Difference between revisions of "Group:Biohacking"

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== Biohacking / DIYBio at LHS ==
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{{Group
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|logo=Biohack_logo.png
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|name=Biohacking
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|when=Every Wednesday
 +
|what=
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|time=19:30
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|recurring=1}}
  
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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.
+
We are the '''biohacking''' or '''DIY biology''' ([http://openwetware.org/wiki/DIYbio/FAQ Official FAQ about DIY-Biology]) group at the London Hackspace, a mix of amateur and professional biologists, attracted by the potential of molecular and synthetic biology. Anyone is welcome, so get involved!
  
−
== Our current projects / schedule==
+
Over the past couple of years we've been developing our equipment, optimising techniques and running some research projects. Here's quite a good short [http://www.bbc.co.uk/news/uk-england-london-19964886 local news video] showing our (previous, smaller) lab and some of what we do in it.
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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. In August and September we worked with the [http://2012.igem.org/Team:University_College_London/HumanPractice/DIYbio 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.
+
We will soon be meeting every month, check back here for our 2019 restart.
 +
We have a list of [[Biohacking FAQ|frequently-asked questions]].
  
−
* [[Public Biobrick]] (in collaboration with the UCL igem team)
+
[[:Category:Biohacking|'''List of biohacker wiki pages.''']]
−
* [[Sex typing with amelogenin]]
+
 
−
* [[Plant species testing]]
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We also maintain an outward facing website at [http://biohackspace.org/ BioHackspace.org]
−
* [[Project:Biohacking/Genetic modification|Genetic modification]]
+
 
−
* [[Blood typing]]
+
== How to find us ==
−
*[[Project:Biohacking/Algal_biodiesel|Algal biodiesel]] (on hold)
+
# Email us [mailto:hello@biohackspace.org here]. You can also sign up to our mailing list where we do most of our communication [https://lists.kentgeek.org/mailman/listinfo/lhs-biohacking here] (if you see a warning ignore it) (Your posts will be moderated unless you're signed up to the list. If you want to be signed up to the list but not receive messages you can change this in the options). You can view the mailing list archives through the previous link or through the [https://groups.google.com/forum/?fromgroups#!forum/london-biohackers google groups] interface. To chat in more detail request a signup to our slack channel using the email address above, or join our irc channel at [http://webchat.freenode.net/?channels=london-biohackers #london-biohackers on freenode]
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*DNA forensics (on hold)
 
−
* [[Other genetic tests to try]]
 
  
−
===Schedule===
+
== Biohackspace Membership ==
−
*November/December 2012 - Refine DNA extraction process to get it working consistently, and complete blood typing and sex typing experiments. Also do the self cloning protocol from NCBE to learn transformation procedures.
+
We're a subgroup of the London Hackspace, and our rent and utility bills are paid as part of the larger space. Therefore it's London Biohackers also need to be members of the hackspace. You can find out how to become a hackspace member [https://london.hackspace.org.uk/signup.php here].  
−
*November 2012 - early 2013 - Get a larger lab space with a licence to do genetic modification, and get the funding to do this.
 
  
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== People ==
+
There is a separate subscription for the biohacking group. Biohacking is more expensive than the typical hackspace activity, and with your membership we can pay for reagents, lab consumables and any equipment we may need for our experiments. The suggested minimum donation is £2 a week, but again, you can come along without joining. If you start to come regularly and use consumables then we'd like you to pay.  Details on how to setup payment to become a biohackspace member are here: [[London Biohackers Membership | Details of Membership]].
−
Andy, Joel, Mike, [[User:Wzdd|Nicholas]], Paddy, Paul, Simon, Taylor, Tom, Tonderai, [[User:mycoplasma|Will]]
 
  
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== How to find us ==
+
We also have an arrangement for people who just want to support the biohackspace work and lab costs, and do not intend to regularly attend the biolab to do science. If you want to become a remote member, or to donate equipment and make a regular contribution, and you can make contact [mailto:hello@biohackspace.org here by email], or see the [[Remote Membership|Donations/Remote members]] page for more details.
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# 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. [mailto:wzdd.lhsb@lardcave.net Email Nicholas] if you can't find the place.
 
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# Post on [https://lists.kentgeek.org/mailman/listinfo/lhs-biohacking the biohacking mailing list]. You can view the mailing list archives through the previous link or through the [https://groups.google.com/forum/?fromgroups#!forum/london-biohackers google groups] interface.
 
