Category Archives: Clipped

Ten simple rules for doing your best research – according to Richard Hamming

There’s an editorial in PLoS Computational Biology presenting condensed thoughts on “first-class research” of mathematician Richard Hamming. It is based on a transcript of a brilliant talk given by Hamming in 1986 at the Bell Communications Research Colloquium Seminar. Definitely a must-read.

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Hamming’s 1986 talk was remarkable. In “You and Your Research,” he addressed the question: How can scientists do great research, i.e., Nobel-Prize-type work? His insights were based on more than forty years of research as a pioneer of computer science and telecommunications who had the privilege of interacting with such luminaries as the physicists Richard Feynman, Enrico Fermi, Edward Teller, Robert Oppenheimer, Hans Bethe, and Walter Brattain, with Claude Shannon, “the father of information theory,” and with the statistician John Tukey.

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Posted by on November 6, 2007 in Clipped, Research skills


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Biology Image Library – scientific stock photography?

(via The Biotech Weblog) BioMed Central has launched the Biology Image Library – online collection of scientifically interesting and meaningful images across biology and biomedicine.

Most of the images at BIL are available free of charge for non-commercial purposes (like teaching), but buying commercial-use rights is also possible. I don’t really agree that the library is aimed at students (teachers, lecturers – maybe), since personal subscriptions are $293 per annum and I could imagine that institute subscriptions are not cheaper. UPDATE: See comments below. To me a corporate client is a main target of this initiative, but I may agree that relatively high subscription rates may be dictated by the nature of the images – most of them come from experiments (almost no computer generated illustrations).

Microstock photography sites hold quite a lot of science-related images, however their scientific value is very often zero (as an example, search for DNA). It is overall nice idea to have a scientific equivalent of a microstock, but I would rather leave the subscriptions out and release low quality (for web/computer screen use) material under non-commercial Creative Commons license.

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What is the Biology Image Library?

The library is a collection of images, illustrations, movies and animations that are useful for research and education. It is also a new, easy way to share your work with others without losing any rights to it or limiting how you use it in the future.

Who publishes the library?

The library is published by BioMed Central, an independent publishing house that offers a wide variety of journals and other online services. BioMed Central is committed to providing immediate open access to peer-reviewed biomedical research. We also publish a number of “value-added” subscription databases and information services, of which the Biology Image Library is an example. Please see for more information about our activities.

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Posted by on October 22, 2007 in Clipped, open-science, Services


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Genome Commons – knowledgebase of human genetic variation

The title says it all – have a look at Steve Brenner’s commentary in Nature (looks like its freely accessible) and the Genome Commons web page.

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The Genome Commons and Genome Commons Navigators are open resources I propose to assist with personal genome interpretation. A commentary describing these has been published in Nature, and additional versions of those musings and more details may be found on the about page of this site.

Thank you very much for your interest. Please explore the site and offer your thoughts. The background page offers some historical context for the Genome Commons idea. More valuable context is given by the resources page, which summarizes some existing resources for personal genome interpretation, with links to much larger lists of resources. The blog will have updates and discussions.

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Posted by on October 17, 2007 in Clipped, Research


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Type VII secretion system

Yet another secretion system was described, this time from Gram-positive bacteria (types I to VI were from Gram-negative). I expect that the further microbiology will go from E. coli, the more secretion systems will be found. Within the large spectrum of bacterial species we still know very little on bacteria outside proteobacterial group.

This is from Nature Reviews Microbiology, and subscription may be required.

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Recent evidence shows that mycobacteria have developed novel and specialized secretion systems for the transport of extracellular proteins across their hydrophobic, and highly impermeable, cell wall. Strikingly, mycobacterial genomes encode up to five of these transport systems. Two of these systems, ESX-1 and ESX-5, are involved in virulence — they both affect the cell-to-cell migration of pathogenic mycobacteria. Here, we discuss this novel secretion pathway and consider variants that are present in various Gram-positive bacteria. Given the unique composition of this secretion system, and its general importance, we propose that, in line with the accepted nomenclature, it should be called type VII secretion.

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Posted by on October 9, 2007 in Clipped, Proteins, Secretion system


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Healia and third party PubMed/Medline tools

David Rothman describes Healia, easy to use interface to the PubMed. But it’s just one of many third party PubMed/Medline tools David had described. Check out his posts related to the one about Healia.

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Healia’s PubMed search (currently in beta) might be one of the best interfaces available for clinicians who don’t have the search skills to effectively search PubMed through its native interface.

Some notable features:

Automatic “AND”
By default, Healia inserts a boolean “AND” between all search terms (as Google does). While the expert searcher might find this unpleasantly limiting, it is a familiar behavior for many clinical searchers who view Google as their ideal, preferred search interface.

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Posted by on October 1, 2007 in Clipped, PubMed, Software


Tenure dossier

Janet D. Stemwedel from Adventures in Ethics and Science publishes photographs of the three-ring binder containing her tenure dossier. She ends this post with the sentence: “I seem to recall that there are important aspects of life that you can’t cram into a three-hole punch.”

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The dossier itself more or less captures the teaching/scholarship/service categories impressed on us as faculty newbies. The faculty member preparing a dossier is handed a set of eight uniform dividers for a three-ring binder. Four of these impose the main structure on the materials the faculty member assembles, marking out sections dealing with teaching effectiveness, service to students and the university, scholarly or creative activity, and what amounts to service within or related to your field of scholarship.

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Posted by on September 27, 2007 in Career, Clipped