Nascent

There's a Commentary in this week's Nature about detecting plagiarism in scientific papers (free access this week) by using eTBLAST, a strange but seemingly effective hybrid of alignment search and heuristics originally designed to help search PubMed. Basically you give it a paragraph of text and it finds papers that contain similar words and phrases.

Here's a summary from the News piece accompanying the story:

As many as 200,000 of the 17 million articles in the Medline database might be duplicates, either plagiarized or republished by the same author in different journals, according to a commentary published in Nature today [... the authors] used text-matching software to look for duplicate or highly-similar abstracts in more than 62,000 randomly selected Medline abstracts published since 1995.

This the second place this week that I've read about bioinformatics techniques being applied to document processing; the other was Deepak's post about IBM using the Teiresias algorithm to detect spam emails with great success. Don't know if there are any other bioinformatics algorithms that have been applied to non-biological problems? BLAST, surely, must have other some novel uses...

Anyway, the authors do mention that:

In general, the duplication of scientific articles has largely been ignored by the gatekeepers of scientific information — the publishers and database curators. Very few journal editors attempt to systematically detect duplicates at the time of submission.

Sort of. CrossRef - the academic publishing industry body that looks after DOIs for scientific papers, amongst other things - is building a plagiarism detection service called CrossCheck in association with the company that makes Turnitin, a popular piece of software used by high schools and colleges to make sure student's don't crib off of each other. If you are going to submit exactly the same paper to multiple journals in the hope of getting multiple citations then do it now...

Posted by Euan Adie at 07:05 AM | Permalink | Comments (1)

We have some new senior positions on the web side of things at Nature Publishing Group (NPG). They might interest Nascent readers, so here are brief descriptions and links:

• Head of Community Business Development: Take our famous range of cutting-edge participative services for scientists, add the huge traffic and vast database of registered users at Nature.com, and help us to (profitably) turn these into the definitive scientific information forum on the web.
• Head of Nature.com User Experience: Take the lead in making the user experience on Nature.com as compelling as it can possibly be, calling on a wide range of skills and resources from across NPG.
• Head of Methods, Products and Protocols: Build on the success of Nature Methods and Nature Protocols to provide life scientists and chemists with all they ever needed to know about scientific procedures, including how to carry them out and which bits of kit they'll need.

All these positions will be based in either London or New York. If you're interested then either write to the address given in the ads or drop me a note via my Nature Network profile page. But hurry: applications close on 31st January 2008.

Posted by Timo Hannay at 03:58 AM | Permalink | Comments (0)

Fancy user interfaces are all the rage nowadays. Did you see Bill Gates 'jamming' with Slash at CES? Jamming as part of a crass marketing excercise, yes, but on a Guitar Hero guitar-shaped controller - in that context a step up in usability and (more importantly) style from a mouse and keyboard.

Well, OK, maybe not style.

Anyway, it turns out that there's exciting stuff happening in the user interface space in science, too.

Deepak at BBGM blogged a while back about a molecular dynamics simulation that used a Wii controller to allow you to interact with the atoms on screen.

Even more excitingly, though, Andrew Walkingshaw at Cambridge has hacked up a tangible user interface that allows you to put together molecules using differently shaped physical markers (each representing a different atom) on a glass table. Custom software written in Processing tracks marker shapes and locations with a webcam, works out which molecule you've built and sends you to the PubChem search page to get more details. It's awesome. I am impressed.

So, to sum up, that’s performing a chemical search by just putting real objects down on a real surface, made really cheaply. Result!
[..]
t’s a usable prototype, and building it cost me under £30. That’s kind of awesome really; playing with this kind of thing really doesn’t have to be hard or expensive any more. It doesn’t even need any really specialist kit.

Posted by Euan Adie at 09:17 AM | Permalink | Comments (1)

The blog posts of four Nature Network bloggers have been chosen to be part of an anthology of the best science blog posts of 2007, called Open Laboratory 2007. The book will be available in bookstores and from Amazon later this month, according to Bora Zivkovic, who led the charge this year in putting together this year's anthology (last year’s anthology, also Bora's doing, was only available online).

Out of more than 450 nominated entries, 52 were chosen by a panel of more than 30 judges; the winning posts include these from Nature Network bloggers:

Deanne Taylor, a research scientist with the Harvard School of Public Health, describes what changes need to be made to boost faculty diversity in science.

Kristin Stephan, a Tufts graduate student, discusses how difficult, but necessary, it is for PhD students in grad school to learn about careers outside of academic science.

Our very own Henry Gee, an editor with Nature, writes lovingly about his 9-year-old daughter with Asperger’s Syndrome and how having Asperger's might help her become a good scientist.

Jennifer Rohn, a postdoc at University College London, documents in this series of four posts her return to the lab and academic science after four years as a journal editor. Required reading for anyone contemplating a career change.

Posted by Corie Lok at 01:01 PM | Permalink | Comments (0)