DoctorBud

//
// Examples of ways to implement a detokenize(vector<string> tokens, string delim) function,
// which will concatenate the tokens in (tokens), with (delim) inserted between, and ensuring
// that no terminal (delim) is inserted.
//
// For example:
//  detokenize( {"aaa", "bbb"}, "/" ) --> "aaa/bbb"
//
// I wrote this as an example for some of my colleagues not as familiar with modern C++.
//

DoctorBud

##"I made a program to generate dot files representing the LR(0) state graph along with computed LALR(1) lookahead for an arbitrary context-free grammar, to make the diagrams I used in this article: http://blog.lab49.com/archives/2471. The program also highlights errant nodes in red if the grammar would produce a shift/reduce or reduce/reduce conflict -- you may be able to go to http://kthielen.dnsalias.com:8082/ to produce a graph more to your liking". Contributed by Kalani Thielen.

##Command to get the layout: "dot -Gsize=10,15 -Tpng thisfile > thisfile.png"

digraph g {
  graph [fontsize=30 labelloc="t" label="" splines=true overlap=false rankdir = "LR"];
  ratio = auto;
  "state0" [ style = "filled, bold" penwidth = 5 fillcolor = "white" fontname = "Courier New" shape = "Mrecord" label =<<table border="0" cellborder="0" cellpadding="3" bgcolor="white"><tr><td bgcolor="black" align="center" colspan="2"><font color="white">State #0</font></td></tr><tr><td align="left" port="r0">&#40;0&#41; s -&gt; &bull;e 

DoctorBud

DoctorBud

Chocolate Chip Cookies (serves 12)

Ingredients:

• Eggs
• Milk
• Chips
• Sugar
• Butter
• Lotta Love

DoctorBud

Welcome to Smartdown

Smartdown is an extension of Markdown that includes several additions:

• The ability to have input, output, and calculation cells that react to user input. Smartdown's cells are similar to those in most spreadsheets.
• Additional media embedding support including Tweets, SVG, Video.
• Integration of P5JS, PlotlyJS, and a GraphViz-compatible viewer.

Math Support

Currently, Smartdown uses LaTeX-style math syntax, so the following formula:

DoctorBud

{
 "name": "flare",
 "children": [
  {
   "name": "analytics",
   "children": [
    {
     "name": "cluster",
     "children": [
      {"name": "AgglomerativeCluster", "size": 3938},

DoctorBud

Simple Example of multiple biological data source acquisition

This notebook is intended as a starting point for other researchers and domain experts to explore and experiment with various data sources and how they can be utilized to build pipelines to support a Blackboard architecture that can address important science. Our initial modest goals are to focus on the Translator competency questions and begin to incorporate and integrate those data sources we anticipate being useful.

Typical Structure

This Notebook, and those that are cloned from it, will follow a typical structure like this:

• Background

DoctorBud

DoctorBud

Sankey diagram

This Sankey diagram shows a correspondence between difference species (taxa?) and their associated Model Organism Database or other data source.

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DoctorBud

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