Michael Ley is visiting Manchester this week, he will be doing a seminar on Wednesday 3rd June, here are some details for anyone who is interested in attending: Date: 3rd Jun 2009 Title: DBLP: How the data get in Speaker: Dr Michael Ley. University of Trier, Germany Time &amp;

Michael Ley is visiting Manchester this week, he will be doing a seminar on Wednesday 3rd June, here are some details for anyone who is interested in attending:

 References

Lincoln Stein (2002). Creating a bioinformatics nation: screen scraping is torture Nature, 417 (6885), 119-120 DOI: 10.1038/417119a

Michael Ley on Digital Bibliographies

The Red Rose of Lancaster is the county flower of Lancashire. Image by Sodacan, created with Inkscape. [CC BY-SA 3.0] via Wikimedia Commons.Once upon a time, there were two football teams, a Northern one (Liverpool F.C.) and a Southern one, (Tottenham Hotspur F.C.). They were due to meet each other in a historic and lucrative match: the 2019 UEFA Champions League Final in Madrid.

Are Liverpool and Manchester still in Lancashire?

bbc.co.uk/programmes as a QR Code by /Sizemore/ Mike Atherton on Flickr available under a creative commons licence  Over at @BBCSport and @BBC2012 there are some Olympian feats of big data wrestling going on behind the scenes for London 2012 [1]. While we all enjoy the Olympics on a range of platforms and devices, a team of twenty engineers is busy making it all happen.

Where did all the BBC programme metadata go? The Infax catalogue online

Last week I attended the first Teaching and Learning conference in the Pendulum hotel, Manchester.

Last week I attended the first Teaching and Learning conference in the Pendulum hotel, Manchester. It was really good and I got lots out of it. The sessions I attended were enjoyable and well organised, I learned heaps, made lots of new contacts and got some useful questions from the audience on my lightning talk about podcasting the student voice.

Improving the Institute for Teaching and Learning (ITL) conference in Manchester for 2024

Following on from our discussion of ungrading, this month we’ll be discussing pass/fail rates in introductory programming courses. [1] Here is the abstract: Vast numbers of publications in computing education begin with the premise that programming is hard to learn and hard to teach.

Following on from our discussion of ungrading, this month we’ll be discussing pass/fail rates in introductory programming courses. [1] Here is the abstract:  As usual, we’ll be meeting on zoom, see sigcse.cs.manchester.ac.uk/join-us for details. Thanks to Brett Becker and Joseph Allen for this months #paper-suggestions via our slack channel at uk-acm-sigsce.slack.com.

Join us to discuss failure rates in introductory programming courses on 1st Feb at 2pm GMT

Learning can be an emotional process and we often don’t realise when we are actually learning. When you’re listening to an expert explain something well, it’s easy to mistake the speaker’s smooth delivery for your own understanding. You might feel like you’re learning, but actual learning is often hard work and feels uncomfortable.

Learning can be an emotional process and we often don’t realise when we are actually learning. When you’re listening to an expert explain something well, it’s easy to mistake the speaker’s smooth delivery for your own understanding. You might

 feel

like you’re learning, but

 actual

learning is often hard work and feels uncomfortable.

Join us to discuss the feeling of learning ❤️ (vs. actual learning) on Monday 4th April at 2pm BST

Some rough and ready notes from day two of the first ChEBI workshop, 20th May 2008. There were two talks, one from Kirill Degtyarenko (European Patent Office) and the other from Janna Hastings (EBI), followed by a discussion.

First ChEBI workshop, Day Two

The fourth International Science Foo Camp (scifoo) 2009 has just concluded. Here are some very brief and incomplete notes and links from some of the sessions on the second day (Saturday), see the scholarly kitchen for a report on the first day.

Science Foo Camp 2009: Scifoo Day Two

Fabio Rinaldi is currently visiting Manchester from the University of Zurich, he will be doing a seminar on Monday 6th July, the details of which are below.

Fabio Rinaldi is currently visiting Manchester from the University of Zurich, he will be doing a seminar on Monday 6th July, the details of which are below.

 References

Rinaldi, F., Kappeler, T., Kaljurand, K., Schneider, G., Klenner, M., Clematide, S., Hess, M., von Allmen, J., Parisot, P., Romacker, M., &amp;

Fabio Rinaldi on OntoGene

The organisers of the Science Online London 2009 conference are asking people to propose their own session ideas (see some examples here), so here is a proposal: Title: Who Are You? Digital Identity in Science Many important decisions in Science are based on identifying scientists and their contributions.

