Group:Biohacking

Biohacking / DIYBio at LHS

We are the biohacking group at the London Hackspace, a mix of amateur and professional biologists, attracted by the potential of DIYbio and synthetic biology. Anyone is welcome, so get involved! It's fascinating, the field and community is growing all the time, together with the ability of amateurs to do cool stuff. Over the past year we've been developing our equipment, optimising techniques and running some research projects.

Our current projects

We're currently working on genetic testing, identifying specific genes using PCR and electrophoresis. We've been working mainly on sex typing with amelogenin, and have just started working on plant species testing to refine our DNA extraction and PCR process. Since August we've also been working with the UCL igem team to develop a 'public biobrick'.

Our big goal for the next year is to begin projects involving genetic modification. For this we'll need to become certified as a class 1 lab, we are currently collecting information on how to do this.

• Public Biobrick (in collaboration with the UCL igem team)
• Sex typing with amelogenin
• Plant species testing
• Genetic modification
• Blood typing
• Algal biodiesel (on hold)
• DNA forensics (on hold)
• Other genetic tests to try

People

Andy, Joel, Mike, Nicholas, Paddy, Paul, Simon, Taylor, Tom, Tonderai, Will

How to find us

1. Come to a meeting: we meet at 7pm every Wednesday in the London Hackspace: Unit 24, Cremer Business Centre, 37 Cremer Street, London E2 8HD. Email Nicholas if you can't find the place.
2. Post on the biohacking mailing list. You can view the mailing list archives through the previous link or through the google groups interface.

Membership

We encourage you to become a member of the biohacking group. Biohacking is more expensive than the typical hackspace activity, and with your membership we can pay for chemicals, primers, and any random equipment we may need.

To become a member, set up a standing order to the London Hackspace with the reference "biohacking". You need to become a hackspace member before you can see the direct debit details. Look here for more information. If you want to become a Biohacking member without joining the space (you really should join the hackspace! It's great), get in contact with Nicholas.

The suggested donation is £2 a week.

Our equipment

• Thermal Cycler (PCR Machine) Perkin Elmer 480
• Gel electrophoresis box
• Incubator with shaker
• Two centrifuges - estimated speed 5000 rpm
• Wet stuff: our inventory of primers, buffers, stains...
• Various pipettes (5-50ul), flasks, beakers, PCR tubes, tip/tube holders, scales (one down to 0.1g, the other down to 0.01g)
• Pressure cooker (goes up to 15PSI and 121°C (this is industry standard, not actually tested) to be used as autoclave. Autoclave tape.

Equipment we want to build / buy in the future

• A better centrifuge. One option is a Dremelfuge - microcentrifuge to be made on a 3D printer. We have one, but using it is a bit ... character building. Need to print a new one, or buy pre printed for £50 from shapeways. Another option could be this £100 13,000rpm centrifuge from ncbe. Says it's only for schools but we can try and persuade them.
• Another PCR machine. One option is the Open Source, Hackable PCR machine. Another is the Light Bulb PCR less than $50 to build this machine (including the $30 arduino)
• Spectrophotometer for measuring DNA concentration.

Our standard protocols / how to's

• DNA extraction using Chelex 100
• DNA extraction with ethanol
• Make and run an agarose gel, then visualise with UV

Standard chemicals and reagents we use

(See suppliers further down the page for where to get these)

• List of possible DNA stains

DNA extraction:

• Chelex 100
• 70% isopropanol (rubbing alcohol) - widely and cheaply available

PCR:

• Taq ReadyMix. Click on bulletin for useful info about procedure for using it.
• dH20 (deionised water bought from garages).

Electrophoresis:

• 1KB DNA ladder. Current ladder is aliquoted with loading dye from a 50 ug sample of concentration 0.2 ug / ul. key
• Ethidium bromide stock solution - 2 ul ethidium bromide solution to 40 ml water.
• Powdered agarose
• Safewhite 1ml
• DNA Ladder
• TBE Concentrate

Shopping list

As of 10 oct, 2012, we need:

• Agarose (nearly run out)
• Taq readymix (nearly run out)
• TE buffer (for storing samples - we currently store dH20, using TE may stop our samples degrading)
• Mini pestle, to grind samples in tubes
• Big gloves

Expenses

Kitty: -£27.19 (as of July 25) (Yes, negative)

Spent on:

• Pressure cooker: £28.95 (May 02)
• Cabinet: £65.94 (July 25)

Resources

Education

• Nature.com comic about Synthetic Biology - Nice introduction to playing with genetic engineering/cloning, though aimed at kids

• Bugs' Crash Course in Molecular Biology - Recorded at the hackspace. Slides
• Sara's Introduction the the Biohacking Community - Recorded at the hackspace

• Good introduction to gel electrophoresis - Explaining one of the core techniques for working with DNA
• Good introduction to the Polymerase Chain Reaction (PCR) - Explaining one of the core techniques for working with DNA
• Nature.com article on Biohacking - Free access. Nice explanation of what's needed in a lab and how different groups are managing it.
• Bioinformatics Resources
• Slides from Bioinformatics workshop August 2012
• Cathal Garvey's beginner's guide to biotech

Community

• Interesting DIYBio community blog - Interesting blog taking articles from a few different groups
• Bio Curious - A well-established bihacking group in California
• Brain-Computer interface at Paris hackspace
• Nature.com article about biohacking community - Not the same one as above. Interesting, but behind a paywall :(.
  • you can access it here: http://www.synbioproject.org/process/assets/files/6452/_draft/nbt-2009-12d_-_biotech_nin_the_basement.pdf -- kanzure 70.114.205.110 19:40, 2 January 2011 (UTC)

PCR primer design

• http://www.cybertory.org/exercises/primerDesign/index.html
• http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
• http://www.premierbiosoft.com/primerdesign/index.htm
• http://molbiol-tools.ca/PCR.htm
• http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome
• http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
• http://bibiserv.techfak.uni-bielefeld.de/genefisher2/

Suppliers

Cf. Suppliers.

• Sigma-Aldrich - Good for custom primers
• Cole-Parmer
• Farnell
• NBSBio - Good for ladders and cheap agarose (only low concentration) [NB: Be sure to navigate to http://www.nbsbio.co.uk NOT http://nbsbio.co.uk, or their payment system doesn't work. Weird.]
• New England Biolabs Good for TAQ
• VWR] - Big supplier of chemicals, glassware and various lab stuff. Sounds very positive about selling to the hackspace. Bugs is in the process of setting up an account with them.
• Invitrogen Don't seem to want to sell to us

Proposed code of conduct

See here: http://wiki.hackspace.org.uk/wiki/Biohacking/Code_of_Conduct

FAQ about DIYBio

• official do-it-yourself biology FAQ