February 28 notes

2014-02-24

Script to download all files from SRA archive in fastq format

Working code to trigger LED/buzzer when laser beam is broken.

const int PHOTOCELL_PIN = A0;
const int BUZZER_PIN = 3;
// voltage readings are in 0-1023 range
const int THRESHOLD = 500;

void setup() {
  pinMode(PHOTOCELL_PIN, INPUT);
  Serial.begin(9600);
}

long alarmEndTime = 0;

void loop() {
  int level = analogRead(PHOTOCELL_PIN);
  Serial.println(level);
  long time = millis();
  if (time < alarmEndTime) {
    long timeLeft = alarmEndTime - time;
    if (timeLeft % 1000 > 300) {
      tone(BUZZER_PIN, 4000);
    } else {
      noTone(BUZZER_PIN);
    }
  } else {
    noTone(BUZZER_PIN);
    if (level < THRESHOLD) {
      alarmEndTime = time + 3000;
    }
  }
}

Pseudo-code to add camera

const int PHOTOCELL_PIN = A0;
const int CAMERA_PIN = 3;
// voltage readings are in 0-1023 range
const int THRESHOLD = 500;

void setup() {
  pinMode(PHOTOCELL_PIN, INPUT);
  Serial.begin(9600);
}

long alarmEndTime = 0;

void loop() {
  int level = analogRead(PHOTOCELL_PIN);
  Serial.println(level);
  long time = millis();
  if (time < alarmEndTime) {
    long timeLeft = alarmEndTime - time;
    if (timeLeft % 1000 > 300) {
//      TAKE PICTURE;
//      SAVE PICTURE TO microSD shield;
    } else {
      noTone(CAMERA_PIN);
    }
  } else {
    noTone(CAMERA_PIN);
    if (level < THRESHOLD) {
      alarmEndTime = time + 3000;
    }
  }
}

Helms Cahan lab meeting

Discussed ApTranscriptome manuscript. Good ideas for improved analyses and figures!

Other

Finished review for Molecular Ecology

2014-02-28

Workstation alarm still going…backup in progress

CCThermBe

Heat shocked ‘blue’ ant group

Meet with Grace to work on beam braker

ApTranscriptome

Working on analyses discussed yesterday

Reading

Fu, X., Sun, Y., Wang, J., Xing, Q., Zou, J., Li, R., Wang, Z., Wang, S., Hu, X., Zhang, L. & Bao, Z. (2014). Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri. Molecular Ecology Resources, 14, 184–198.

interesting and clear use of network analysis
identifies Hsp90 as a ‘hub’ which we also find in Aphaenogaster!
seems like they could have used regression approach with time-series dat