Synthetic Biology

Synbio Future talk: Video and Retrospective

So, I gave a talk at the Synbio Future conference in Cork, which was organised by SynbioAxlr8r and brought in some top talent in Synthetic Biology to speak about their work and the prospects for the future of the field, and Ireland’s role in it. My own talk was in the “translation” block, so I tried to discuss my experiences making a business out of Synbio. At the time, I was trying to raise money for IndieBB (an effort which failed), but I tried to keep that out of the talk except where it was relevant.

IndieBB - Technical FAQ

As I am redesigning the main pitch-page for IndieBB in order to appeal more to the currently-untechnical audience, what little technical detail I’ve reserved for the main page will have to be stripped out; I’m taking this opportunity to write up a “Frequently Asked Questions” post to address the more technical queries I’m seeing in the survey, tweets, comments and other correspondence. I will soon also post a less technical FAQ, but given that “Less Technical FAQ” is now the design goal for the main IndieBB crowdfunding page, I’m considering it a lower priority.

Codon Optimisation: A Hidden Process Behind IndieBB

I’ve posted twice recently after a prolonged blogging absence, and here I am again. Perhaps I should always be running a crowdfunding campaign, so that I have a stake in blogging; I’d be far more prolific! I’m too principled (or, to some “dogmatic”) to include advertisement on this or any blog, and flattr revenue is far too thin to encourage more than the occasional post otherwise. In any case, today I’d like to share something with you all that I’ve been meaning to write up for ages anyway, but which becomes especially relevant in light of my IndieBB DIYbio/Biohacking/Teaching plasmid design project.

A Primer on Plasmid Design (For IndieBB)

So, in the preceding blogpost I introduced my current crowdfunding project, IndieBB: ..If you navigate to the “updates” panel on that crowdfunding page, I’ve been busy keeping things current. Among the promises I’ve made lately was to run through my workflow for total-plasmid-design as I plan to apply to IndieBB. So, here we go. Before clicking “more”, be aware that you do not need to understand any of the below to complete the IndieBB kit.

Reasons to be in Ireland this October: Synbio AXLR8R, Grow Your Own

As is often the case when I fail to post for months, I’ve been busy. In addition to my own work in the lab, which currently entails bypassing and leapfrogging existing affinity chromatography standards while making DIY protein purification trivial (!), I’ve been roped into organising an ambitious Synthetic Biology business accelerator programme in my home city, Cork, and I’m officially a co-curator for the upcoming Synthetic Biology exhibition in Science Gallery, “Grow Your Own”.

Hacking Your Own Fluorescent Yogurt

There is a common conceit among we DIYbio enthusiasts, namely to suggest that one could opt to create “glow-in-the-dark yoghurt” using DIYbio-oriented techniques as a nigh trivial matter. Indeed, this conceit led to my recently being queried by twitter and email about the possibility; where are the guides and how-tos, if it is so trivial? While a conceit it may be to suggest that glow-in-the-dark yoghurt would be trivial, that’s not to say it’s at all out of reach to the dedicated biohacker.

DNA Logic for Chronic HIV Infection

I was just reading through this really encouraging sum-up of progress on preventing and treating HIV: On the whole, it’s great news. I mean, as much as I dislike making circumcision mainstream, if it saves lives in a continent where AIDS is at full epidemic strength, it’s a no-brainer. I just hope we can move past it with more advanced methods at some point in the future. However, the bit that caught my attention was the ongoing (though low-level) debate as to whether a practical cure for HIV will ever be possible.

Irish law, ethics and Biohacking - Tomorrow, 1-4pm at Science Gallery

Hey all, Tomorrow is the last session of the first biohacking workshops in Ireland. It’s been awesome fun (even though much of the hastily prepared stuff didn’t work as intended!) and really informative to me and hopefully my excellent participants. Sadly a lot of people couldn’t make the weekdays due to pernicious blights such as employment, but tomorrow might be a chance to get a more diverse group together before it’s all over.