The organisers of the Science Online London 2009 conference are asking people to propose their own session ideas (see some examples here), so here is a proposal: If this is a successful proposal, I’ll need some help. Any offers? If you are interested in joining in the fun, more details are at scienceonlinelondon.org

 References

Bourne, P., &amp;

Who Are You? Digital Identity in Science

I look at the world and I notice it’s turning While my keyboard gently weeps With every mistake we must surely be learning Still my keyboard gently weeps Oh oh oh oh oh oh oh oh oh, oh oh, oh oh Yeah yeah yeah yeah yeah yeah yeah yeah.

I look at the world and I notice it’s turning  While my keyboard gently weeps  With every mistake we must surely be learning  Still my keyboard gently weeps  Oh oh oh oh oh oh oh  oh oh, oh oh, oh oh  Yeah yeah yeah yeah  yeah yeah yeah yeah.

While My Keyboard Gently Weeps

With apologies to Jonathan Swift: So what happened was, Carole Goble asked on the myExperiment mailing list, “is there a list of scientist social networking sites”? Here is first attempt at such a list (

 not

comprehensive), you’ll have to decide for yourself which are the great, greater, little and lesser sites. For simplicity, I’ll break social software down into social networking, data sharing, blogging, ranking and video.

myScience: “social software” for scientists

Details of two-day conference titled “Biological Complexity: From Molecules to Systems” at University College London (UCL) in June 2008 have recently been announced. Speakers and topics are described in the link above and also by Martyn Amos on his blog.

Details of two-day conference titled “Biological Complexity: From Molecules to Systems” at University College London (UCL) in June 2008 have recently been announced. Speakers and topics are described in the link above and also by Martyn Amos on his blog. Speakers from the UK include: Martyn Amos, Cyrus Chothia, Jasmin Fisher, Mike Hoffman / Ewan Birney, Jaroslav Stark, Michael Sternberg and Perdita Stevens.

Biological Complexity

Long jumper for Snohomish. Creative Commons licensed picture by by Philo Nordlund on Flickr  If Science were an Olympic sport, which events would scientists excel at?  During the Beijing Olympics in 2008, I wondered what Olympic activities scientists would be good at, with a list of events.

Olympic Science: The Long Jump to Conclusions

UK news-rag The Grauniad has a series of interviews with some of the people behind the next generation web, so-called Web 2.0. After reading these interviews, I can’t help wondering, who are the equivalent pioneers in bioinformatics? The interviews include… Wikipedian Jimmy Wales WordPresser Matt Mullenweg Technorati’s Dave Sifry …and several others too.

UK news-rag

 The Grauniad

has a series of interviews with some of the people behind the next generation web, so-called Web 2.0. After reading these interviews, I can’t help wondering, who are the equivalent pioneers in bioinformatics? The interviews include… Wikipedian Jimmy Wales WordPresser Matt Mullenweg Technorati’s Dave Sifry …and several others too.

People 2.0: Pioneers of the next generation Web

Today, the 20th July 2009, is the 40th anniversary of the first lunar landing. There has been plenty of global coverage, stargazing, astronautical analysis and heavenly commentary recently. But for me personally, the Apollo 11 anniversary brings back fond memories of rocket science lessons [1] – specifically, the things I learned in Chemistry at school.

How to be a Rocket Scientist

A brief report (well just some scribbled notes, bullet points and links really) on the third and final day of Network Applications and Tools in Biology (NETTAB) 2009 in Catania, Sicily. There was a special section on Methods and Tools for RNA Structure and Functional Analysis.

A brief report (well just some scribbled notes, bullet points and links really) on the third and final day of Network Applications and Tools in Biology (NETTAB) 2009 in Catania, Sicily. There was a special section on

 Methods and Tools for RNA Structure and Functional Analysis

. Disclaimer: RNA mania isn’t really my thing – so the RNA presentations and papers are grossly under-represented in this mini-report (sorry).

Nettab 2009 Day Three: Semantic Integration

In my inbox this morning, an intriguing email from Timo Hannay, Tim O’Reilly and Chris DiBona: Duncan, We’d like to invite you to join us for Science Foo Camp (or “Sci Foo”), a unique, invitation-only gathering organized by Nature, O’Reilly Media, and Google, and hosted at the Googleplex in Mountain View, California.

In my inbox this morning, an intriguing email from Timo Hannay, Tim O’Reilly and Chris DiBona:  Obviously I’m thrilled to bits to receive such an email, I’ve been to scifoo once before and it was a fantastic mind-blowing experience. This time, I’m invited as a consolation prize for being a runner-up in the international science blogging challenge 2009 which challenged younger scientists to get a senior scientist to blog.

