Diybio

Cork Biomakerspace, AKA Forma Biolabs: Some Updates

In the considerable time since my last update, much has changed around our biomakerspace project. All for the better, thankfully, though things remain a bit precarious (as ever). Firstly, as hinted in the title, the Cork biomakerspace project has a name: “Forma”! This name was inspired by that of La Paillasse (“The Bench”) transliterated to Irish. Given the choice between idiomatic but Anglicised “Bínse” or the probably Latin-derived “Forma” we chose the latter because the spelling is more obvious to non-Irish speakers and it sounds exactly as it is spelled in most English dialects.

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.

What Will Your IndieBB Be?

IndieBB stands for “Indie Biotech Backbone”. When I started this blog, I had intended “Indie Biotech” to be a phrase that could be generally used, not a “trademark” for my own work, yet people sometimes still refer to my project/company as “Indie Biotech” (I do have a company for this, and it’s called “Glowbiotics”, not “Indie Biotech”!). With the same spirit in mind, I named my plasmid backbone “Indie Biotech Backbone” because I wanted it to be something that could be used by “indie” genetic engineers worldwide to make their own stuff.

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.

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”.

Performing Minipreps with Homebrew Buffers

The alkaline-lysis miniprep is a critical tool in the arsenal of a molecular biologist. It allows one to rapidly isolate only plasmid DNA from a bacterial cell by leveraging the increased resilience of this (usually supercoiled) form of DNA against highly basic conditions. Minipreps are routinely performed to isolate plasmids that serve as substrates for further assembly work, for PCR amplification of specific gene segments, for direct application in other species or strains, or simply for archival uses (DNA can be easier and cheaper to store than the cells containing it).

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.

DIYbio UK Summit, Manchester Madlab

Here’s a belated notice for those able to make last-minute flightplans. This weekend, the Manchester Madlab are hosting a DIYbio Summit, and the lineup looks great. You can book places for the DIYbio Summit on Eventbrite; please come if you’re able, there’s already a great crowd due to attend. As for Indie Biotech, yours truly will be giving a 30 minute keynote on the first day. I’ll also be helping to facilitate several workshops over the weekend, with plans ranging from in-silico gene design (or, “How do I go from Concept to Ordered DNA?”), a rundown on Irish GMO Licensing Law (which is rather similar to the UK system), and assisting Brian Degger of Transitlab.org in giving a Webcam-Microscope hacking workshop.

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.

Biohacking and Ireland: A Forum on Future Prospects, Ethics and Law

It’s not too late for you to take part in the biohacking workshops that I’ve been facilitating in the Science Gallery this past week. It’s true, the wet-work is officially out of the way, and tomorrow’s session assumes some grounding that has been provided in prior days. However, the last day will focus not on the methods, nor even the knowledge of biotech. Instead, we’ll focus on the role of biohacking in society, with a particular focus on the transformative power of DIY biotech, the social responsibility and ethics that this calls for, and the particulars of Irish law regarding biohacking.

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

Hey all, Over at IndieBiotech.com 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.

Current Projects at Indie Biotech

Update: I deleted my Google account so the video is broken. If I find it later I’ll re-up. :) Here’s some stuff I’m doing at the moment that you might find interesting. If you’re going to say “Hey, aren’t you supposed to be biohacking and genetic engineering and such?”, I’m awaiting a verdict from the Irish EPA regarding a site license. I’ll detail my experiences with the Irish GMO regulation system when I’ve come out the other end, one way or another.

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.

Current Work: Kombucha

By way of apology for the prior wall-of-text post, I’ll include here some information on what I am currently doing in the lab. Nothing’s ready or completed, but I figure some insight into my workings and goals at present might be nice. In keeping with my general intention to make it as easy as possible for amateurs to get into Biotech, I would like to offer a number of pretty easy starter cultures that people can get started with while not requiring too much early investment in equipment.

Post Mindfield 2011

Needless to say for many of my visitors, doubtless directed here by a surprisingly popular video of a DNA extraction I performed on a Banana at Mindfield, the event was a big hit for DIYbio/Amateur Biotech. Indeed, it was a hit from almost every angle I can personally imagine, although I’ll save a full round-up of events for my personal blog (my mind was somewhat blown open by the festival). Here, I’ll just share the highlights that might be relevant to DIYbioers.

