Everyone knows that Vim is the greatest of all editors but the story of it’s esoteric beginnings sourced to the late 60’s was too good to not share! Check it out!
https://twobithistory.org/2018/08/05/where-vim-came-from.html
Planet DNA goes to Cheltenham!
StandardLast week we took Bioprospecting On Mars on the road with a new updated hardware (but the same fundamentals) to Cheltenham science festival! The aim of the game to educate the young and old about how changing DNA sequences underlie different species, and how we can process those sequences and decode them to find the species and genetics it comes from.
Is it really science communication if you don’t gesticulate wildly?
Installed for 6 days, we had over 9,000 attendees to our tent, including school trips, the general public and the Friday night event for 18+, and had a consistent stream of enthusiastic individuals of all ages! It took 3 of us manning the stall at all times to handle the students hunting for the 12bp DNA sequences, decoding them into the raspberry pi computer (which has all keys except A, T, C & G removed), and then talking to them about the implications of those species:
- How could Rhizosphere bacteria be useful in growing plants?
- What does it mean that you found Salmonella enterica in the Astronaut kitchen?
- Is it important that we found Human DNA? Other humans on the planet or did you contaminate your sample?
- Why is there a DNA sequence for Jar Jar Binks?
The Maker-shack in its glory
If you want to see more photos and a making of, check out this link, or to see the coding and resources for the raspberry pi see the PlanetDNA github or the full documentation to go along with the DNA Guess who activity.
K-means clustering is not a free lunch
StandardI came across this awesome blog post and had to share here for posterity: http://varianceexplained.org/r/kmeans-free-lunch/
It makes great points about the underlying assumptions of using K-means clustering to find groups in your data and suggests other methods that perhaps you should be using instead. I know I’ve previously fallen in to the trap of just throwing data at k-means and hoping for the best.
Enjoy!
Example of a wrong thing!
Careers Week at Priory Community School
StandardI was very happy to get asked to speak to the pupils at my old Secondary School this week, as part of the careers event they have organised.
Going back to Priory was pretty astounding given all of the new facilities and building that have sprung up since I left 12 years ago! I set up in front of 50 science-interested year 10s and an enthusiastic year 7 to give them a rundown of how you go from GCSEs to a working research scientist, and why I think it’s a cool job! 
I also think it’s important not just to shill my own path, so gave a section over to the ecologists, doctors, industrial scientists and non-scientists that came the same route but spit off.
The session was rounded off with two additional Priory Alumni giving their paths since leaving into law or business. Hopefully the students get a lot out of the week and fingers crossed for some world-class scientists coming out of Priory in the years to come!
STEM live: Bioprospecting on Mars!
StandardIn the summer I was tasked with setting up an outreach activity to fit in with the Cardiff University STEM event themed around Life on Mars aimed at year 8 pupils (12/13 year olds). The invite was to all STEM schools and incorporated Biosciences, Chemistry, Physics, Computer Science, Maths and more. So I set my mind to what we could do on topic for a place renowned for its lack of life (so far!).
Mmmmm, Marsy
The underlying principle of the DNA Guess Who! activity was to explain the connection between a DNA sequence and the observed phenotype (i.e. ‘DNA is instructions’) and I set to retooling it as an example of an environmental DNA survey of a barren landscape in-fitting with the theme. With a region to search, a battleship-style peppering with simulated 12 base sequences, and a decoding computer for species identification, we had a DNA treasure hunt on our hands.
‘The Plan’
After a fair amount of work building a Mars-esque terrain, habitat pods, and coloured straws acting as DNA sequences, we were good to go (photo album, polystyrene everywhere). Obviously, we can’t go around telling the students that we’re actually finding life on Mars, so the plan was to develop a ‘test site’ for the proto-astronauts to hone their DNA decoding skills on.
On top of the spaced out (waaay, pun!) DNA sequences corresponding to various potential Martian inhabitants, we had some dangerous things (Salmonella in the kitchen pod), and the cautionary tale of finding ‘human-related DNA sequence’ in the field (aka contamination). On top of the full sequences, the students could search the terrain, test module bedrooms, kitchen or W.C. and build consensuses from incomplete ones mastermind style.
The setup
On the day we set up in the Sherman theatre, decked out in Mars themed banners, red light, and a spacey soundscape. Mission control was in the adjacent building with a more Earthy environment. The students rotated between the different schools in 20 minute blocks and we gave them an onverview and set them on their mission. Turns out we were working to a bit too complex of a concept to get across in 20 minute sessions so we mainly stuck to the complete sequences, but we got the message across!
Credit: Cardiff University photographer
Once they had the sequences translated from the magnetic straws via the 3D printed Mars Rovers into the ‘DNA signal’, they had to move it around to the decoding computers to find out what the sequence coded for. This was a little perl script which added some theatrics to the dictionary lookup, and then some fact sheets about the species found to act as discussion points.
All in all, the students seemed very on board with the activity and we held our own alongside the obviously very exciting Nerf gun and explosion-based activities from the other schools!
For more photos from the day check out this album (we were too busy to take too many photos unfortunately 😦 ) and I’ll be adding a materials and methods document similar to the Guess Who! page shortly.
Cardiff Awarded Silver at iGEM!
StandardAfter a great summer of work and a last minute rush to get the documentation written up and onto the wiki, the last part of the iGEM experience was the trip to Boston for the students to present the project to both the Judges and the other competitors.
After all the fun of a transatlantic flight and passing American security we managed to get to the booked AirBnB which was in a neighborhood about as American as one could expect. The evening and next day was committed to preparing and practicing the presentation which was being given by David, Andrew, and Asal, with Chris taking point on finishing up the poster.
Smoothing off the edges!