Upcoming Gig: Science Foo Camp (scifoo) 2009

Despite what some people think (see “the myth of the lone inventor” in [1]) most scientists are usually pretty sociable people. Science is an inherently social activity [2], just take a look around you. Most laboratories are full of like-minded people working on related problems, our lab is no exception.

The Loneliness of the Long Distance Researcher

At the Microsoft e-Science workshop in Indianapolis, earlier this week Carole Goble was awarded with the first Jim Gray 2008 e-Science award, pictured here collecting the prize from Tony Hey of Microsoft Research.

At the Microsoft e-Science workshop in Indianapolis, earlier this week Carole Goble was awarded with the first Jim Gray 2008 e-Science award, pictured here collecting the prize from Tony Hey of Microsoft Research. You can read all about it in the Seattle Tech Report which says:  It is very inspiring when colleagues win prizes and awards.

Congratulations Carole Goble, e-Scientist

If you travel back in time, to around 2002, it isn’t difficult to find people claiming that Web services were going to be the new silver bullet technology to create world peace, eradicate global poverty and finally make some sense of all the data produced by the human genome project. Over hyped? Just a bit.

Embracing Registries of Web Services

Nature Publishing Group are organising a workshop on science blogging, this Saturday 30th August 2008 at the Royal Institution of Great Britain in London. Why would you care? Because there are: Lots of interesting people… …talking about a range of interesting subjects … .. in a distinguished venue that has recently been refurbished.

Nature Publishing Group are organising a workshop on science blogging, this Saturday 30th August 2008 at the Royal Institution of Great Britain in London. Why would you care? Because there are: Lots of interesting people… …talking about a range of interesting subjects … .. in a distinguished venue that has recently been refurbished. It is also home to the fantastic Christmas lectures and much more besides.

Science blogging at the Royal Institution, London

With sincere apologies to Jamaican reggae singer-songwriter Eric Donaldson, “ChEBI, Oh ChEBI, Oh Baby, don’t you know I’m in need of thee”? Chemical Entities of Biological Interest (ChEBI) is a dictionary, controlled vocabulary, database, ontology of small (low molecular-weight) chemical entities that are considered to be biologically interesting, (like amphetamine (CHEBI:2679) for example). After a […]

With sincere apologies to Jamaican reggae singer-songwriter Eric Donaldson, “ChEBI, Oh ChEBI, Oh Baby, don’t you know I’m in need of thee”?  Chemical Entities of Biological Interest (ChEBI) is a dictionary, controlled vocabulary, database, ontology of  small (low molecular-weight) chemical entities that are considered to be biologically interesting, (like amphetamine (CHEBI:2679) for example). After a couple of recent meetings, ChEBI is going

ChEBI, Oh ChEBI, Oh Baby!

This thing called Science, whatever it is, who actually owns it? Scientists? Technology companies? Industrial Biotechnology and Pharmaceutical companies? Investors? Shareholders? Governments? Universities? Philanthropists? Charities? Publishers? Joe Public? Or none of the above…? The Scientists.

This thing called Science, whatever it is, who actually owns it? Scientists? Technology companies? Industrial Biotechnology and Pharmaceutical companies? Investors? Shareholders? Governments? Universities? Philanthropists? Charities? Publishers? Joe Public?

Who Owns Science?

Michael Ashburner at the University of Cambridge once famously quipped that “Biologists would rather share their toothbrush than share a gene name” [1]. And so we have many different colourful and imaginative names for genes. The same mis-naming rule applies the reactants and products (input and output) of metabolism.

Michael Ashburner at the University of Cambridge once famously quipped that “Biologists would rather share their toothbrush than share a gene name” [1]. And so we have many different colourful and imaginative names for genes. The same mis-naming rule applies the reactants and products (input and output) of metabolism. Here are some example names, would you like to share my toothbrush chemical name?

Would you like to share my toothbrush?

(To be spoken in the best SoCal Valley Speak you can muster) I went down to the beach and saw Yahoo She was, like, all “semantic web” And I was, like, “whatever!” References Liam Lynch (2003) (Well this is my) United States of Whatever Yours Truly (2007) Burn, Semantic Web Burn!

(To be spoken in the best SoCal Valley Speak you can muster) I went down to the beach and saw Yahoo She was, like, all “semantic web” And I was, like, “whatever!”

