Duncan Hull › Comments

"There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia (http://www.getutopia.com) and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses: Blogs for biomedical science Biomedical Ontologies – OBO etc Project Prospect and the Royal Society of Chemistry The Chemspider Journal of Chemistry The FEBS Letters experiment PubMedCentral and BioLit [2] Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3] The Elsevier Grand Challenge [4] Liquid Publications The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it? The Semantic Biochemical Journal project with Utopia Documents [5] The review asks what advances these projects have made and what obstacles to progress still exist.... more... - Duncan Hull from Bookmarklet

Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9 - joergkurtwegner

Excellent, this is a much better approach than an author ID system... - Greg Tyrelle

2% false negatives is not nearly good enough on its own. It would be a great way to pre-populate an author ID system and then finish it off by hand, though. - Björn Brembs

A comprehensive update on the human protein resource - Frank from iPhone

Egon, It was just made with the titles of the articles. Anyway, the word "RDF" doesn't appear in the abstracts - Pierre Lindenbaum

Quite a milestone :) - Graham Steel

@Jason Any idea how many of those are duplicates? See also buggotea http://www.google.com/search... - Duncan Hull

Viva la interwebs! - Duncan Hull

The Fourth Paradigm: Data-Intensive Scientific Discovery, download here: http://research.microsoft.com/en-us... - Greg Tyrelle

sent! - JJ

It's barely worth reading, Duncan... - Graham Steel

If you weren’t able to attend this years Christmas lectures in person, they are televised tonight in the UK on More4 from 7pm. This year, they are given by Professor Sue Hartley [1] (pictured right) from the University of Sussex. Here is some blurb on the series from the Royal Institution called “The 300 million year war“... - Duncan Hull

"If Agile is the teachings of Jesus, Scrum is every abuse ever perpetrated in his name. In many ways, Scrum as practiced in most companies today is the antithesis of Agile, a heavy, dogmatic methodology that blindly follows a checklist of "best practices" that some consultant convinced the management to follow." - Duncan Hull

"Throughout the course of 2009, PLoS has been adding a range of Metrics to each and every article that it has published. In addition to the many metrics already displayed (article pageviews and downloads, citations, social bookmarks, notes, comments and ratings), we are pleased to now add data relating to the blog coverage of any article, as measured by ResearchBlogging.org. You can find out more about the Article Level Metrics program here. Every interested author and user can now see how many times an article has been downloaded (split into HTML Pageviews, PDF and XML downloads and displayed in a month-by-month format); how often an article has been cited (as measured by PubMed Central, Scopus and CrossRef); how many times it has been ‘socially bookmarked’ (at CiteULike and Connotea); how many times users have Commented, or left Notes, or provided Ratings; and how many blog articles have been written about it (as measured by the blog aggragators Postgenomic, Blog Lines, Nature Blogs and, from today, ResearchBlogging.org)." - Duncan Hull from Bookmarklet

Google Browser Size is a visualization of browser window sizes for people who visit Google. For example, the "90%" contour means that 90% of people visiting Google have their browser window open to at least this size or larger. This is useful for ensuring that important parts of a page's user interface are visible by a wide audience. On the example page that you see when you first visit this site, there is a "donate now" button which falls within the 80% contour, meaning that 20% of users cannot see this button when they first visit the page. 20% is a significant number; knowing this fact would encourage the designer to move the button much higher in the page so it can be seen without scrolling. To view your own Web site with this same visualization overlaid on it, simply type its URL into the "Enter URL here" textbox at the top of the window and click Go. - Duncan Hull

"Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races." - Itachi from Bookmarklet

Certainly, one could never use knowledge of how drugs work differently in different genetic backgrounds to help cure disease, right? - Mr. Gunn

We present ChemAxiom as the first ontological framework for chemistry in science. ChemAxiom enables discourse about chemical objects in a computable language and is useful for the management of chemical concepts and data, the retrospective typing of resources, the identification of ambiguity and supports chemical text mining. - Duncan Hull

Hi Jean-Claude. I am sure it will be possible. I'll email you offline. Duncan, thanks for the ping! - Nico Adams

Had the pleasure of visiting the exhibit a couple of months ago. Highly recommend the Wellcome Collection, if you find yourself in Euston with some time to kill. - Neil Saunders

Thanks, Neil, that sounds like a great idea! - Cesar Sanchez

@Neil aye: see http://www.wellcomecollection.org/ - Duncan Hull

"Don't rely on your host or anyone else to back up your important data. Do it yourself. If you aren't personally responsible for your own backups, they are effectively not happening." - Duncan Hull

Nice article. Not sure about "Exaflood"?! Add that to "the metaphors of doom used to describe the phenomenal pace of data acquisition (from data floods, deluges, surging oceans and tsunamis, to icebergs, avalanches, earthquakes and explosions)"... http://pubmed.gov/19929850 - Duncan Hull

Now I have scenes from a disaster movie in my head, as scientists race to save the world from the data deluge... - Neil Saunders

Good idea putting this PDF up. It's my opinion that you should go for option B, as it will allow you to not only have the extra attributes (souce/value etc), but will allow you to later add new attributes of the Synonym class if you ever need it. I haven't worked much with annotation properties - can the reasoner see them in the same way as it can see the datatype and object properties? - Allyson Lister

@Duncan, that is certainly one synonym you could apply to it, I can think of many others.. :) - Frank

