Embedded Ruby

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Slide 1

MBARI 2005

Embedding Ruby into a Robotic MarineEmbedding Ruby into a Robotic Marine

LaboratoryLaboratory

Brent Roman,

Christopher A. Scholin, Dianne I. Greenfield

Monterey Bay Aquarium Research Institute

www.mbari.org


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Slide 2

MBARI 2005

About MBARIAbout MBARIMonterey Bay Aquarium Research Institute

Part of our stated mission is to develop betterinstruments, systems, and methods for scientificresearch in the deep waters of the ocean

Founded in 1987 by David Packard of HP Funded largely by the Packard Foundation

Employs >200 in Moss Landing, CA


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Slide 3

MBARI 2005

What it does

How it works

Current applications

Future directions

Ruby's Central Role

MBARI's 2MBARI's 2ndnd

GenerationGeneration

Environmental Sample ProcessorEnvironmental Sample Processor


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Slide 4

MBARI 2005A.C. Hardy. 1936. Discovery Reports Vol. XI, pp. 457-510.A.C. Hardy. 1936. Discovery Reports Vol. XI, pp. 457-510.

Machines to collect microbes are not new

Continuous Plankton

Recorder (CPR)

First deployed on the R.R.S.

Discovery 1925-27.

Design driven by need todocument patchiness of

zooplankton

Many modifications over the

years

took ~10 yrs to become

operational

A.C. Hardy. 1936. Discovery Reports Vol. XI, pp. 457-510.A.C. Hardy. 1936. Discovery Reports Vol. XI, pp. 457-510.


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Slide 5

MBARI 2005

Functional Requirements for Instruments that

Detect Microorganisms and Gene Products

Sample collection

Cell concentration, preservation and disruption

Separation of molecules based on physical properties

Use of intermolecular reactions to reveal target molecules

lectin/carbohydrate

antibody/antigen

nucleic acid hybridization receptor/target

enzyme mediated processing

Optical and electrochemical signal transduction common

Functional Requirements for Instruments that

Detect Microorganisms and Gene Products

Sample collection

Cell concentration, preservation and disruption

Separation of molecules based on physical properties

Use of intermolecular reactions to reveal target molecules

lectin/carbohydrate

antibody/antigen

nucleic acid hybridization receptor/target

enzyme mediated processing

Optical and electrochemical signal transduction common


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Slide 6

MBARI 2005

The Environmental Sample Processor (ESP)The Environmental Sample Processor (ESP) Rotating carousel with 100, 25mm pucks holding user-defined

filters or solid phase media

Fluid handling system permitsautonomous collection of samplesand timed application of multiplereagents in situ, subsurface

Sample processing protocolswritten as a series of simplecommands such as Load Filter,Pullx ml reagenty, heatzoC30 min, etc.

Two-way communication


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Slide 7

MBARI 2005

Environmental Sample Processor MooringEnvironmental Sample Processor Mooring


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MBARI 2005


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MBARI 2005

Functions of the ESP

Development of DNA probe arrays (near real-time)

collect sample create cell homogenate

discharge sample collection filter > load probe array filter

develop probe array > image > transmit result

Sample Archival for whole cell analysis (probes, microscopy)

for nucleic acids (gene libraries)

for toxins (domoic acid)

Whole Cell Hybridization(FISH -- Fluorescent In-Situ Hybridization) collect, fix sample

label target species with probes

recover filter and view using epifluorescence microscopy

Functions of the ESP

Development of DNA probe arrays (near real-time)

collect sample create cell homogenate

discharge sample collection filter > load probe array filter

develop probe array > image > transmit result

Sample Archival for whole cell analysis (probes, microscopy)

for nucleic acids (gene libraries)

for toxins (domoic acid)

Whole Cell Hybridization(FISH -- Fluorescent In-Situ Hybridization) collect, fix sample

label target species with probes

recover filter and view using epifluorescence microscopy


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MBARI 2005

controls/orient image

16,000

cells/ml

lysateP.

australis

27 28 29

23 26 30 31 32

20 22 25 33 34 35 36

19 21 24 6 3 1

18 17 16 15 7 4 2

14 13 12 8 5

11 10 9

auD1 muD2 NA-1 HET1

Heterosigmaakashiwo

Alexandrium

catenella

Pseudo-nitzschia

australis

Pseudo-nitzschiamultiseries

Array map species/group specific DNA probes

Sandwich hybridization assay (SHA) chemistry

Image stored & sent to shore via radio modem

ESP's DNA Probe ArraysESP's DNA Probe Arrays


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MBARI 2005

The Sandwich Hybridization AssayThe Sandwich Hybridization Assay

18S rRNA

rRNA-targeted capture

probe (streptavidin)

signal probe

(dioxygenin)

HRP conjugate

enzyme

substrate

Verification

by matching

96-well bench

run

Imaged

array

array spot intensity

absorbance (450 nm)

