;
  padding-right: 5px; }
  
.editorFooter .button:hover { 
  border-top:    2px solid #ccc; 
  border-left:   2px solid #ccc; 
  border-bottom: 1px solid #ccc; 
  border-right:  1px solid #ccc; 
  margin-left: 3px;
  padding-top: 1px;
  padding-bottom: 1px;
  padding-left: 5px;
  padding-right: 5px; }
/*}}}*/

/***
To use, add {{{[[Styles HorizontalMainMenu]]}}} to your StyleSheet tiddler, or you can just paste the CSS in directly. See also HorizontalMainMenu and PageTemplate.
***/
/*{{{*/

#topMenu br {display:none; }
#topMenu { background: #39a; }
#topMenu { padding:2px; }
#topMenu .button,  #topMenu .tiddlyLink { padding-left:1em; padding-right:1em; color:white; font-size:115%;}
#displayArea { margin: 1em 15.7em 0em 1em; }

/* just in case want some QuickOpenTags in your topMenu */
#topMenu .quickopentag { padding:0px; margin:0px; border:0px; }
#topMenu .quickopentag .tiddlyLink { padding-right:1px; }
#topMenu .quickopentag .button { padding-left:1px; border:0px; }


/*}}}*/

/***
Styles SideBarOptions
***/
/*{{{*/
#sidebarOptions .sliderPanel {
  border: 0px solid #ccc; 
  background-color: #eee;
  margin: 0px;
  margin-left: 0.5em;
  padding: 0px;
  -moz-border-radius: 1em; }

#sidebarOptions .sliderPanel .tabSelected{
  border: 1px solid #ccc; 
  background-color: #fff;
  margin: 0px;
  padding-top: 5px;
  padding-bottom: 0px;
  padding-left: 2px;
  padding-right: 2px;
  -moz-border-radius-topleft: 1em; 
  -moz-border-radius-topright: 1em;}

#sidebarOptions .sliderPanel .tabUnselected{
  border:    1px solid #ccc; 
  background-color: #eee;
  margin: 0px;
  padding-top: 5px;
  padding-bottom: 0px;
  padding-left: 2px;
  padding-right: 2px;
  -moz-border-radius-topleft: 1em; 
  -moz-border-radius-topright: 1em;}

#sidebarOptions { 
  border-top:    1px solid #ccc; 
  border-left:   1px solid #ccc; 
  border-bottom: 3px solid #ccc; 
  border-right:  3px solid #ccc; 
  padding: 0.5em; 
  margin: 0.5em; 
  -moz-border-radius: 1em; }

#sidebarOptions .button {
  margin: 1px;
  border-color:white;
  color:#fff;
  border-top:    1px solid #ccc; 
  border-left:   1px solid #ccc; 
  border-bottom: 2px solid #ccc; 
  border-right:  2px solid #ccc; 
}

#sidebarOptions .button:hover {
  color: #000;
  background: #000
  border-top:    2px solid #ccc; 
  border-left:   2px solid #ccc; 
  border-bottom: 1px solid #ccc; 
  border-right:  1px solid #ccc; 
}

#sidebarOptions .button:active {
  color: #fff;
  background: #000
}
/*}}}*/

/***
To use, add {{{[[Styles TagglyTagging]]}}} to your StyleSheet tiddler, or you can just paste the CSS in directly. See also ViewTemplate, EditTemplate and TagglyTagging.
***/
/*{{{*/
.tagglyTagged li.listTitle { display:none;}
.tagglyTagged li { display: inline; font-size:90%; }
.tagglyTagged ul  { margin:0px; padding:0px; }
.tagglyTagging { padding-top:0.5em; }
.tagglyTagging li.listTitle { display:none;}
.tagglyTagging ul  { margin-top:0px; padding-top:0.5em; padding-left:2em; margin-bottom:0px; padding-bottom:0px; }

/* .tagglyTagging .tghide { display:inline; } */

.tagglyTagging .button { display:none;  margin-left:3px; margin-right:3px; }
.tagglyTagging .button, .hidebutton  { color:#aaa; font-size:90%; border:0px; padding-left:0.3em;padding-right:0.3em;}
.tagglyTagging .button:hover, .hidebutton:hover { background:#eee; color:#888; }
.selected .tagglyTagging .button { display:inline; }

.tagglyLabel { color:#aaa; font-size:90%; }


.editLabel { font-size:90%; padding-top:0.5em; }
/*}}}*/

This website is a [[TiddlyWiki|http://www.tiddlywiki.com/]].  I dont know anything about web design but played around with the base template using some tips from [[tiddlywikitips |http://tiddlywikitips.com/]] and a [[tiddly tutorial|http://www.blogjones.com/TiddlyWikiTutorial.html]]. Hopefully this entirely gratuitous use of the awesome ~TiddlyWiki will encourage me to add some more content at some point.

I'm a first year student in the Department of Biomedical Informatics with an interest in bioinformatics and especially systems biology.  Right now I'm taking a lot of courses but hopefully I'll have more interesting information for this page in the future. For now here's a picture of the view of the George Washington bridge last fall.
[img[gw.fall.JPG]]

config.macros.toggleSideBar={};

config.macros.toggleSideBar.settings={
         styleHide :  "#sidebar { display: none;}\n"+"#contentWrapper #displayArea { margin-right: 1em;}\n"+"",
         styleShow : " ",
         arrow1: "«",
         arrow2: "»"
};

config.macros.toggleSideBar.handler=function (place,macroName,params,wikifier,paramString,tiddler)
{
          var tooltip= params[1]||'toggle sidebar';
          var mode = (params[2] && params[2]=="hide")? "hide":"show";
          var arrow = (mode == "hide")? this.settings.arrow1:this.settings.arrow2;
          var label= (params[0]&&params[0]!='.')?params[0]+" "+arrow:arrow;
          var theBtn = createTiddlyButton(place,label,tooltip,this.onToggleSideBar,"button HideSideBarButton");
          if (mode == "hide")
             { 
             (document.getElementById("sidebar")).setAttribute("toggle","hide");
              setStylesheet(this.settings.styleHide,"ToggleSideBarStyles");
             }
};

config.macros.toggleSideBar.onToggleSideBar = function(){
          var sidebar = document.getElementById("sidebar");
          var settings = config.macros.toggleSideBar.settings;
          if (sidebar.getAttribute("toggle")=='hide')
             {
              setStylesheet(settings.styleShow,"ToggleSideBarStyles");
              sidebar.setAttribute("toggle","show");
              this.firstChild.data= (this.firstChild.data).replace(settings.arrow1,settings.arrow2);
              }
          else
              {    
               setStylesheet(settings.styleHide,"ToggleSideBarStyles");
               sidebar.setAttribute("toggle","hide");
               this.firstChild.data= (this.firstChild.data).replace(settings.arrow2,settings.arrow1);
              }

     return false;
}

setStylesheet(".HideSideBarButton .button {font-weight:bold; padding: 0 5px;}\n","ToggleSideBarButtonStyles");