How To

Fit for Purpose: Linux Mint Debian Edition on Sony Vaio Flip 13

Update: Since writing this, I have two things to add. Firstly, Linux Mint are terrible custodians of a distro and should no longer be trusted; they end-of-life’d LMDE mid-cycle with no upgrade/escape path to Debian, which is simply sloppy, and their packaging system for stock Linux Mint has come under scrutiny for being amateur-hour BS. Secondly, all of the below is now outdated, because Ubuntu works perfectly out of the box on this laptop, without any further hax or modifications.

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.

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.

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).

The Shortlist of Free-Speech Software For Our Newly Censored Ireland

So, our great and glorious Minister Sean Sherlock just signed SOPA into law in Ireland, despite a huge civil outcry. The poorly defined statutory instrument will allow anyone claiming “Copyright Infringement” to seek a court injunction against any website, without having to present evidence and without a consultation with the accused website. The form of the resulting censorship is unclear, but will probably require ISP-level DNS censorship of websites outside Ireland, or direct seizing of those within the Irish jurisdiction.

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 and I will be hosting a little workshop on a few DIYbio experiments and fun stuff).

Internet Security: Chapter 1

Well, I promised a post on Privacy and Security online, and it’s been long in coming. I’ll admit that’s because for all that I’d love to waffle on ad infinitum, I haven’t done enough research to know that everything I’m saying is up-to-date. So, to strike a nice middle ground I’ll split the post instead. In this installment, rather than offering “active” advice (such as what to install and how to browse), I’ll offer the groundwork and the basics of how to “passively” be more secure online and how to preserve your security.

Digital Privacy: An Upcoming How-To

I have a personal interest in my privacy both online and in the physical world. There’s no real reason behind it besides a knowledge that it is my right not to have my privacy invaded, and a feeling of insult that it is invaded anyway on probably a daily basis. Sources of this invasion include my ISP, Marketing Widgets on the internet, Possibly the odd hacker and the NSA, who are doubtless running programs that scan my email and monitor browsing statistics to identify them terrur-wrists at work on the internet.