  
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== Membership ==
+
However it's not essential to become a member just to come along initially and find out what we do.
−
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.
 
  
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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. [https://london.hackspace.org.uk/signup.php 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 [mailto:wzdd.lhsb@lardcave.net Nicholas].
+
== Organization ==
  
−
The suggested donation is £2 a week.
+
The biohackspace operates as a Company Limited by guarantee. The legal details of this are [[London Biological Laboratories|here]]
  
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== Our standard protocols / how to's ==
+
== Projects ==
 +
We are currently well equipped to carry out molecular biology experiments.  The lab space on Hackney Road was a CL1 approved lab and we are aiming to reestablish that in Wembley.
  
−
*[[DNA extraction using Chelex 100]]
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=== Current Projects ===
−
*[[DNA extraction and precipitation with ethanol / isopropanol]]
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* Hacking the lab
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*[[Biohacking/Equipment/Thermal_Cycler_(Perkin_Elmer_480)#How_to_use_it:|Run PCR]]
+
* * Recommissioning RO water system
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*[[Make and run an agarose gel]], then visualise with UV
+
* * Recommissioning Laminar Flow system
 +
* * Building Laminar Flow System into a hood
 +
* Culturing Local Algae
 +
* Lab Automation
 +
* Stirling Engine for Cryogenics
  
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== Our reagents + equipment ==
+
=== Completed Projects ===
−
*[[Biohacking/Equipment/Thermal_Cycler_(Perkin_Elmer_480) | Thermal Cycler (PCR Machine) Perkin Elmer 480]]
 
−
*[[Gel electrophoresis box]]
 
−
* [[Incubator with shaker]]
 
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* Two centrifuges - estimated speed 5000 rpm
 
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*[[Biohacking/Wetstuff | 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)
 
−
* 0.65ml tubes. 1000 for £18 from [http://www.nbsbio.co.uk/product.asp?pID=11982&cID=275 nbsbio]
 
−
* 1.5ml tubes. 1000 for £18 from [http://www.nbsbio.co.uk/product.asp?pID=11995&cID=275 nbsbio]
 
−
* Tips for 1-10ul pipette. Available for £27.60 from [http://www.nbsbio.co.uk/product.asp?pID=11817 NBSbio]
 
−
* Pressure cooker (goes up to 15PSI and 121°C (this is industry standard, not actually tested) to be used as autoclave. Autoclave tape.
 
  
−
=== Shopping list in priority order (See [[Biohacking/Wetstuff|wet stuff]] for sources and prices not listed here) ===
+
* [http://2015.igem.org/Team:London_Biohackspace iGEM 2015]
 +
* [[Project:iGEM 2014]]
 +
* [[Project:Flow Hood]]
 +
* [[E. coli transformation]]
 +
* [[Image Focus Stacking]]
 +
* [[CL1_BSO_SOP_GLP|Lab Containment Level 1]]
 +
* [[Project:Growing bacteria|Growing V. fischeri]]
 +
* [[Project:Sex typing with amelogenin]]
 +
* [[Project:Public Biobrick]] (in collaboration with the UCL igem team)
 +
* [[Blood typing]]
 +
* [[Project:Plant species testing]]
 +
* [[Project:Gel electrophoresis box]]
 +
* [[Project:Shaker platform]]
  
−
'''These prices are the first I found. We should look for better ones.'''
+
=== Future Projects ===
 +
* [[Project:Making our own reagents]]
 +
*[[MindControlBacteria]]
 +
* More and more becoming current project :)
 +
Add your own!
  
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* Ladder (only enough left for 1 gel of current ladder + a few more gels for the an older one)
+
== Our lab ==
−
* Agarose (nearly run out, less than 10 more gels)
+
Our lab is small in size but we have tried to make good use of the tight space to incorporate all the equipment we need to carry out interesting projects. You can see a [[Lab|floor plan of the lab here]].  
−
* KPN1 (£27 for 1000 units from [http://www.sigmaaldrich.com/catalog/product/sigma/r1258?lang=en&region=GB sigma] - a unit is "the enzyme activity that completely cleaves 1 µg λ DNA in 1 hr. at 37 °C in a total volume of 25 µl of Buffer SL for restriction enzymes.") and ALU1 (£18.90 for 100 units from [http://www.sigmaaldrich.com/catalog/product/sigma/r6885?lang=en&region=GB sigma] - can also buy 500 units for £33.80) for blood typing. I guess we will be using it on minimum 20ng of DNA, which gives us 50 reactions for Kpn1 and 5/25 reactions for Alu1.
 