 References

Liam Lynch (2003) (Well this is my) United States of Whatever Yours Truly (2007) Burn, Semantic Web Burn! Yours Truly (2005) Rethinking the Semantic Web, The Semantic Web (stack): Will It All End In Tiers?

Semantic Web? Yeah, Whatever!

There are a growing number of biomedical services out there on Wild Wild Web for performing various computations on DNA, RNA and proteins as well as the associated scientific literature. Currently, using and debugging these services can be hard work.

There are a growing number of biomedical services out there on

 Wild Wild Web

for performing various computations on DNA, RNA and proteins as well as the associated scientific literature. Currently, using and debugging these services can be hard work. SOAP UI (SOAP User Interface) is newish and handy free tool to help debug services and get your

 in silico

experiments and analyses done, hopefully more easily.

Debugging Web Services

Chemical Entities of Biological Interest (ChEBI) release 67 is now available, containing 548,850 total entities, of which 20,565 are annotated entities and 720 were submitted via the ChEBI submission tool.

Chemical Entities of Biological Interest (ChEBI) release 67 is now available, containing 548,850 total entities, of which 20,565 are annotated entities and 720 were submitted via the ChEBI submission tool. New in this release, the ChEBI ontology is now available in the Web Ontology Language (OWL), which is part of an ongoing research project to automate the classification of small molecules in ChEBI.

8-OHdG: Entity of the Month

Many people are still trying to work out exactly what twitter is good for [1] but with more than 100 million users worldwide making around 50 million tweets per day, the website is clearly popular with those who like to communicate via short “sound bites” of 140 characters or less.

Many people are still trying to work out exactly what twitter is good for [1] but with more than 100 million users worldwide making around 50 million tweets per day, the website is clearly popular with those who like to communicate via short “sound bites” of 140 characters or less. Communication is an important part of what Universities are all about, so how many UK universities are on twitter?

The University of Twitter, UK: A Quick Survey

Cartoonist and engineer Tim Hunkin is probably best known for his exhibits at the Science Museum in London and his Under The Pier Show “a mad arcade of home-made slot machines &amp; simulator rides on Southwold Pier, Suffolk”.  His website is a treasure trove of weird and wonderful things.

Hunkin’s Hypothesis: Technology Is What Makes Us Human

There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd.

The Semantic Biochemical Journal experiment

Wandering the Immeasurable: A sculpture at CERN by Gayle Hermick, picture re-used with permission from the artist  Even if you’re not a Physicist, there is plenty to see and do above and below ground at the European Organization for Nuclear Research (CERN). Home to the worlds largest experiment on what is arguably the worlds largest machine near Geneva in Switzerland, CERN is a very inspiring place to visit.

Seven things to do at CERN if you’re not a Physicist

The year 2016 will go down as an interesting one, but was it magnificent, horrible or stupid? Or perhaps all three Annus mirabilis? 🇬🇧 For some people, 2016 was a good year, an annus mirabilis. If you voted for Trump or are brexiteer who voted to leave the European Union, 2016 was a good year.

The year 2016 will go down as an

 interesting

one, but was it magnificent, horrible or stupid? Or perhaps all three

 Annus mirabilis?

For some people, 2016 was a good year, an

 annus mirabilis

. If you voted for Trump or are brexiteer who voted to leave the European Union, 2016 was a good year. If you are a climate change denier, you probably enjoyed 2016 too.

2016: Annus mirabilis, annus horribilis or annus stupidus?

Sometimes, being a PostDoctoral researcher is a tough life. Thankfully, help is at hand in Philip Bourne and Iddo Friedberg‘s guide Ten Simple Rules for Selecting a Post-Doctoral Position published in PLOS Computational Biology.

Sometimes, being a PostDoctoral researcher is a tough life. Thankfully, help is at hand in Philip Bourne and Iddo Friedberg‘s guide Ten Simple Rules for Selecting a Post-Doctoral Position published in PLOS Computational Biology. This article is part of a series of editorials [1,2,3] which discuss various aspects of the weird and wonderful world of scientific research.

Postdoc Hell: Should I Stay Or Should I Go?

The Manchester Interdisciplinary Biocentre (MIB) is officially opening on 25/26th October 2006. The centre has been about a decade in the making, and aims to be a world-class research centre, with around £37 million (~$70 million) of initial funding from the Wellcome Trust charity, UK Research Councils and others.

The Manchester Interdisciplinary Biocentre (MIB) is officially opening on 25/26th October 2006. The centre has been about a decade in the making, and aims to be a world-class research centre, with around £37 million (~$70 million) of initial funding from the Wellcome Trust charity,  UK Research Councils and others.