Mindfield Workshop

As mentioned previously, I’ll be offering a repeat of the Cork workshop at Mindfield this Friday. You can register here if you think you’d like to come along; it’s free! The workshop is tailored toward absolute beginners, and starts with an introduction to Biology, Microbiology and Biotechnology, followed by a discussion on DIYbio and Amateur or “Indie” Biotech, an introduction to a specific bacteria I particularly like, and a chance for participants to actually start growing the bacterium then and there.

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 in Dublin, 2pm April 12th (Tomorrow!)

Dear all, there will be a DIYbio meetup in the cafe of the Science Gallery (Pearce Street, Dublin) tomorrow at 2pm. The event is better documented here, with a list of currently registered attendees: [http://diybiodublin.eventbrite.com][] It’s free and informal. If you like DIYbio to some extent and you’re free, please come along! The point? To meet, greet, and perhaps discuss not-so-weighty matters like forming a regional identity for Irish DIYbio. I’ve been informed by the great people at the Science Gallery that they’ll be closing early to prepare for their next exhibition, so the event is set to begin at 2 and end at 4.

Maker Faire 2011 Debriefing

Maker Faire 2011 was, true to expectations, even bigger and better than last year. Expecting as much, Brian Degger and I were prepared. Our DIYbio table was a big improvement on last year, with more interaction and more experimentation on our part than before. As bad luck would have it, our location was very poor compared to last year; our stand was in the Convention Center, a room of wonders that was thoughtfully omitted from the maps and for which there were no signs to follow.

Maker Faire Setup

Maker Faire UK 2011 begins tomorrow, and today exhibitors are being given a chance to set things up and prepare. As we’re offering a DIY microbiology event, we’ll need happy plates of microbes to work with, so our incubator is getting set up and our HEPA will be running on low speed to prepare for the day to come. By way of update, we actually have only 50 plates to give out due to damaged dishes in the package I received.

Maker Faire UK and DIYbio Dinner

Maker Faire is creeping up on me, and I have limited time to prepare as I’m leaving for Scotland/NW England early for a bit of a holiday. So, my last few days have been spent in hectic preparation for the event. Myself and Brian Degger will be hosting a table on DIYbio and Indie Biotech, as we did last year, but we are making a strong effort this time around to include more interactive exhibits.

DIYbio and Indie talk, Ignite Dublin #6

Work is progressing very well on the first Indie Biotech wetware product, a plasmid vector for DIYbio. To my knowledge, nobody has yet attempted to produce a novel cloning vector by total synthesis before, certainly not for Bacillus subtilis. I’m attempting something largely unprecedented, which ought to be worrying but instead feels exciting. I don’t want to share too much at this stage (familiarity breeds contempt, after all), but I will say that I’m attempting to hit as many birds with one stone as possible.

2010, an Excellent Year In Review

Well, everyone is doing it so I may as well jump on board. As it happens, 2010 has been a really, really exciting year for me, so writing this will be an indulgent remembrance. In fact, looking back this morning, I was surprised at how much of the things I’ve lately been happy with took place in 2010; some of them seemed like so long ago. Like any year, it’s been full of good, bad and ugly, but for the most part good.

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.

Garage Biotech at Barcamp Cork, Ignite Dublin

Introductory Note Perhaps a quick word of introduction. If you don’t know me yet, welcome to Indiebiotech.com, my name is Cathal Garvey, and I live in Cork City in Ireland. I’m an avid DIYbio enthusiast, a trained and fairly experienced molecular biologist (specifically, a Geneticist). I believe that everyone with an interest in DIYbio and Synthetic biology should be able to learn and access easily what they need to start experimenting, because I know that until that happens nobody will trust this amazing, transformative technology, even as it grows and develops without them.

Biocurious: Final Lap, Nature Publication. Jump On Board!

I’ve written before about Biocurious, the nascent Hackerspace for Biology that is raising money to rent out a real, no-kidding biotech lab full of professional equipment for community and citizen science. It’s ambitious, it’s brilliant, and it’s already resulted in a study that’s been published in Nature Medicine (a very prestigious journal even for well-equipped lab scientists), long before they reach their funding goal. The study in question was an excellent example of the power of citizen science and collaborative work.