−
* 0.65ml tubes (or whatever size will fit in PCR machine) (around 30 tubes left)
 
−
* Some 1.5ml tubes for reactions of higher volume (such as ethanol precipitation). Don't need too m
 
−
* Taq readymix (less than 20 reactions left).
 
−
* 10X TBE (running low)
 
−
* Jim paid 108.99 for company formation + registered office etc. Needs to be reimbursed.
 
−
* Would be good to get some tubes that can hold up to 10ml for spinning down stuff in the big centrifuge.
 
  
−
=== Suppliers ===
+
We <strike> are currently working towards being </strike> are a certified Containment Level 1 Lab ([[BioSafety|more details on biosafety classifications]]).
  
−
* [http://www.sigmaaldrich.com/united-kingdom.html Sigma-Aldrich] - Good for custom primers
+
The Lab is the registered office of our limited company, [[London Biological Laboratories]], used to deal with suppliers.
−
* [http://www.coleparmer.co.uk/ Cole-Parmer]
 
−
* [http://uk.farnell.com/ Farnell]
 
−
* [http://www.nbsbio.co.uk/ 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. Standard shipping cost is £15
 
−
* [http://www.neb.com New England Biolabs] They sell very cheap taq. We could also look at their restriction enzymes. However atm they won't sell to us. See [https://lists.kentgeek.org/pipermail/lhs-biohacking/2012-August/000817.html this post]. Once we have all our registrations for LBL sorted we could try again.
 
−
* [http://www.vwr.com VWR] - Big supplier of chemicals, glassware and various lab stuff. Sounds very positive about selling to the hackspace. [[User:Bugs|Bugs]] is in the process of setting up an account with them.
 
−
* [http://www.invitrogen.com/site/us/en/home.html Invitrogen] Don't seem to want to sell to us
 
  
−
Also see general hackspace [[suppliers]] page.
+
=== How to use the Lab ===
 +
Please do not touch things in the lab if you do not know what they are or how to use them. Many items may be hazards to your health if used incorrectly.
  
−
=== Wish list ===
+
Our [[BioLab Manual|lab manual]] details our equipment, reagents, strains and our established protocols.
  
−
* If extractions keep failing, lets look at some extraction kits. [http://www.promega.com/products/dna-and-rna-purification/genomic-dna-purification-kits/wizard-genomic-dna-purification-kit/ This one] recommended by Tom is &sim;£100 for 100 reactions or &sim;£250 for 500 extractions.
+
=== Starting your own lab? ===
−
* A more consistent and effective way of crushing/homogenising small amounts of tissue for DNA extraction. Blenders are good but not for small quantities. Pestles are ok, but not great. One idea is to make a small pestle by melting a pipette tip then using a PCR tube as a mortar. Some labs use liquid nitrogen or a sonicator.
+
We have some notes on [[Starting your own biolab|starting your own biolab]] based on our experiences.
−
* Spectrophotometer for measuring DNA concentration. Simon and Tom are on this.
 
−
* Another centrifuge, if ours breaks down, or a dremelfuge. One option is a [http://www.thingiverse.com/thing:1483 Dremelfuge] - microcentrifuge to be made on a 3D printer. Can print a new one, or buy pre printed for £50 from shapeways. Another option could be this £100 13,000rpm centrifuge from [http://www.ncbe.reading.ac.uk/ncbe/materials/dna/microcentrifuge.html ncbe]. Says it's only for schools but we can try and persuade them. If we want a chilled centrifuge we can put it in the fridge / freezer.
 
−
*Another PCR machine. One option is the [http://openpcr.org/ Open Source, Hackable PCR machine]. Another is the [http://www.russelldurrett.com/lightbulbpcr.html Light Bulb PCR] less than $50 to build this machine (including the $30 arduino)
 
  
−
===Costs (assuming prices on [[Biohacking/Wetstuff|wet stuff]])===
+
=== Equipment we made ===
 +
Our hope is to be able to use self-developed or open source hardware equipment where possible in order to carry out our projects. Here is what we have done so far:
  
−
'''Per Chelex DNA extraction:'''
+
* [[Project:Gel electrophoresis box]]
−
* Chelex: Not calculated
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* [[Biobot]]
−
* Pasteur pipettes: Not calculated
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* [[Project:Shaker platform]]
−
* Tubes: £0.04 (1 for chelex incubation, 1 to save supernatant)
 
−
* Tips: £0.06 (1 for mixing chelex, 1 removing supernatant)
 
−
Total per sample: £0.10 + chelex and pasteur pipettes
 
  
−
'''Per PCR reaction'''
+
A list of biohacking hardware projects is here [[Project:Biohardware]]
−
Assume 25ul total reaction volume. 12.5ul Taq, 5ul primers.
 