Current Stuff: "Biotech for Homesteaders", CyclerCan, Biohacking Workshops

Hey all, Over at I’ve shared some of what I’m up to, and I may as well mirror it here! In a nutshell, I’m preparing for a five-day course of Biohacking workshops in the Science Gallery in Dublin, starting Tuesday and ending Saturday afternoon. I’ve had to prepare some mad inventions to make it happen due to equipment restrictions, which you might find amusing or exciting. The aim of the workshops is to deliver a crashcourse in literacy and skills in biohacking; you should come out of the workshops with a basic understanding of how DNA, RNA and Protein work, how bacteria work, and how to design and build your own GMOs.

Biohacking Crashcourse in Science Gallery, 14th - 18th June

It’s terribly late of me to share this on my own website, but here it is: This Tuesday next, 14th June, I’ll be commencing a five-day workshop in DIYbio and biohacking. The course is €150 and runs from 10am-3pm weekdays and 1-4pm on Saturday. Bookings through the Science Gallery please. Rough content breakdown by day: Introduction to Microbiology, Evolution, Genetics, Bacterial physiology, Synthetic Biology. Practical skills: Sterilising, maintaining sterility, basics of microbiology.

On Forensic DNA Evidence and Forged DNA

For context’s sake, let me say that at time of writing I am between Cork Airport and somewhere in London, attending the EU DIYbio Continental Congress, with the collective goal of developing a community code of bioethics and biosafety that we can hopefully ask the community at large to adhere to. I’ll be summarising and expounding on the experience afterwards, but for now I’m motivated to discuss something mostly unrelated. DNA Evidence; Great for a Portfolio, Bad in a Database There are rumblings here in Ireland of a Garda DNA database, as have been established elsewhere for law-enforcement purposes.

Dear all, my DIYbio plasmid has arrived

Some time ago I placed an order for a labour of love of mine: IndieBB. It’s a plasmid I designed to make cloning in Bacillus subtilis easier, faster and more reliable. Crucially, it’s also supposed to make the whole process antibiotic-free and DIYbio friendly. It’s going to be the flagship product of Indie Biotech if it works, and if it sells well enough I’m planning to offer additional cassettes that extend and enhance the plasmid, allowing customers to start performing practical synthetic biology with a minimal lab setup requirement.

Cork/Dublin Workshoppery

This Friday and Saturday, I’m hosting three daily sessions of a DIYbio workshop, focusing on Amateur Microbiology and Biotechnology. The DIYbio workshops are in the Camden Palace Building, in Nexus Cork (the Cork Makerspace). Following that, I’m hosting another DIYbio workshop at Mindfield on April 29th in the Hackerspace tent at 8PM, which will follow the same format as the above. This workshop will focus on microbiology, genetic engineering and synthetic biology as topics of discussion, and participants will be shown the basic techniques of Microbiology.

DIYbio talk at Barcamp Cork, Nov 20th

In case it’s up your alley, I’ll be giving a talk on Garage Biotech and DIYbio at Barcamp Cork on the 20th. It’s a free conference, it’s held in the webworks in Cork City Center, and there’ll be a ton of other interesting talks. My own talk will be a 35 minute affair, and I’ll be covering the “why” of Synthetic Biology, some crucial elements of Bacterial Physiology (specifically B.subtilis) you’ll need to know to get started, and some information on how _you_ can set up and get started performing synthetic biology experiments at home or with friends.

Follow-Through in Synthetic Biology Research

I have just read a pair of papers, both of which outline theoretical methods of creating synchronised oscillation circuits in bacterial cells. Synchronising Genetic Relaxation Oscillators by Intercell Signalling Modelling a Synthetic Multicellular Clock: Repressilators Coupled by Quorum Sensing In essence, the idea is to make bacteria who “blink” as whole colonies, by creating and destroying a fluorescent protein in an on-off manner at the same time as a group. This has been done in single cells, but as you might imagine the pattern of on-off gets lost in the crowd of a whole colony of millions, so the effect isn’t clear to the naked eye.