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Revision as of 10:45, 23 June 2013
Notes on hardware of interest:
- 19,8 x 12,0 cm
- 340 g
- 1 GB RAM
- 1,2 Ghz quad-core CPU
Pris: ~ 2000 NOK (uten 3G)
- 26,4 x 17,8 cm
- 2 GB RAM
- 1,7 Ghz dual-core CPU
- 603 g
- 24,12 x 18,57 cm
Pris: ~ 3600 NOK
POGO Oligonucleotide synthesizer: http://www.bioinformatics.org/pogo/
DIY scanning Electron microscope: http://benkrasnow.blogspot.nl/2011/03/diy-scanning-electron-microscope.html
DIY Bioprinter: http://www.instructables.com/id/DIY-BioPrinter/?ALLSTEPS
Tekla labs - research grade DIY instructables: http://guides.teklalabs.org/
Automated fluid handling
Tecan Infinite 200 PRO: http://www.tecan.com/platform/apps/product/index.asp?MenuID=1812&ID=1916&Menu=1&Item=220.127.116.11
- Measurments of absorbance and fluorescence in 96-well plate and cuvette
- Temperature control and shaking
Infinite 200 downloads: http://www.tecan.com/platform/apps/product/index.asp?MenuID=1816&ID=1922&Menu=1&Item=18.104.22.168.4
Fluorescence-Based DNA Quantification in Small Volume Samples : http://www.tecan.com/platform/apps/checkdoc/index.asp?doc_Id=708,148&prot=1,1
Tweaking fluorescence scans: http://www.tecan.com/platform/apps/checkdoc/index.asp?doc_Id=1719,276&prot=1,1
Improved Detection of Green Fluorescent Protein (GFP) in the Infinite® 200 PRO: http://www.tecan.com/platform/apps/checkdoc/index.asp?doc_Id=1031,148&prot=1,1
The BioRad Gene Pulser II electroporation system requires the Gene Pulser II Core unit and an acessory unit (Pulse Controller II or Capacitance Extander) The BioRad Gene Pulser II core unit (110 V) has been spotted on sale for 400 USD on EBay: http://www.ebay.com/itm/Bio-Rad-BioRad-Gene-Pulser-II-2-Apparatus-340BR-/290868541376?pt=LH_DefaultDomain_0&hash=item43b91db7c0 Shipping (~200 USD) and import tax would bring total cost to ~ 4500 NOK.
Pulse Controller spotted for ~200 USD:
Recent development in low-cost electroporation: http://www.eurekalert.org/pub_releases/2013-02/f-sf-asb020713.php Appears to be only usable for electroporation of adherent cells.
List price for BioRad MicroPulser electroporator is 20 000 NOK: http://www.bio-rad.com/prd/en/NO/adirect/biorad?ts=1&cmd=BRCatgProductDetail&vertical=LSR&catID=83527990-34fb-4b33-b955-ca53b57bf8b9
- Used in majority of smartphones.
Single-board microcontroller based on Atmel's ATMEGA8 and ATMEGA168 AVR microcontrollers. Arduino is a fork from the Wiring development platform.
10 ways to destroy an arduino: http://www.ruggedcircuits.com/html/ancp01.html
Language reference: http://arduino.cc/en/Reference/HomePage
Power supply: http://playground.arduino.cc/Learning/WhatAdapter
- 9-12 V DC
- Minimum 250 mA, recommended 500mA - 1A.
- 2.1 mm power plug, centre positive
Arduino products: http://arduino.cc/en/Main/Products
Getting started: http://arduino.cc/en/Guide/HomePage
- Runs on Windows, Macintosh OSX, and Linux operating systems.
MAKE Magazine - Arduino section: http://blog.makezine.com/category/arduino/
MAKE Magazine Arduino blog: http://blog.makezine.com/arduino/
Clones and derivate products:
SimDuino, an iPad Arduino simulator: http://arduino.cc/forum/index.php/topic,107629.0.html
Official Arduino boards:
- Microcontroller board based on ATmega328.
- Can be powered by USB or external power supply.
- 14 digital input/output pins, 6 analog inputs. 16 MHz ceramic resonator.
Arduino Mini: http://arduino.cc/en/Main/ArduinoBoardMini
Arduino Mega 2560:
- 54 digital input/output pins, 16 analog inputs.
- Compatible with most shields designed for the Arduino Duemilanove or Diecimila.