−
* Taq: £0.72
 
−
* Primers: Not calculated
 
−
* Tubes: £0.02 (1 tube for PCR)
 
−
* Tips: £0.15 (Assuming 1 tip for template, 1 for PF, 1 for PR, 1 for dH20, 1 for Taq)
 
−
* Paraffin: Negligible
 
−
Total per sample: £0.89
 
  
−
'''Per gel:'''
+
=== Equipment Pledges ===
−
For each sample:
 
−
* Tubes: £0.02 (1 to mix loading buffer with PCR product)
 
−
* Tips: £0.03 (1 to add product to loading buffer and then load into well)
 
−
* Loading buffer: Negligible
 
−
Total per sample: £0.05
 
  
−
For each gel:
+
[[Biohacking Wishlist]]
−
Assume a 1% 50ml agarose gel with 100ml buffer and 2.2ul EtBr
 
−
* Agarose: £0.23
 
−
* TBE: £0.60
 
−
* Ladder: £0.30
 
−
* Tips: £0.03 (1 to add loading buffer to all tubes)
 
−
* dH20: Negligible
 
−
* EtBr: Negligible
 
−
Total per gel: £1.16
 
  
−
So for a chelex extraction, PCRx4 and gel it costs at least £5.32
+
* [[Pledge: Flow Hood]]
 +
* [[Pledge:Lab Microscope]]
 +
* [[Pledge:vacum forming machine]]
 +
* [[Pledge:Gluconacetobacter_hansenii]]
  
 
== Resources ==
 
== Resources ==
Line 138: Line 114:
 
*[http://wiki.london.hackspace.org.uk/w/images/4/43/Biohacking_workshop_Aug2012.pdf Slides] from Bioinformatics workshop August 2012
 
*[http://wiki.london.hackspace.org.uk/w/images/4/43/Biohacking_workshop_Aug2012.pdf Slides] from Bioinformatics workshop August 2012
 
*[http://en.wikipedia.org/wiki/User:Cathalgarvey/Books/A_Beginner's_Guide_to_Biotechnology Cathal Garvey's beginner's guide to biotech]
 
*[http://en.wikipedia.org/wiki/User:Cathalgarvey/Books/A_Beginner's_Guide_to_Biotechnology Cathal Garvey's beginner's guide to biotech]
 +
*[https://docs.google.com/drawings/d/1hXO4uu_TZ_yI3amJ1jGo9zu2XU3gX9yXMchC9gGZT6k/edit Flowchart diagram of DNA extraction protocol]
  
 
=== Community ===
 
=== Community ===
 
*[http://diybio.org/blog Interesting DIYBio community blog] - Interesting blog taking articles from a few different groups
 
*[http://diybio.org/blog Interesting DIYBio community blog] - Interesting blog taking articles from a few different groups
−
*[http://biocurious.org/index.php?title=Main_Page Bio Curious] - A well-established bihacking group in California
+
*[http://biocurious.org/index.php?title=Main_Page Bio Curious] - A well-established biohacking group in California
 
*[http://www.tmplab.org/wiki/index.php/Brain_Computer_Interface Brain-Computer interface at Paris hackspace]
 
*[http://www.tmplab.org/wiki/index.php/Brain_Computer_Interface Brain-Computer interface at Paris hackspace]
 
*[http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1077.html Nature.com article about biohacking community] - Not the same one as above. Interesting, but behind a paywall :(.
 