This workshop will present how scientists are currently using the Web, and discuss the functionality that is required to make the Web an ideal platform for both cutting edge scientific collaboration and for managing health care and life science related data. We would encourage submission of papers covering the following topics: Web 2.0 applications for large, heterogeneous and complex data sets, Models for collaborative scientific annotations, Tools and applications for aggregating information across web sites, Provenance, attribution, trust, and intellectual property and Policy for data access, sharing, and anonymization - Duncan Hull

See also http://esw.w3.org/topic... - Duncan Hull

Do you feel scientifically isolated? Do you find yourself sitting on the side-line while others take the field by the nose and lead it? Are you unable to publish a model that summarizes your data and ideas because reviewers label it as being too speculative and unsupported? Can't get those experiments published in any regular journal? Do you find that nobody is citing your papers? Haven't published in your field for some time, but want to show that you are still a player? Well, no need to worry! There is a special category of publication for you, 'the invited review', and even specialized journals, the 'review journals', that cater to every part of your neurosis. - Duncan Hull

I still think stand-alone reviews should be abandoned in favour of collaboratively written updatable documents (who said wiki?). - Daniel Mietchen

The accompanying online Database Collection, available at http://www.oxfordjournals.org/nar..., now lists 1230 carefully selected databases covering various aspects of molecular and cell biology. - Duncan Hull

what do you think of this? "By contrast, early bioinformatics work was almost invariably founded on biological concepts from the onset. A biological issue was raised and then a technique to address that issue was presented. That is, theoretical biology was the foundation on which [early] bioinformatics was built. I fear this is being lost in the mass-data and technology-hype driven bioinformatics. It seems to me that unless companies and research groups are careful many will waste time and money “stamp collecting and cataloging”. Certainly the organized data is useful, but only if it is applied with biological principles." - Attila Csordas from Bookmarklet

Grant: it's really good to see you here, every time I cite somebody living here I have the hidden motive to draw the author into this community, get her/him involved, make him/her part of a 'community of equals'. The paragraph cited is itself a good source to initiate a standalone conversation here w/o reflecting to everything in your article. That sad, I encourage people to continue this conversation here. :) - Attila Csordas

A senior scientist once told me "We all work in public relations"... - Duncan Hull

I think they were right. - f1000

the lights will go out automatically due to having no money to pay the bills - Frank

I guess I won't be moving back any time soon :-( - Sarah Kendrew

This article is now most viewed in the last 30 days at Genome Biology http://genomebiology.com/article... with >4000 views - Duncan Hull

ABSTRACT: As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU... more... - Duncan Hull

Traditional wisdom and empirical observation unite in recommending a 7 year unit for measuring human life - including individual and institutional science. But, because of astronomy and the decimal system, things tend to be measured either in years, five years or in decades. A year is too short while a decade is too long to measure the trends and transitions of individual or institutional life. And the half decade, such as the 'five year plan' beloved by politicians and bureaucrats seems too short. Therefore, seven years should become the standard unit for tracking trends and measuring attainment. Precedents for using a seven year unit include the notorious Jesuit saying: 'Give me the child until he is seven, and I will show you the man'; and the 'ninth commandment' of Leo Szilard: 'Do your work for six years; but in the seventh, go into solitude or among strangers, so that the memory of your friends does not prevent you from being what you have become'. In a scientific career, seven... more... - Duncan Hull

Wonder if Bruce Charlton is the seventh son of a seventh son? http://www.ncbirofl.com/2009... - Duncan Hull

Oh brother. I'm quite positive that I could find similar anecdotes supporting 4 years, 5 years, 6 years, etc. I hope the article was tongue-in-cheek. - Chris Miller

"NASA’s Jet Propulsion Laboratory (JPL) created the first American satellite and are now using Taverna for their Web Services-based infrastructure.[..] One of the challenges faced by the research team is the integration of various models that are used to explore the science behind the JPL’s missions. These models have been developed independently and run on different platforms, so their integration is not straightforward. The JPL’s solution is to wrap each model as a Web Service and drive them with a Web Services-enabled workflow." [From the OMII-UK newsletter: http://www.omii.ac.uk/wiki...] - 'Mummi' Thorisson

?!? - Neil Swainston

Rocket Science? - Duncan Hull

With the US National Institute of Health’s Molecular Library Initiative and the EMBL-European Bioinformatics Institute’s chemogenomics and cheminformatics programmes, large-scale drug discovery and biological screening data have entered the public domain. We are also witnessing the first efforts to sequence individual human genomes, and are making impressive progress in understanding the genomes of some of the world’s most significant disease-causing organisms. Integration of genomic sequence information with proteomics and metabolomics data provides an unprecedented chance to systematically attack disease on a molecular level. Open access to bioinformatics and cheminformatics data also opens up exciting new opportunities for academic–industrial collaboration. TACBAC 2010 will bring together experts from both the biomedical and the computational domains to explore these novel developments, discuss how to overcome the major challenges, and create new opportunities for applying computational biology and chemistry to disease management and prevention. - Duncan Hull

#qotd "I believe if a man has something to say that interests him, and he knows how to say it, they he need never be dull. Unfortunately some people have the desire for publication but nothing more. They have nothing to say, and they do not know how to say it." --Richard Asher - Duncan Hull

For all the adrenaline junkies out there... - Duncan Hull

#qotd "New scientific truth usually becomes accepted, not because opponents become convinced, but because opponents die, and because the rising generation is familiar with the new truth at the outset. " - Duncan Hull

Interesting phrase "new truth." - Andrew Lang

@Andy I hadn't noticed that. It is translated from German, so maybe something has been lost (or gained) in translation? - Duncan Hull

#qotd "I'm playing my part in the slow strangulation of innovative blue-skies research - but hey, I've got to eat, right? " - Duncan Hull