Photo courtesy of A. Haywood

rRNA-targeted capture

probe (streptavidin)

signal probe

(dioxygenin)

HRP conjugate

enzyme

substrate

Verification

by matching

96-well bench

run

Imaged

array

array spot intensity

absorbance (450 nm)

Photo courtesy of A. Haywood

HRP = Horse Radish Peroxidase


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MBARI 2005


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MBARI 2005

Current ApplicationsCurrent Applications

Develop DNA probe arrays (~2 h) for identification of:

Harmful Algal Blooms (plankton)

Bacteria

Invertebrate Larvae

Sample archival to preserve cell structure

whole cell archival

(FISH) hybridization

Domoic acid analysis (in progress)

Current ApplicationsCurrent Applications

Develop DNA probe arrays (~2 h) for identification of:

Harmful Algal Blooms (plankton)

Bacteria

Invertebrate Larvae

Sample archival to preserve cell structure

whole cell archival

(FISH) hybridization

Domoic acid analysis (in progress)


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MBARI 2005

Future DirectionsFuture Directions

Deep ESP: Deploy on Ocean Bottom at >2000m

The 2G ESP is a sampling tool - protocols can be

tailored for user requirements

Modifying chemistry as appropriateDevelopment of new probes

Adjusting sampling procedures

Other uses?

Complete in situ domoic acid analysis methodology

Increase array sensitivity

Integrate PCR module


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MBARI 2005

NASA ASTEP: Astrobiology Science and Technology for Exploring Planets


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MBARI 2005

AcknowledgmentsAcknowledgments

The David and Lucile Packard Foundation

National Oceanographic Partnership Program (NOPP) funds allocatedby the National Science Foundation (NSF OCE-0314222)

R. Marin III, S. Jensen, A. Haywood, C. Preston, M. Adachi, T. Walsh,

J. Jones, C. Braby, A. Gough


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MBARI 2005

Why Choose Ruby for anembedded system like ESP?

Can be configured to run in small memory footprint

Open Source Universities have cheap labor and little $$$

We can fix (or break) it ourselves as we see fit

Readable, but terse syntax No white space rules and no excess punctuation

Make it suitable for use as an interactive shell

Useful subset of Ruby is approachable for non-programmers

Everything is an Object! But, no OO baggage creeps into procedural definitions.

Most molecular biologists don't get OO. They write recipes.

User defined Exception Objects

Multi-Threading

Why Choose Ruby for anembedded system like ESP?

Can be configured to run in small memory footprint

Open Source Universities have cheap labor and little $$$

We can fix (or break) it ourselves as we see fit

Readable, but terse syntax No white space rules and no excess punctuation

Make it suitable for use as an interactive shell

Useful subset of Ruby is approachable for non-programmers

Everything is an Object! But, no OO baggage creeps into procedural definitions.

Most molecular biologists don't get OO. They write recipes.

User defined Exception Objects

Multi-Threading


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MBARI 2005

ESP Software Overview

Mission

Hardware

System Libraries

User Libraries

Device Drivers

Device Models

via I2C Gateway

Simulation Normal Operation


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MBARI 2005

2nd Generation ESPElectrical Block Diagram

PC/104

Host Processor

Interconnect /Motherboard

5V & 3.3V Power Supplies

Sampler

Collection

Process

Manipulator

Storage

I2C

ContextualSensors

3 x RS-232

External

Power 10 - 16V

RFModem

Analytical Modules

3 x RS-232

RS-232

Serial Bus

Distributed Controllersaka Dwarves

~2 Watts

~450 mW


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MBARI 2005

2G ESPPC/104 Host Processor

Inexpensive (


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MBARI 2005

Trimming Ruby

Fitting Linux/Ruby in 16MB flash requires some thought

Use of JFFS2 filesystem compresses flash by ~40% But, Linux kernel takes 2MB leaving 14MB

Ruby core interpreter is small ( ~ 500kByte )

Native code libraries are large (~8MB base install!)

Pure Ruby ASCII code is extremely compact! Avoid use of Native Libraries in favor of pure Ruby

Example: curses.so links with libcurses.so, libterm.so

Curses support brings in close to 1MB of binary

Hack core Makefile to skip building unneeded libraries

Removed tcltk, tk & curses from Ruby 1.68 build

Reduced /usr/lib/ruby to


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R b Th d


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Slide 28

MBARI 2005

Ruby Threads:More Bad

Thread.sleep does not clear Thread.critical

Ruby code cannot clear Thread.critical before sleeping

Just as one can't clear it explicitly before Thread.stop

Another thread my run between the clear & stop

This is why Thread.stop clears Thread.critical

My solution was to add the 'C' extension: Thread.doze

Just like .sleep, but clears Thread.critical first

Is there any reason Thread.sleep should not be changed?

Could one ever want to sleep with Thread.critical set?!

BTW -- there is a similar issue with the select method...

See ruby-core:4053


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