*[http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1077.html 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 http://www.synbioproject.org/process/assets/files/6452/_draft/nbt-2009-12d_-_biotech_nin_the_basement.pdf] -- [http://heybryan.org/ kanzure] [[Special:Contributions/70.114.205.110|70.114.205.110]] 19:40, 2 January 2011 (UTC)
 
** you can access it here: [http://www.synbioproject.org/process/assets/files/6452/_draft/nbt-2009-12d_-_biotech_nin_the_basement.pdf http://www.synbioproject.org/process/assets/files/6452/_draft/nbt-2009-12d_-_biotech_nin_the_basement.pdf] -- [http://heybryan.org/ kanzure] [[Special:Contributions/70.114.205.110|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/
 
  
 
== Proposed code of conduct ==
 
== Proposed code of conduct ==
 
See here: http://wiki.hackspace.org.uk/wiki/Biohacking/Code_of_Conduct
 
See here: http://wiki.hackspace.org.uk/wiki/Biohacking/Code_of_Conduct
  
−
== FAQ about DIYBio ==
+
[[Category:Biohacking]]
−
* [http://openwetware.org/wiki/DIYbio/FAQ official do-it-yourself biology FAQ]
+
[[Category:Groups]]

Latest revision as of 06:16, 1 May 2019

Biohacking
Biohack logo.png
When Every Wednesday, from 19:30
Members

We are the biohacking or DIY biology (Official FAQ about DIY-Biology) group at the London Hackspace, a mix of amateur and professional biologists, attracted by the potential of molecular and synthetic biology. Anyone is welcome, so get involved!

Over the past couple of years we've been developing our equipment, optimising techniques and running some research projects. Here's quite a good short local news video showing our (previous, smaller) lab and some of what we do in it.

We will soon be meeting every month, check back here for our 2019 restart. We have a list of frequently-asked questions.

List of biohacker wiki pages.

We also maintain an outward facing website at BioHackspace.org

How to find us

  1. Email us here. You can also sign up to our mailing list where we do most of our communication here (if you see a warning ignore it) (Your posts will be moderated unless you're signed up to the list. If you want to be signed up to the list but not receive messages you can change this in the options). You can view the mailing list archives through the previous link or through the google groups interface. To chat in more detail request a signup to our slack channel using the email address above, or join our irc channel at #london-biohackers on freenode

Biohackspace Membership

We're a subgroup of the London Hackspace, and our rent and utility bills are paid as part of the larger space. Therefore it's London Biohackers also need to be members of the hackspace. You can find out how to become a hackspace member here.

There is a separate subscription for the biohacking group. Biohacking is more expensive than the typical hackspace activity, and with your membership we can pay for reagents, lab consumables and any equipment we may need for our experiments. The suggested minimum donation is £2 a week, but again, you can come along without joining. If you start to come regularly and use consumables then we'd like you to pay. Details on how to setup payment to become a biohackspace member are here: Details of Membership.

We also have an arrangement for people who just want to support the biohackspace work and lab costs, and do not intend to regularly attend the biolab to do science. If you want to become a remote member, or to donate equipment and make a regular contribution, and you can make contact here by email, or see the Donations/Remote members page for more details.

However it's not essential to become a member just to come along initially and find out what we do.

Organization

The biohackspace operates as a Company Limited by guarantee. The legal details of this are here

Projects

We are currently well equipped to carry out molecular biology experiments. The lab space on Hackney Road was a CL1 approved lab and we are aiming to reestablish that in Wembley.

Current Projects

  • Hacking the lab
  • * Recommissioning RO water system
  • * Recommissioning Laminar Flow system
  • * Building Laminar Flow System into a hood
  • Culturing Local Algae
  • Lab Automation
  • Stirling Engine for Cryogenics

Completed Projects

Future Projects

Add your own!

Our lab

Our lab is small in size but we have tried to make good use of the tight space to incorporate all the equipment we need to carry out interesting projects. You can see a floor plan of the lab here.

We are currently working towards being are a certified Containment Level 1 Lab (more details on biosafety classifications).

The Lab is the registered office of our limited company, London Biological Laboratories, used to deal with suppliers.

How to use the Lab

Please do not touch things in the lab if you do not know what they are or how to use them. Many items may be hazards to your health if used incorrectly.

Our lab manual details our equipment, reagents, strains and our established protocols.

Starting your own lab?

We have some notes on starting your own biolab based on our experiences.

Equipment we made

Our hope is to be able to use self-developed or open source hardware equipment where possible in order to carry out our projects. Here is what we have done so far:

A list of biohacking hardware projects is here Project:Biohardware

Equipment Pledges

Biohacking Wishlist

Resources

Education

A primer for synthetic biology

Community

Proposed code of conduct

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

Retrieved from ‘https://wiki.london.hackspace.org.uk/w/index.php?title=Group:Biohacking&oldid=52868’