User:Jarle Pahr/Hardware

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Notes on hardware of interest:

http://www.synbio.org.uk/hardware.html

http://www.instructables.com/

http://hackaday.com/

http://opensourceecology.org/wiki-gvcs.php

http://sonen.ifi.uio.no/

http://makezine.com/

http://pittcon.org/

http://www.openlabtools.org/

http://en.wikipedia.org/wiki/Open-source_hardware

Contents

Minicomputers

http://cubox-i.com/


Lab equipment

Qubit fluorometer: http://products.invitrogen.com/ivgn/product/Q32866


OpenPCR:

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

http://myspectral.com/

Tekla labs - research grade DIY instructables: http://guides.teklalabs.org/


See also http://www.laboratoryequipment.com/


Stirrers

http://www.kptkomet.no/produkter/no_89/biologi/vnr/065200/

Spectrometry

http://openspectrometer.com/

DNA synthesizers

http://www.ebay.com/itm/ABI-PRISM-6700-Automated-Nucleic-Acid-Workstation-/330815488973?pt=LH_DefaultDomain_0&hash=item4d0623c3cd

Chromatography

ABI Kratos Spectroflow 757: http://www.ebay.com/itm/ABI-Kratos-Spectroflow-757-Lab-Analytical-Absorbance-Detector-9000-7571-HPLC-/130908497938?pt=LH_DefaultDomain_0&hash=item1e7ac12812

Automated fluid handling

http://forums.reprap.org/read.php?194,32936

http://88proof.com/synthetic_biology/blog/archives/407

http://unterbahn.com/2010/02/diy-lego-liquid-handling-robot-for-gene-synthesis/

http://2009.igem.org/Team:Washington-Software

http://openwetware.org/wiki/Mike_Barnkob:Projects/Liquid_handling_robot

https://groups.google.com/forum/?fromgroups=#!topic/diybio/D5-eOnJjw_A

https://groups.google.com/forum/#!topic/diybio/Cp8n7p3kPMc

https://forum.sparkfun.com/viewtopic.php?f=14&t=23561

http://88proof.com/synthetic_biology/blog/archives/461

www.andrewalliance.com

http://forums.reprap.org/read.php?1,11439,11494

https://github.com/delinquentme/LH001#readme

http://hackteria.org/wiki/index.php/DIY_Micro_Dispensing_and_Bio_Printing

Microfluidics

http://hackteria.org/wiki/index.php/DIY_Microfluidics

http://wetpong.net/wetpong/?page_id=115

http://fab.cba.mit.edu/classes/S62.12/people/tsai.liz/index.html

http://fluidicmems.com/2010/04/21/diy-microfluidics/http://fluidicmems.com/2010/04/21/diy-microfluidics/


Plate readers

Tecan Infinite 200 PRO: http://www.tecan.com/platform/apps/product/index.asp?MenuID=1812&ID=1916&Menu=1&Item=21.2.10.1

  • Measurments of absorbance and fluorescence in 96-well plate and cuvette
  • Temperature control and shaking

http://www.cnsi.ucsb.edu/facilities/nanostructures/biological/tecan-reader.pdf

Infinite 200 downloads: http://www.tecan.com/platform/apps/product/index.asp?MenuID=1816&ID=1922&Menu=1&Item=21.2.10.1.4


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 InfiniteĀ® 200 PRO: http://www.tecan.com/platform/apps/checkdoc/index.asp?doc_Id=1031,148&prot=1,1

Electroporation

http://biotech.wku.edu/online_manual/Bio-Rad%20Gene%20Pulser%20II.pdf

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.


http://www.ebay.com/itm/BioRad-GenePulser-Gene-Pulser-II-Apparatus-Electroporation-System-/181067560006?pt=LH_DefaultDomain_0&hash=item2a2877b446

Pulse Controller spotted for ~200 USD:

http://www.ebay.com/itm/BIORAD-PULSE-CONTROLLER-BIO-RAD-1652098-FOR-GENE-PULSER-/280907232003?pt=UK_BOI_Medical_Lab_Equipment_Lab_Equipment_ET&hash=item4167603303


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.

See also http://www.ncbi.nlm.nih.gov/pubmed/1368271


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

Processors

http://en.wikipedia.org/wiki/ARM_architecture

  • Used in majority of smartphones.