Poster Positioned Perfectly
Come Friday, and Cardiff was up to present straight after lunch and by that point the talk ran like a well-oiled machine. Donning our team T-shirts, we were cheering on from the sidelines. They did a great job and represented the project flawlessly (see more about the project here!), but we’d need to wait until Monday for the judges to give their verdict (spoiler: It’s in the blog title). In true Woodhousian fashion, the Hamburg team following us gave a stellar performance of a quite similar project, but we were happy with our job.
Over the next 2 and a half days there was ample opportunity to watch 1/8th of the sessions going on (hugely parallel!), or visit the huge poster hall and talk with the incredibly enthusiastic students (seriously, I’ve never been to a conference or scientific event of any kind where people were so upbeat!). The range, scope and detail of projects was incredible, especially given the short working schedule, and the integrated STEM and Design work lead to some amazingly complete products.
Once Monday came around, we were delighted to be awarded a Silver Award for the project which was well deserved by the work of the students. The winning teams of the major awards were incredible and you can check out more of their work at the official igem 2016 website.
Post-Silver Award Happiness!
With a day and a half left before the flight back there was time to see a bit of Boston and I picked up a bike for a cycling tour of MIT, Harvard, and the Downtown area. After visiting a slightly awkward reenactment of the Boston Tea Party (for an Englishman!) and the best lobster dinner of my life, off to the plane for the long flight back.
Incredible science, incredible cause, incredible venue. Roll on iGEM 2017
Brit on tour.
If you were so inclined, you can view the rest of the trip photos here!
iGEM Cardiff wrap up the project!
StandardThis summer I had the opportunity to act as an adviser to the Cardiff iGEM (International Genetically Modified Machines) team, the first entrant to the global competition from Wales since it’s inception in 2004. The competition is basically to design, produce, and test a novel Synthetic Biology product utilising both denovo designs and the wealth of materials that have been produced by teams over the previous years in and deposited in the BioBricks repository. Truly ‘Standing on the shoulders off giants’.
The International Genetically Engineered Machine (iGEM) Foundation is an independent, non-profit organization dedicated to education and competition, the advancement of synthetic biology, and the development of an open community and collaboration.
iGEM runs three main programs: the iGEM Competition – an international competition for students interested in the field of synthetic biology; the Labs Program– a program for academic labs to use the same resources as the competition teams; and the Registry of Standard Biological Parts – a growing collection of genetic parts use for building biological devices and systems.
-http://igem.org/About
The team was led by Dr Geraint Parry as the lead PI and I was on hand for the bioinformatic training and support, among other advisors who were specialists in synthetic biology (as I’m certainly not!). The 7 applying students took part in project conception and design, with some suggestions from the advisory team as to what was feasible (!) and they worked over the summer.
We’ve now submitted the project after a few bumps along the road, and the students have documented all their progress, successes, and issues on the wiki which I urge you to check out!
Next stop is the competition in Boston, USA, where we will be showcasing the project and going for a award!
Gene Sequencing practical for the Learn About Life: School Biosciences event
StandardI gave the first run of his gene sequencing practical for the Secondary School children visiting the university today for the Learn About Life annual BIOSI event for visiting Schools.
The School of Biosciences runs an annual event for visiting primary school pupils (9-11 years). This year’s event was run on Wednesday 3rd & Thursday 4th June, consisting of a series of rotating 15 minute workshops, run by staff and postgrad students. The workshops are divided into themed sessions on cells in the body, the natural environment, neuroscience and physiology.
Find out more, including all the downloadable resources at https://passdan.github.io/genesequencepractical/
Gene Sequencing Practical
Near-optimal RNA-Seq quantification with kallisto
Standard“The quantification of 78.6 million [RNAseq] reads takes 14 minutes on a standard desktop using a single CPU core.”
Currently the hot-topic on twitter, this new method of RNAseq quantification using psuedoalignment looks incredible, and could revolutionise our approach. Lior Patcher describes the process himself here, the arxiv here, and get to the github here.
Source: https://liorpachter.wordpress.com/2015/05/10/near-optimal-rna-seq-quantification-with-kallisto/
The Earthworm Microbiome – PhD thesis now available online
StandardMy thesis has now been ratified by the university and deposited in the database! You can download it here. The summary is below to whet your appetite!
Abstract
Background: Host-associated microbial communities play a significant role in a species’ environmental interactions, often performing functions unachievable by the eukaryotic host, and is essential in developing a comprehensive understanding of the species and its impact on the local and global ecosystem.
Earthworms (Lumbricina) habituate almost every type of soil environment globally, including sites of severe environmental stress and is an essential ecosystem engineer, central to healthy natural and agricultural soils. To date, only a singular symbiotic species (Verminephrobacter sp.) has been identified, but the earthworm impact on transient microbial communities and the surrounding soil microbiome is profound.
Methods: Previous culture and molecular based studies found earthworm-associated microbiota unlikely however, this has not been explored using High Throughput Sequencing. Utilisation of Illumina, 454 and Ion Torrent sequencing has enabled production of the highest resolution microbial analysis of host-associated bacteria of any single eukaryotic species to date, including spatial bacterial localisation of the entire Lumbricus rubellus organism and impact analysis of a wide range of anthropogenic contaminants and environmental stressors on the basal microbiomic community.
Results: A core bacterial community has been described which is distinct from the surrounding soil. A number of novel species have been associated with the earthworm crop, body wall and hindgut, contravening claims that the earthworm has limited or no impact on ingested soil bacteria. This demonstrate that the host properties impart significant effects on the transient population, demanding further analysis to determine potential symbiotic functionality. However, while a biologically important community has been described, the significant impact of anthropogenic contamination on the host microbiome must be considered given the observed eradication of the Verminephrobacter symbiont during the host’s exposure to arsenic and the potential subsequent implications on host health.
Dr Daniel Pass 