Manchester Biocentre Launch

The BBC programme catalogue has recently gone online, and provides a demonstration of the applications that can be built using web technology such as Ruby on Rails, RDF, FOAF, web feeds, tag clouds and sparklines.

Bioinformatics at the BBC: Demonstrating the power of metadata

Open Access (OA) publishing aims to make the results of scientific research available to the widest possible audience.

The Open Access Irony Awards: Naming and shaming them

Androids by etnyk. What are they thinking? With more than three million Android devices activated on the 24/25th December 2011 [1] and something like 200 million (or more?) Android devices in total, there are nearly enough droids around to build a primitive brain.

Does Android Dream of Electric Sheep?

A crude score for benchmarking scientists Have you ever wanted to compare different scientists by their publication record? It’s not always an easy task, but here is a crude and handy way to benchmark people by their journal publications in Nature, Science or PNAS using PubMed.

A crude score for benchmarking scientists

Have you ever wanted to compare different scientists by their publication record? It’s not always an easy task, but here is a crude and handy way to benchmark people by their journal publications in

 
 N
 
 ature

,

 
 S
 
 cience

or

 
 PNAS
 

using PubMed.

NSPNAS: Nature, Science or PNAS?

Alan Turing Binary code, Shoreditch High Street, London by Chris Beckett on Flickr (CC-BY-NC-ND license)  Over at democracy corner, Manchester Digital is interviewing all of its elected council members.

Two big challenges facing the technology &amp; digital industries (IMHO)

The Small Scale Experimental Beer Machine (aka Manchester Beerby) has its name in neon lights and was switched on on the 21st June 2019. A new pub has opened opposite where I work. Set up by some enterprising scotsmen from Aberdeenshire ( och aye laddie!), it has its very own microbrewery.

The Small Scale Experimental Beer Machine aka “Manchester Beerby”

In 2013, 44% of newly elected Fellows of the Royal Society had biography pages on wikipedia. Earlier this month confusingly-named “Royal Society” announced their new fellows for 2013. The society is made up of (quote):  A quick-and-dirty measure of the scientific coverage of wikipedia is the percentage of these fellows that have a profile on wikipedia at the time of their election to the prestigious Society.

Measuring scientific coverage of @Wikipedia: Fellows of the Wiki Society index 2013

Thirteen year old Amy Mather aka @MiniGirlGeek steals the show at Manchester Raspberry Jam 2013  Last Saturday, the first ever Raspberry Jamboree rolled into town, organised by the unstoppable force of nature that is Alan O’Donohoe (aka @teknoteacher). The jamboree looked at the educational value of the Raspberry Pi (a $25 computer) one year on from its launch on the the 29th February 2012. Here are some brief and incomplete

Creating with the Raspberry Pi vs. Consuming Apple Pie at the Manchester Raspberry Jamboree

There’s an interesting article [1] by Chelsea Wald in Science magazine published today, about Open Science including Open Source Code, Open Notebook Science, Open Data and Open Access Publishing.

There’s an interesting article [1] by Chelsea Wald in

 Science

magazine published today, about Open Science including Open Source Code, Open Notebook Science, Open Data and Open Access Publishing.

Embracing Open Science

So, I’m going to San Francisco and on to the Googleplex in the heart of Silly Valley, California for Science Foo Camp (scifoo) 2009.

So, I’m going to San Francisco and on to the Googleplex in the heart of Silly Valley, California for Science Foo Camp (scifoo) 2009. As I put the Flowers In My Hair (what’s left of it) and confirm my booking at the Hotel California I’m not just California Dreamin’ but California Googlin’. Just how many American and Californian musical clichés it is possible to cram into one blog post and accompanying iPod playlist?

California Googlin’

It’s Friday, so here’s another one of those cool RSA Animate videos by Cognitive Media. This one is narrated by Microsoftie Manuel Lima and describes how the tree structures that we know and love, such as the infamous tree of life are becoming inadequate for organising knowledge, despite having been useful for thousands of years.

From Useful Trees to Powerful Networks: A talk by Manuel Lima from Microsoft

An equation of love (x² + y² − 1)³ − x² y³ = 0  Former Mancunian James Lovelock runs the kind of a laboratory most scientists can only fantasise about working in as they grind through the humdrum bureaucracy of peer-review and never-ending grant applications. Lovelock is fortunate enough to run a completely independent, self-funded lab located in the beautiful West Country.