Digit shield: http://www.makershed.com/Digit_Shield_Green_p/mkntd3.htm
Networking & communication:
GPS shield: http://www.ladyada.net/make/gpsshield/
GSM/GPRS and GPS shield: http://store.open-electronics.org/?_route_=/Arduino/Shield/GSM_GPRS_GPS_SHIELD
Lithium backpack: http://www.liquidware.com/shop/show/MBP/Lithium+Backpack
MicroSD shield: http://www.sensor-networks.org/index.php?page=0827727742
- Sketch: The term for an Arduino program. A unit of code that is uploaded and run on an Arduino board. Sketches are saved with the file extension .ino.
- Shields: Printed circuit expansion boards called "shields" can be plugged into the Arduino pin-headers to provide specialized functions such as GPS, ethernet, LCD display etc.
The Arduino programming environment is based on the Processing programming environment (http://www.processing.org/).
The Arduino language is based on C/C++. After processing, Arduino codes is handed of to a C/C++ compiler (avr-g++).
Because Arduino uses Atmel's microprocessors, Atmels development environments AVR Studio and Atmel Studio may also be used for software development. Functions/methods:
Building Research Equipment with Free, Open-Source Hardware: http://www.sciencemag.org/content/337/6100/1303.summary
ArduPilot Mega - Arduino-based autopilot: http://code.google.com/p/ardupilot-mega/wiki/APM2board
Programming Arduino: Getting started with Sketches: http://www.amazon.com/Programming-Arduino-Getting-Started-Sketches/dp/0071784225/ref=sr_1_3?ie=UTF8&qid=1366760346&sr=8-3&keywords=Arduino
Practical Arduino: Cool projects for open source hardware: http://www.amazon.com/Practical-Arduino-Projects-Hardware-Technology/dp/1430224770/ref=tag_dpp_lp_edpp_ttl_in
Costs $100, free shipping.
Getting Started with Arduino Kit v3.0: http://www.makershed.com/Getting_Started_with_Arduino_Kit_V3_0_p/msgsa.htm
Costs ~ 80€. ( + shipping + import duty)
Adafruit Budget Pack for Arduino (Arduino Uno R3) - Uno w/328: http://www.adafruit.com/products/193
Adafruit Starter Pack for Arduino (Includes Arduino Uno R3) - 1.0: http://www.adafruit.com/products/68
Sparkfun Inventors Kit (SIK) solgt av Robonor, for NOK 889,-
- Boots from SD card (Not included in price). Minimum size 2 GB. Minimum 4GB recommended. Pre-loaded SD cards can be bought. (for example: http://www.amazon.co.uk/For-Raspberry-preloaded-operating-partitioned/dp/B008IU78EK) If not, an SD card reader is needed to prepare the card. High-speed category 4 is recommended. See http://elinux.org/RPi_Easy_SD_Card_Setup and http://elinux.org/RPi_SD_cards
- Programs must be compilable for ARMv6 architecture. (Windows/x86 not supported)
- Video output through HDMI or Composite. No VGA.
- Power through micro USB port. Standard phone charger with micro USB plug can be used (minimum 700mA at 5 volts).
- No Real Time Clock (RTC) on board. Time is updated over internet after each boot.
- Not all peripherals (keyboards, mice, etc.) may work (may draw too much power). See http://elinux.org/RPi_VerifiedPeripherals
- Two models: A and B. B model draws 3.5 W, the A model 2 W.
- B model specifications: 700 Mhz ARM1, 256 MB SDRAM
Official downloads: http://www.raspberrypi.org/downloads
Official forum - basic setup and usage: http://www.raspberrypi.org/phpBB3/viewforum.php?f=26
Unofficial wiki: http://elinux.org/RPi_Hub
Buying guide: http://elinux.org/RPi_Buying_Guide
Introducing the raspberry pi - getting started: http://www.h2g2.com/approved_entry/A9143796
Introducing the raspberry pi - peripherals you'll need: http://www.h2g2.com/approved_entry/A13413584
Raspberry Pi Stack exchange: http://raspberrypi.stackexchange.com/
The Pi Hut - accessories: http://thepihut.com/
"The true cost of Raspberry Pi - essential accessories": http://www.penguintutor.com/blog/viewblog.php?blog=6354
Gotcha's and new users tips: http://www.keyboardmaven.com/2013/04/raspberry-pi-gotchas-and-newbiebuyer.html
Gray Girling: Rapsberry Pi Owners workshop manual: http://www.amazon.co.uk/Raspberry-Pi-Manual-practical-revolutionary/dp/0857332953
Mike McGrath: Raspberry Pi in easy steps: http://www.amazon.com/Raspberry-Easy-Steps-Mike-McGrath/dp/1840785810
Review of Raspberry pi books: http://www.theregister.co.uk/2013/04/18/feature_getting_into_the_raspberry_pi_books/
Richardson & Wallace. Getting Started with Raspberry Pi. Published December 2012: http://shop.oreilly.com/product/0636920023371.do
Upton & Halfacree: Raspberry Pi User Guide: http://www.amazon.com/Raspberry-User-Guide-Gareth-Halfacree /dp/111846446X Published September 2012. Somewhat dated already?
