March 12, 2009

Defrosting the Digital Seminar

The Lecture by James M ThorneCasey Bergman suggested it, Jean-Marc Schwartz organised it, so now I’m going to do it: a seminar on our Defrosting the Digital Library paper as part of the Bioinformatics and Functional Genomics seminar series. Here is the abstract of the talk:

After centuries with little change, scientific libraries have recently experienced massive upheaval. From being almost entirely paper-based, most libraries are now almost completely digital. This information revolution has all happened in less than 20 years and has created many novel opportunities and threats for scientists, publishers and libraries.

Today, we are struggling with an embarrassing wealth of digital knowledge on the Web. Most scientists access this knowledge through some kind of digital library, however these places can be cold, impersonal, isolated, and inaccessible places. Many libraries are still clinging to obsolete models of identity, attribution, contribution, citation and publication.

Based on a review published in PLoS Computational Biology, http://pubmed.gov/18974831 this talk will discuss the current chilly state of digital libraries for biologists, chemists and informaticians, including PubMed and Google Scholar. We highlight problems and solutions to the coupling and decoupling of publication data and metadata, with a tool called http://www.citeulike.org. This software tool exploits the Web to make digital libraries “warmer”: more personal, sociable, integrated, and accessible places.

Finally issues that will help or hinder the continued warming of libraries in the future, particularly the accurate identity of authors and their publications, are briefly introduced. These are discussed in the context of the BBSRC funded REFINE project, at the National Centre for Text Mining (NaCTeM.ac.uk), which is linking biochemical pathway data with evidence for pathways from the PubMed database.

Date: Monday 16th March 2008, Time: 12.00 midday, Location: Michael Smith Building, Main lecture theatre, Faculty of Life Sciences, University of Manchester (number 71 on google map of the Manchester campus). Please come along if you are interested…

[CC licensed picture above, “The Lecture” at Speakers Corner by James M Thorne]

January 22, 2007

DNA mania

Filed under: bio — Duncan Hull @ 10:29 pm
Tags: , , , ,

What does DNA do when it’s not being transcribed into RNA? It causes DNA mania…

Quote of the Day

“DNA, you know, is Midas’ gold. Everyone who touches it goes mad.”

Maurice Wilkins

Read the rest in [1,2]

Do you or your colleagues ever suffer from DNA mania [3,4]? A biochemist friend of mine once semi-jokingly remarked that people’s manic obsession with DNA is a bit like buying some food and being more interested in the bar-code on the packaging, than the food inside. In his particular area of research, DNA is about as exciting as bar-codes, because it doesn’t even leave the nucleus of the cell, at least in Eukaryotes. I wonder what readers of nodalpoint think of this analogy? Anyway, as a result of this philosophy, most of his community have developed an unhealthy and manic interest in proteins rather than DNA. You could call this particular obsessive-compulsive disorder “protein mania”.

Depending on the scientific obsession(s) of your particular community, you might need to substitute Protein or RNA for DNA in the above quote, as appropriate. And if that is all too molecular for you, substitute any other of your favourite bioinformatics buzzwords.


  1. Horace Freeland Judson (1996) The Eighth Day of Creation: Makers of the Revolution in Biology
  2. John Sulston (2006) Won for All: How the Drosophila Genome was sequenced: a book by Michael Ashburner
  3. André Pichot (1999) Histoire de la notion de gène (one of the first documented uses of the phrase “DNA mania”)
  4. Denis Noble (2006) The Music of Life: Biology Beyond the Genome (an antidote to DNA mania and the Dawkinian gene-centric view of Life)
  5. DNA Photograph taken by Unapersona in Ciutat de les Arts i les Ciències, Calatrava building, Valencia, Spain.

November 28, 2006

Postdoc Hell: Should I Stay Or Should I Go?

Postdoc Hell? "Please dispose thoughtfully of your used postdocs"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. They are worth reading if you’re at an early stage of your career, although you may not always agree with all the advice given. For example, the article advises PostDocs to:

Think very carefully before extending your graduate work into a postdoc in the same laboratory where you are now – to some professionals this raises a red flag when they look at your resume. Almost never does it maximise your gain of knowledge and experience, but that can be offset by rapid and important publications.