The Lovelock Laboratory: A fantasy workplace in the West Country

As Tom Lehrer once sang on his christmas carol:  Which must mean it’s also time for another seasonal tradition: the Royal Institution Christmas lectures.

Happy Christmas Lectures 2010

If you took an infinite number of Professors, added some comedians, recording studios (instead of typewriters) and got them to record random radio shows you might just end up with a program like the Infinite Monkey Cage.

If you took an infinite number of Professors, added some comedians, recording studios (instead of typewriters) and got them to record random radio shows you

 might

just end up with a program like the Infinite Monkey Cage.

The Infinite Professor Theorem

♫ PCR, When you need to know who the Daddy is ♫ …  When you’ve finished chuckling at that ridiculous viral marketing video, go and Dance Naked in the Mind Field with Kary Mullis. Found via Respectful Insolence: Scientists for better PCR.

Who’s the Daddy? PCR…

Maybe you wrote that code and maybe you didn’t. If Artificial Intelligence helped you, such as the OpenAI Codex in GitHub Copilot, how did it solve your problem? How much did AI help or hinder your solution?

Maybe you wrote that code and maybe you didn’t. If Artificial Intelligence helped you, such as the OpenAI Codex in GitHub Copilot, how did it solve your problem? How much did AI help or hinder your solution? Join us to discuss a paper by Michel Wermelinger from the Open University published in the SIGCSE technical symposium earlier this month in Toronto on this very topic.

Join us to discuss using AI to solve simple programming problems on Monday 3rd April at 2pm BST

A thought experiment with lots of money The Biotechnology and Biological Sciences Research Council (BBSRC) is the United Kingdom’s funding agency for academic research and training in the non-clinical life sciences.

A thought experiment with lots of money

The Biotechnology and Biological Sciences Research Council (BBSRC) is the United Kingdom’s funding agency for academic research and training in the non-clinical life sciences.

How to spend a £400 million Science budget

Writing good code is often harder than it looks via Randall Munroe at xkcd.com  Manchester Digital is the independent trade association for the thriving digital sector in the North West of England. Last night they held their AGM and elections for new members of their council.

Manchester Digital and Higher Education in 2013

This years Reith Lectures by Martin Rees are being broadcast on BBC Radio 4 during June. An important theme in the lectures this year is scientists relationship with society.

Martin Rees on Science and the Citizen

The organisers of the Science Online London 2009 conference are asking people to propose their own session ideas (see some examples here), so here is proposal: Title: Blogging For Profit: Costs and Benefits What are the costs and benefits of blogging and how can you make sure the latter justifies the former?

The organisers of the Science Online London 2009 conference are asking people to propose their own session ideas (see some examples here), so here is proposal:  If this is a successful proposal, I’ll need some help. Any offers?

Blogging For Profit: Costs and Benefits

Via the Official Google Research Blog at the University of Google, Alon Halevy, Peter Norvig and Fernando Pereira have published an interesting expert opinion piece in the  March/April 2009 edition of IEEE Intelligent Systems: computer.org/intelligent.

The Unreasonable Effectiveness of Google

Any budding biomedical scientists out there, interested in doing a PhD, take note: The European Molecular Biology Laboratory (EMBL) – European Bioinformatics Institute (EBI) is having an open day on Monday 3rd November 2008.

PhD studentships at EMBL-EBI, UK

I’m not much of an evolutionary biologist, but Jonathan Eisen asked for help and I can’t resist. So, in the name of Science, here is some deserved Google Juice for various Trees of Life on the Web.

The Tree of Life

What exactly is a drug? A project I’m currently working on requires a good solid definition, at the very least comprehensible to humans, and preferably understandable by more intelligent, semantically aware computers too.

The drugs don’t work, they just make you worse

There are a number of “Molecule of the Month” style mini-reviews on the web, which highlight one particular molecule (usually a protein) every month, in an accessible style.

There are a number of “Molecule of the Month” style mini-reviews on the web, which highlight one particular molecule (usually a protein) every month, in an accessible style. Two of my personal favourites are protein spotlight: one month, one protein written by Vivienne Baillie Gerritsen of the Swiss-Prot team and Molecule of the Month at the Protein Databank PDB edited by David Goodsell.

This month’s molecule is…

Many computer scientists and software engineers are not familiar with basic biology or bioinformatics. Many biologists and bioinformaticians are not familiar with basic computer science or software engineering. This article points to some resources that can help with the former, and asks, what can be done about the latter?