News and reviews:
See also: http://reprap.org/wiki/PrintingMaterials
Food safe printing:
Solidoodle 3D printer 3d generation: http://store.solidoodle.com/index.php?route=product/product&product_id=79
- 799 USD
Solidoodle 3D printer 2nd generation: http://store.solidoodle.com/index.php?route=product/product&product_id=56
- 499 USD
Makerbot Replicator 2: http://store.makerbot.com/replicator2.html
- 2200 $ USD
- 200 USD. Uses PLA filament. 6-10 weeks lead time.
Reviews and discussion
DAVID 3D Scanner
FabScan hardware: https://hci.rwth-aachen.de/fabscan_hardware
FabScan 100 Linux Version: https://groups.google.com/forum/?fromgroups=#!topic/fabscan/oIMZYx_utjo
FabScan Arduino shield: http://hci.rwth-aachen.de/fabscan_shield
Objective: Obtain automatation and decreased variability in the handling of cells during heat-shock transformation.
Input materials: Eppendorf tubes (containing supercompetent cells or DNA), water, ice, sterile liquid growth medium, pipette tips. Should perform: Add DNA, heat shock, addition of medium, incubation. Should produce: Transformed cells ready for plating out.
Technical requirements: Must be able to open and close eppendorf tubes. Must be able to regulate temperature for heat shock and incubation chambers/water baths. Must be able to transfer all tubes simultaneously. Must be able to transfer tubes rapidly between ice bath and heat shock bath.
Challenges: Opening/closing tubes. Tubes must be kept firmly in place when opening/closing lids. Either lid closing/opening operation must be very reliable, or the machine must be able to detect a failure to correctly open/close all lids (the latter option probably hard to implement).
Idea: Place all tubes in a single row on a movable rack (movable in direction y). For adding DNA and medium, use two standard autopipettes (volume must be adjusted manually) mounted to the side (direction x) of the rack. Use an overhead rail to move the pipettes over the tubes, using a stepper motor to ensure that the pipette stops at the correct position above each tube. Two additional motors are needed to operate the pipette: One to push the piston, and one to operate the pipette-tip discard mechanism. Use a lifting mechanism and rail system to move the rack between the water baths.
To open/close the tubes, use one or several metal or plastic bars mounted along the tube rack so that the lids rest on the bar (all tubes must be placed on the rack with the lid in the right orientation), the bar being connected to a rotation mechanism, which when rotated causes the lids to be opened. A similar mechanism can be used to close the tubes. For this to work, the tubes must be kept firmly in place and be well supported from below (otherwise, tubes will be pushed downwards without the lid closing properly).
Questions: How can the pipettes be moved? How can the rack be moved between the bath?
Motors Temperature sensors Heating elements Rails and movement mechanisms
Input materials: Plastic petri dishes with agar, sterile glass beads, eppendorf tubes containing cells.
Core functionality: Remove cover from plates, transfer cells to plates, add glass beads to plates, replace cover on plates, spread cells by shaking plastes.
Nice to have: Invert plates (while avoiding cover falling off), transfer plates to incubation chamber.
Should accomplish the following: Pouring a consistent volume of molten agar into a number of petri dishes.
Miniprepper: Purpose: Achieve greater consistency in handling and treatment of miniprep samples.
Input: Resuspended cells. Intermediate samples.
Output: Intermediate and final samples for centrifugatin. Should add equal amounts of solutions to each sample, incubating for approximately the same time (for a limited number of samples) and shake tubes, such that all tubes are treated as similarly as reasonably possible.