Do any experienced postdocs (or post-postdocs) out there have an opinions on the importance of moving labs after a PhD? What if you’re already in a great lab and like where you work? To what extent is it important to move, just to get new experience and skills? Or as The Clash once put it [4]:

♫ If I go there will be trouble, if I stay it will be double.
So come on and let me know, should I cool it or should I blow? ♫


  1. Phillip Bourne (2006) Ten Simple Rules for Getting Published PLOS Computational Biology
  2. Phillip Bourne and Leo Chalupa (2006) Ten Simple Rules for Getting Grants PLOS Computational Biology
  3. Phillip Bourne and Alon Korngreen (2006) Ten Simple Rules for Reviewers PLOS Computational Biology
  4. Joe Strummer and Mick Jones (1981) Should I stay or should I go?
  5. Jawahar Swaminathan (2006) A ten step plan for PostDoc training nodalpoint.org
  6. this post originally on nodalpoint with comments
  7. Postdoc Hell, a collection of articles describing the plight of the postdoctoral researcher on citeulike

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update: Mysteriously, Nature jobs used the Clash as a theme to their careers supplement, two weeks after this post was published. See How to ask yourself questions about major career decisions and Should I Stay Or Should I Go?. Coincidence? I wonder if they read nodalpoint?

October 20, 2006

Manchester Biocentre Launch

MIB: Spot the test tubeThe 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. If you’re looking for a bioinformatics job, PhD, PostDoc etc in the UK, MIB is continuously hiring and looks like a good place to work, if the opening programme (which follows) is anything to go by.

Unfortunately the MIB web pages aren’t quite world class yet, the promotional launch material is only available in pdf format, *sigh*, see references below. So I’m blogging the MIB Symposium launch programme here to put the stuff online. Talks scheduled for the second day of the opening, 26th October 2006, are listed below, and these can be attended by free registration (see references):

Session 1: Bio-molecular machines, 9.00-11.00

Session chaired by Alan North, Dean of the Faculty of Life Sciences

  • John E. Walker (MRC Dunn Human Nutrition Unit, Cambridge, UK): Biomolecular rotary motors.
  • Yoshi Nakamura (Tokyo University, Japan): Aptamer as RNA-made super antibody for basic and therapeutic applications
  • John McCarthy, (Manchester Interdisciplinary Biocentre): Molecular mechanisms underlying post-transcrptional gene expression.
  • Refreshment break

Session 2: Biomolecular Structure and Dynamics, 11.00-12.40

Session chaired by Bob Ford, Professor of Structural Biology, Faculty of Life Sciences.

Session 3: Systems and Information, 13.35-15.45

Session chaired by John Perkins, Dean of Faculty of Engineering and Physical Sciences.

Session 4: Biocatalysis, 16.10-17.00

Session chaired by Hans Westerhoff, Manchester Interdisciplinary Biocentre

  • Nigel Scrutton (MIB and Faculty of Life Sciences): ‘Squeezing’ barriers – a dynamical view of enzyme catalysis.
  • Gill Stephens, (MIB and School of Chemical Engineering): Redox biocatalysis – the next generation of enzymes for manufacturing pharmaceutical intermediates and specialty chemicals.

Session 5: Bionanoscience and engineering: 17.00-18.00

Session chaired by Peter Fielden, Chemical Engineering

  • Joseph Wang (Arizona State University, USA): Nanomaterials for monitoring and controlling biomolecular interactions.
  • Milan Stojanovich (Columbia University Medical School, New York, USA): Deoxyribozyme-based devices.

Session 6: Postgenomic Analytical Technologies, 18.00-19.10

Session chaired by Roy Goodacre, MIB and School of Chemistry

  • Ruedi Aebersold (ETH Zürich): Quantitative Proteomics and Systems Biology
  • Simon Gaskell, MIB and School of Chemistry: New analytical science in proteomics and metabolomics.
  • Concluding remarks.

October 8, 2006

Bio-Ignorance: Communicating Biology to Computer Scientists

The Human GenomeMany 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?

Progress in both computer science and biology is closely linked and dependent on people understanding each others strange language, cross-pollinating ideas and creating technology which hopefully has hybrid vigour. So for example, biologists and bioinformaticians have a healthy apetite for all kinds of better, cheaper, faster and sometimes novel computation. This requires they understand basic computer science and software enginnering. In the other direction, computer scientists often need realistic scenarios to motivate the invention, development and testing of genuinely novel technology. As for the software engineers, more on them later…

It sounds great, but before you can even say the words “inter-discplinary”, there are considerable barriers to communication. The various camps speak different languages, and have radically different cultures. To illustrate this communication breakdown, here is a story from the lab where I work. A while ago, I was discussing the Gene Ontology with a colleague, who shall remain anonymous. This colleague was educated, doing PhD level research and what I’d consider a fairly typical computer scientist. Soon the conversation turned to chromosomes, and they asked me:

“What is a Chromosome?”