Some cool resources for Homebrew Science

While researching homebrew chromatography, I got seriously sidetracked by several cool blogs on DIY science. DIYBIO4Beginners is over a year old, and has a huge number of posts covering mostly practical aspects of learning about Biotech and DIYbio. Of particular interest are the posts that contain video series’ teaching you about Biotech/Biochem, or “How-To”, etc. There’s a lot of stuff in there, much of it news coverage, but the signal-to-noise is really excellent.

An Analysis of What #DIYbio Has and What It Needs

DIYbio and its more professionally oriented cousin, Garage Biotech, are undergoing a revolution at present. Essential equipment that used to cost thousands is now available at affordable prices, in many cases under open licensing schemes and open to community development. Knowledge of biology, genetics and the procedures underlying it all is being disseminated in ever-more-abstracted forms to make it easier to get started. And soon, even the biological components: strains, enzymes and substrates, will likely become mass-marketable.

Makerfaire Newcastle Update: A DIYbio Success Story

Folks from Makerfaire: Here’s a link to the Instructions for Making DIY Microbial Media (the homebrew petri dishes) and Isolating Bioluminescent Bacteria! Give them a read through, and let me know if you try them and what results you got! Take care! I’ve just returned this evening from Makerfaire: Newcastle. I had an amazing time, and I was thoroughly inspired by the people I met there and the things they’re doing.

Newcastle Maker Faire

Tomorrow, I disappear to Maker Faire Newcastle to meet Brian Degger of Transitlab.org, see loads of Makers and made things, and help give a workshop on DIYbio. Should be fun! If you’re about Newcastle, look us up at the event!

Isolation and Culture of Bioluminescent Bacteria

Update: Keep your bacteria in the dark. I had been doing this without meaning to, and was confused to hear a fellow microbiologist growing a derivative of my cultures in her lab and getting no glow. When she grew them in the dark, they glowed again! Brief exposures have no effect. It’s the prevailing light conditions that seem to decide whether to stay active. This may be due to the light breaking down the little peptide the bacteria use to detect whether there are enough of them to glow meaningfully, or it might be a deliberate evolutionary adaptation.

Homebrew Bacterial Media for the Microbiology Hobbyist or DIYbio Enthusiast

Update: The links to these files have always been precarious, sorry.. I’ve just re-uploaded the two main files, and soon I’ll be reworking them into my “biohacking protocols” repository on Github in Markdown format with separate images. Enjoy! Life is, as ever these days, quite busy! I have two trips coming up, one to Ignite in Dublin and one to the Newcastle Maker Faire (where Brian Degger of Transitlab.org and I will be hosting a little workshop on a few DIYbio experiments and fun stuff).

Cargo Cults and Electrophoresis

Toward the latter half of WWII, landing strips and airbases were being built all over the Pacific on small, otherwise totally isolated islands. Little contact was made with the natives to explain what was going on, and in some cases the locals were incredulous to see the new arrivals performing strange rituals on their tarmac runways and receiving airdropped “gifts” from the gods/ancestors. When the bases were abandoned, in some cases the locals started replicating the structures and activities of the base personnel, performing marches and drills, talking into replica radios, and waving lit firebrands on the runways and waving them.

Dremelfuge: It works, and it's Available

Long Overdue Update: I’m very proud to say that, some time back, I updated the Dremelfuge design with better tolerances and a better shape to handle tubes. When I tested it (only once so far) at full speed on a dremel with two tubes full of fruit smoothie, it didn’t eject or break the tubes at all. So there you go, Dremelfuge can now be considered the world’s cheapest midi-ultra-centrifuge, capable of putting about 52,000g on up to six 1.5ml eppendorf tubes.

DremelFuge, First Go

I’ve had on my mind an idea for some time that I’ve wanted to try. Having a Makerbot has enabled me to experiment with mad science on a level I’ve not been able to before, so here it is: DremelFuge, a printable drill/rotary tool attachment that spins microcentrifuge tubes! I uploaded a quickly mashed-together first draft to Thingiverse, but didn’t have a chance to print it that day as planned because I lost my laptop in town while Christmas shopping.

First Test Setup of OpenThermo Project

Long Overdue Update: This post has turned out to be one of the all-time most popular on my site, which surprises me to no end. Who’d have thought my crummy heatsink-and-tin thermal cycler would be cooler than isolating glowing bacteria or printing a 52,000g centrifuge? But, who am I to question human interest. It’s not like my interests are particularly normal anyway. However, I do think this post needs updating, since people keep returning to it and asking questions.