http://en.wikipedia.org/wiki/X86

Electronics

http://en.wikipedia.org/wiki/Bug_Labs


Udoo: http://www.kickstarter.com/projects/435742530/udoo-android-linux-arduino-in-a-tiny-single-board

http://www.pcduino.com/

http://blog.makezine.com/2013/04/15/arduino-uno-vs-beaglebone-vs-raspberry-pi

http://freak.no/forum/forumdisplay.php?s=df6e715254c0b9035b3108b2ec531dbc&f=152

Arduino

See Arduino

Raspberry Pi

See Raspberry pi

Tinkerforge

http://en.wikipedia.org/wiki/Tinkerforge

http://www.tinkerforge.com/en

3D Printing

http://www.cartesianclassroom.com/

Filaments

ABS plastic


PLA: http://reprap.org/wiki/PLA


See also: http://reprap.org/wiki/PrintingMaterials


Food safe printing:

http://www.3dprintingera.com/food-safe-3d-printing/

http://www.dezeen.com/2013/03/27/food-is-the-next-frontier-of-3d-printing-janne-kytannen/

http://reprage.com/post/36869678168/is-3d-printed-pla-food-safe

Links

http://blog.makezine.com/category/workshop/3d-printing-workshop/

http://reprage.com/

http://www.shapeways.com/

http://www.3dprintingera.com/

http://www.3dprintingera.com/what-are-3d-printers-bad-at/

http://vort.org/2012/11/20/why-doesnt-your-lab-have-3d-printer-yet/

http://forums.somethingawful.com/showthread.php?threadid=3365193

http://whatabout.no/

http://www.reprapcentral.com/vmchk.html

http://cubify.com/cube/index.aspx?hp_bn_cube

http://www.ultimaker.com/

www.3ders.org/

http://www.3ders.org/articles/20121123-meet-metalbot-new-all-metal-reprap-compatible-3d-printer.html

http://www.robo3dprinter.com/

http://www.thingiverse.com/

http://www.pp3dp.com/

http://www.lulzbot.com/catalog

http://vort.org/2011/09/19/how-sequence-10000-metagenomes-3d-printer/

Solidoodle

http://www.solidoodle.com/


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

www.makerbot.com


Makerbot Replicator 2: http://store.makerbot.com/replicator2.html

  • 2200 $ USD

RepRap

http://en.wikipedia.org/wiki/RepRap_Project

http://reprap.org/wiki/Main_Page

http://forums.reprap.org/list.php?1

http://www.reprap.org/wiki/Main_Page

http://reprap.org/wiki/RepRap_Buyers%27_Guide

http://www.robonor.no/mage/default/


http://www.3dstuffmaker.com/

http://www.makergear.com/products/3d-printers

http://reprappro.com/

Other printers

http://pinterest.com/finklean/diy-3d-printers/

http://makibox.com/products

http://makibox.com/details/product/A6-LT

  • 200 USD. Uses PLA filament. 6-10 weeks lead time.

Software

http://replicat.org/

https://github.com/SolidCode/SolidPython#readme

Reviews and discussion

http://reviews.cnet.com/3d-printers/makerbot-replicator-3d-printer/4505-33809_7-35266602.html

http://freak.no/forum/showthread.php?t=219137

http://www.treehugger.com/gadgets/28-affordable-3d-printers-you-can-buy-now.html

http://blog.makezine.com/2013/03/25/will-3d-printers-save-the-world/

Vendors

http://www.reprapdiscount.com/

http://adafruit.com/

http://www.makershed.com/default.asp

http://www.raspberry-pi-buy.com/

https://www.sparkfun.com/

http://www.creativetools.se/

3D scanners

MakerScanner

http://www.makerscanner.com/

http://www.makerscanner.com/docs/1-makerscanner.html

http://www.thingiverse.com/thing:3946

http://abarry.org/makerscanner/2-makerscanner-building.html

DAVID 3D Scanner

http://www.david-laserscanner.com/

http://shop.david-vision-systems.de/

FabScan

FabScan: http://hci.rwth-aachen.de/fabscan


FabScan hardware: https://hci.rwth-aachen.de/fabscan_hardware

https://groups.google.com/forum/?fromgroups=#!forum/fabscan

https://github.com/francisengelmann/FabScan100

http://shop.mariolukas.de/de/Fabscan-Kit


FabScan 100 Linux Version: https://groups.google.com/forum/?fromgroups=#!topic/fabscan/oIMZYx_utjo

FabScan Arduino shield: http://hci.rwth-aachen.de/fabscan_shield

http://www.watterott.com/de/Arduino-FabScan-Shield


Ideas

ShakeFlaskBot: Setup for incubation in and automatic sampling from shake flasks. Connect a rack for holding shakeflasks to a shaking mechanism. When not moving, the rack should be in a defined position to allow automatic sampling. Possible to incorporate heating?


Bacteria transformer:

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?


Needed components:


Motors Temperature sensors Heating elements Rails and movement mechanisms


Plate spreader:

Input materials: Plastic petri dishes with agar, sterile glass beads, eppendorf tubes containing cells.

Should perform:

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.


Plate pourer:

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.

Milling and machining

Othermill:

http://otherfab.com/products/

http://blog.arduino.cc/2013/05/06/othermill-on-kickstarter/?utm_source=buffer&utm_medium=facebook&utm_campaign=Buffer&utm_content=buffer2e4db

http://www.kickstarter.com/projects/otherfab/the-othermill-custom-circuits-at-your-fingertips

Personal tools