Initially I was shocked. How could somebody not know what a chromosome was? Had they never read a newspaper? Never watched the television? Surely, most people have at least a vague idea what a chromosome is? After recovering from the shock, I told this person that according to the Gene Ontology a chromosome is “a very long molecule of DNA and associated proteins that carries hereditary information.” Perhaps this bio-ignorance is an extreme case, but unfortunately, it is all too common. Many computer scientists and software engineers I know stopped studying biology as soon as they possibly could, opting for the so-called “harder” sciences: physics, chemistry and mathematics. Consequently, many (but not all) computer scientists are bio-ignorant. What can we do about it? We really need to understand each other if we are going to make any progress. How can we improve communication between biologists and computer scientists?

Part of the solution to this problem is well-written literature that explains basic concepts quickly and clearly without getting bogged down in jargon or stuck on esoteric details, see the references below for some examples. One of my personal favourites is a little book called The Human Genome: a beginner’s guide to the chemical code of life authored by Jeremy Cherfas. This book is lavishly illustrated and beautifully written, but most importantly of all at 72 pages it is blisteringly concise, so stands a chance of being read by computer geeks and nerds. It is even funny in places, the Nobel laureate and geneticist Thomas Hunt Morgan is amusingly depicted as a red-eyed wild type, just like the fruit flies he studied. Anyway, I lent my copy of said book to my computer science buddy, and they learnt not just what chromosomes are, but also a little bit about why Biology and Genetics are such fascinating subjects.

The literature listed below can help one-way understanding of biology by outsiders, but communication is a two-way street. What about the other direction? Is there any literature that explains computer science and software engineering specifically to biologists and bioinformaticians? I don’t know of any particularly good examples, that are concise, well written and illustrated, but perhaps you do. I’ve frequently found bioinformaticians and biologists misunderstand what computer science is about, and confuse it with software engineering, but that is another story. The moral of this story is, don’t be surprised if people working in different fields to you lack a basic understanding of what you consider fundamental concepts that everybody knows. If they are bio-ignorant computer scientists, you should patiently and tirelessly explain yourself and maybe point to some of the resources below. Maybe we can understand each other just a little better.


  1. Anonymous GO:0005694 Chromosome: A very long molecule of DNA AmiGO! Your friend in the Gene Ontology
  2. Alvis Brazma, Helen Parkinson, Thomas Schlitt and Mohammadreza Shojatalab (2001) All you need to know about biology in twenty pages European Bioinformatics Institute (EMBL-EBI) (A technical introduction, written for EBI employees, but useful elsewhere)
  3. Jeremy Cherfas (2002) The Human Genome: a beginner’s guide to the chemical code of life (isbn:0751337161) Dorling Kindersley (A quick but informative introduction that your granny could understand)
  4. Jeremy Cherfas (2006) International Plant Genetic Resources Institute (IPGRI) public awareness blog IPGRI, Rome, Italy. (Some deserved nodalpoint Google Juice for these news and press releasess)
  5. Carole Goble and Chris Wroe (2005) The Montagues and the Capulets: In fair Genomics, where we lay our scene… Comparative and Functional Genomics 5(8):623-632 (A paper describing communication breakdown between two different research “houses”, very possibly the only paper on genomics that will make you laugh. seeAlso Shakespearean Genomics: a plague on both your houses)
  6. John Gribbin Dorling Kindersley’s Essential Science: Human Genome, Global warming, Expanding universe, Food for the future, Digital revolution and How the brain works http://www.dk.com (Some interesting books here)
  7. John W. Kimball Chromosomes Kimball’s Biology Pages (How does John Kimball manage to write so much good introductory material sabout Biology?)
  8. John Bonham, John Paul Jones and Jimmy Page (1969) Communication Breakdown Led Zeppelin (Communication breakdown, it’s always the same, I’m having a nervous breakdown, drive me insane!)
  9. This post was originally published on nodalpoint with comments.

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