Bio-Ignorance: Communicating Biology to Computer Scientists

Today, Tuesday the 14th of October 2008, is Open Access Day. Like many others, this blog post is joining in by describing why Open Access matters – from a personal point of view.

Today, Tuesday the 14th of October 2008, is Open Access Day. Like many others, this blog post is joining in by describing why Open Access matters – from a personal point of view. According to the wikipedia article Open Access (OA) is “free, immediate, permanent, full-text, online access, for any user, web-wide, to digital scientific and scholarly material, primarily research articles published in peer-reviewed journals.

Open Access Day: Why It Matters

Wiki Loves Scientists   Jess Wade, editor extraordinaire, in 2017. Portrait by Dave Guttridge via Wikimedia Commons CC BY-SA  Today Jess Wade published her one thousandth new Wikipedia article, a wiki-biography of Sylvie Briand. This biography joins 999 others Jess has written at a rate of one per day since September 2017.

Congratulations and thank you Jess Wade for 1000 new biographies @Wikipedia 🏆

Delegates at the Computing at School conference 2017 #CASConf17 answering diagnostic questions, picture by Miles Berry. The Computing At School (CAS) conference is an annual event for educators, mostly primary and secondary school teachers from the public and private sector in the UK. Now in its ninth year, it attracts over 300 delegates from across the UK and beyond to the University of Birmingham, see the brochure for details.

Nine ideas for teaching Computing at School from the 2017 CAS conference

There is growing interest in Wikipedia, Wikidata, Commons, and other Wikimedia projects as platforms for opening up the scientific process [1]. The first Wikipedia Science Conference will discuss activities in this area at the Wellcome Collection Conference Centre in London on the 2nd &amp; 3rd September 2015.

Wikipedia Science Conference @WellcomeTrust in London, September 2nd &amp; 3rd 2015 #wikisci

The artist Andy Warhol once said:  This well worn saying has been quoted and misquoted in hundreds of different ways in the forty years since Warhol first coined it [1].  Bad Scientist Ben Goldacre, in his keynote speech* at Science Blogging (sciblog) 2008, highlighted one of these deliberate misquotes, which he attributed to NTK.net (Need To Know: Britain’s most sarcastic high-tech weekly newsletter). It goes a little something like this:  This

Famous for fifteen people

Christmas lectures 2014 by @Ben_Nuttall  Our homes are full of technology that we typically take for granted and understand little. Your average smartphone or tablet, for example, is a “black box”, that deliberately discourages modification by tinkering and hacking.

Makey Christmas and a Hacky New Year!

According to the urban myth, the eskimos have hundreds of words for snow. But meteorologists, especially British weather forecasters, have just as many words for rain. Take this typical forecast for example: TODAY: Showers will continue in the north and west, but become more lighter and more isolated as the night progresses.

Sunny intervals? Really? According to the urban myth, the eskimos have hundreds of words for snow. But meteorologists, especially British weather forecasters, have just as many words for rain. Take this typical forecast for example:  Many people just want to know will it rain today and should I take a brolly?

Weasel Words of Weather Forecasters: Will it rain today?

I’m Sorry I Haven’t A Clue, also unavailable on Samsung Android devices. I’m Sorry I Haven’t A Clue (ISIHAC) is a superbly funny comedy show broadcast by the BBC since 1972 and currently airing it’s sixtieth (yes 60th!) series. Unlike many other BBC programmes, ISIHAC is mysteriously unavailable as a podcast, which makes it difficult to listen to offline. Why is this?

I’m Sorry I Haven’t A Podcast, now on BBC Radio 4

“I have learned much from my teachers and even more from my friends, but from my students I have learned most of all” Graduation is one of the most enjoyable milestones in the academic calendar.

“

 I have learned much from my teachers and even more from my friends, but from my students I have learned most of all

” Graduation is one of the most enjoyable milestones in the academic calendar. It’s a chance to celebrate and reflect on what students have learned and how they have grown during the time they have spent at University.

…from my students I have learned most of all

All your dreams are made, when you’re chained to the lecture and the teaching trade. Was that lecture, lab or lesson a dream or a nightmare? Exactly what did you learn from the experience? When you reflect on it, how will you tell yourself and others the stories of your study?

What’s the Story, Learning Glory? How we can start telling better stories about teaching in Higher Education

Creative Commons licensed picture of a DayGlo Raspberry Pi by @kevinv033 on Flickr  STEMNet is an organisation in the UK which creates opportunities to inspire young people in Science, Technology, Engineering and Mathematics (STEM). Recently, along with about 15 PhD students from the CDT in Manchester, I became an STEM Ambassador. This post briefly describes what STEMNet is all about, why you would want to get involved and how you can do so.

