This is for the OSU ATLAS Group, just a proof of concept so far. Very far from feature complete.

Arduino Yun 40 to 50 Channel Data Acquisition System

/*
 40 to 50 channel data acquisition
 
 TODO: Detection of optional channels 41 to 50
 TODO: Collect only when data is incoming
 
 created 09 April 2014
 by Joseph Warner
*/

#include <Bridge.h>

// Define the pins on the MUX from lsb
#define MUX_PIN_1 2
#define MUX_PIN_2 3
#define MUX_PIN_3 4
#define MUX_PIN_4 5
#define MUX_PIN_5 6
#define MUX_PIN_6 7

// Define the ADC pins from LSB
#define ADC_PIN_1 8
#define ADC_PIN_2 9
#define ADC_PIN_3 10
#define ADC_PIN_4 11

// Current channel we're getting data from
int addr = 0x0;
// Last channel currently available
int last_addr = 40;
// Time of the collection period (ms)
int collection_period = 100;

void setup() { 
  // Set MUX pins as output pins
  pinMode(MUX_PIN_1, OUTPUT);
  pinMode(MUX_PIN_2, OUTPUT);
  pinMode(MUX_PIN_3, OUTPUT);
  pinMode(MUX_PIN_4, OUTPUT);
  pinMode(MUX_PIN_5, OUTPUT);
  pinMode(MUX_PIN_6, OUTPUT);

  // Set ADC pins as input pins
  pinMode(ADC_PIN_1, INPUT);
  pinMode(ADC_PIN_2, INPUT);
  pinMode(ADC_PIN_3, INPUT);
  pinMode(ADC_PIN_4, INPUT);

  // Begin the Bridge to the Atheros processor
  Bridge.begin();
  Serial.begin(9600);

  while(!Serial);
  Serial.println("Serial data logger started\n");
}

void loop() {
  int i = 0;
  int data = 0;
  String dataString;

  // Reset addr to 0
  addr = 0;
  writeAddrToMux();
  
  // Start timing
  int startTime = millis();
  int endTime = startTime + collection_period;

  while (endTime < millis()) {
    dataString = "";
    dataString += millis() - startTime;
    dataString += ";";
    dataString += addr;
    dataString += ";";
    dataString += getDataFromAdc();
    Serial.println(dataString);
    nextAddrToMux();
  }
}

// Gets data from the ADC
int getDataFromAdc() {
  int data = 0x0;

  data ^= digitalRead(ADC_PIN_1);
  data ^= (digitalRead(ADC_PIN_1) << 1);
  data ^= (digitalRead(ADC_PIN_1) << 2);
  data ^= (digitalRead(ADC_PIN_1) << 3);

  return data;
}

// Increments the MUX to the next address
void nextAddrToMux() {
  if (addr != last_addr) {
    addr++;
  } else {
    addr = 0x0;
  }
  writeAddrToMux();
}

// Writes the current addr to the MUX
void writeAddrToMux() {
  digitalWrite(MUX_PIN_1, addr & 1);
  digitalWrite(MUX_PIN_2, addr & (1 << 1));
  digitalWrite(MUX_PIN_3, addr & (1 << 2));
  digitalWrite(MUX_PIN_4, addr & (1 << 3));
  digitalWrite(MUX_PIN_5, addr & (1 << 4));
  digitalWrite(MUX_PIN_6, addr & (1 << 5));
}