May 11, 2012

Journal Fire: Bonfire of the Vanity Journals?

Fire by John Curley on Flickr

Fire by John Curley, available via Creative Commons license.

When I first heard about Journal Fire, I thought, Great! someone is going to take all the closed-access scientific journals and make a big bonfire of them! At the top of this bonfire would be the burning effigy of a wicker man, representing the very worst of the vanity journals [1,2].

Unfortunately Journal Fire aren’t burning anything just yet, but what they are doing is something just as interesting. Their web based application allows you to manage and share your journal club online. I thought I’d give it a whirl because a friend of mine asked me what I thought about a paper on ontologies in biodiversity [3]. Rather than post a brief review here, I’ve posted it over at Journal Fire. Here’s some initial thoughts on a quick test drive of their application:


On the up side Journal Fire:

  • Is a neutral-ish third party space where anyone can discuss scientific papers.
  • Understands common identifiers (DOI and PMID) to tackle the identity crisis.
  • Allows you to post simple anchor links in reviews, but not much else, see below.
  • Does not require you to use cumbersome syntax used in ResearchBlogging [4], ScienceSeeker and elsewhere
  • Is integrated with citeulike, for those that use it
  • It can potentially provide many different reviews of a given paper in one place
  • Is web-based, so you don’t have to download and install any software, unlike alternative desktop systems Mendeley and Utopia docs


On the down side Journal Fire:

  • Is yet another piece social software for scientists. Do we really need more, when we’ve had far too many already?
  • Requires you to sign up for an account without  re-using your existing digital identity with Google, Facebook, Twitter etc.
  • Does not seem to have many people on it (yet) despite the fact it has been going since at least since 2007.
  • Looks a bit stale, the last blog post was published in 2010. Although the software still works fine, it is not clear if it is being actively maintained and developed.
  • Does not allow much formatting in reviews besides simple links, something like markdown would be good.
  • Does not understand or import arXiv identifiers, at the moment.
  • As far as I can see, Journal Fire is a small startup based in Pasadena, California. Like all startups, they might go bust. If this happens, they’ll take your journal club, and all its reviews down with them.

I think the pros mostly outweigh the cons, so if you like the idea of a third-party hosting your journal club, Journal Fire is worth a trial run.


  1. Juan Carlos Lopez (2009) We want your paper! The similarity between high-end restaurants and scientific journals Spoonful of Medicine, a blog from Nature Medicine
  2. NOTE: Vanity journals should not to be confused with the The Vanity Press.
  3. Andrew R. Deans, Matthew J. Yoder & James P. Balhoff (2012). Time to change how we describe biodiversity, Trends in Ecology & Evolution, 27 (2) 84. DOI: 10.1016/j.tree.2011.11.007
  4. Shema, H., Bar-Ilan, J., & Thelwall, M. (2012). Research Blogs and the Discussion of Scholarly Information PLoS ONE, 7 (5) DOI: 10.1371/journal.pone.0035869

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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