On becoming a STEMnet ambassador: What, why and how?

Any list of 100 best anything is going to be riddled with biases, flaws and omissions, but here’s a list of albums you might enjoy listening to from 100best.music.apple.com.

Any list of

 100 best

anything is going to be riddled with biases, flaws and omissions, but here’s a list of albums you might enjoy listening to from 100best.music.apple.com. I’ve posted them here because my family are listening to three albums a week throughout 2025, and discussing them as we go. The albums are listed in reverse order of “greatness“ below, as we’re starting from the top.

One hundred albums you might enjoy listening to

Airplane by By Kuster &amp; Wildhaber Photography  The Software Sustainability Institute www.software.ac.uk has launched a Fellowship programme that recognises outstanding UK-based researchers who use software. The Fellowships come with £3000 funding which can be used for travel, collaboration and running events.

Fancy becoming a Software Fellow?

The Parthenon at night by Konstantinos Dafalias, creative commons licensed picture available on Flickr. If you look carefully, you can see the inscription “Elgin woz ‘ere, 1801” where the Marbles were stolen from. Here is a recipe and serving suggestion for delicious Parthenon Marbles cake, originally developed by Thomas Bruce, better known as Lord Elgin.

Delicious Parthenon Marbles Cake, stolen from Athens

Have you ever been asked WHAT SCHOOL DID YOU GO TO? I was once asked this in a high-stakes job interview and my answer was that of a startled rabbit caught in the headlights before becoming squashed roadkill on the highway to hell. Nobody has asked me that question before or since.

Have you ever been asked WHAT SCHOOL DID YOU GO TO? I was once asked this in a high-stakes job interview and my answer was that of a startled rabbit caught in the headlights before becoming squashed roadkill on the highway to hell. Nobody has asked me that question before or since. How can such a simple question be so difficult to answer?

SO, WHAT SCHOOL DID YOU GO TO?

The British Monarchy are preparing to exploit new advertising opportunities and boost royal revenue during the 2012 Olympics in London. Photo credit: gokart.co.uk.  Advertising agencies are everywhere, there is no escaping them. But who’s the daddy of the advertising world? The mother of all ad agencies? According to wikipedia, WPP is the “world’s largest advertising group by revenues”. This is hogwash.

Who is the World’s Largest Advertising Agency?

Forty two years ago I wrote my first bit of software on a BBC Micro in the Code Club at Fitzmaurice Primary School.

Hello World: GOTO Christmas 1981

Science, is a big word that gets used and abused with reckless abandon. Virtually any discipline can award itself extra kudos by adding the magic S word at the end. For example, which sounds weightier, sports studies or sports science?

Science, is a big word that gets used and abused with reckless abandon. Virtually any discipline can award itself extra kudos by adding the magic S word at the end. For example, which sounds weightier, sports studies or sports science? This phenomenon has been noticed many times before, for example, the philosopher John Searle once remarked that:  So let’s make a list.

Anything that calls itself a Science, probably isn’t…

Whatever your views on Facebook [1], you can’t deny that from space, “Planet Facebook” looks rather intriguing. The wonderful diagram below of Facebook connections has been made by Paul Butler.

Planet Facebook

Madder than the Mad March Hare, more entertaining and surreal than Alice down-a-rabbit-hole in Wonderland: today marks the start of this years Cambridge Science festival: “Delve into the diversity of science at the Cambridge Science Festival 2010!

Madder than the Mad March Hare, more entertaining and surreal than Alice down-a-rabbit-hole in Wonderland: today marks the start of this years Cambridge Science festival:  A team of scientists and engineers from the Wellcome Trust Sanger Institute and The EBI will be participating, on Saturday 13th March with a session on DNA, diversity and you and also tackling the thorny issue of Who Owns Science? on Friday 19th March.

Cambridge Science Festival, 8th-21st March 2010

If you wanted to write a guide to Biomedical and Biological Ontologies [1], especially the what, why, when, how, where and who, there are at least three choices for publishing your work: Journal publishing in your favourite scientific journal. Book publishing with your favourite academic or technical publisher.

If you wanted to write a guide to Biomedical and Biological Ontologies [1], especially the

 what

,

 why

,

 when

,

 how

,

 where

and

 who

, there are at least three choices for publishing your work:

 Journal publishing

in your favourite scientific journal.

 Book publishing

with your favourite academic or technical publisher.

O'Really?