Las Vegas SUN: German Researcher Stripped of Doctoral: "Schoen, now 34, was fired by Bell Laboratories in New Jersey in September 2002 after an outside review committee concluded that he made up or altered data 16 times while working in the hot fields of superconductivity and molecular electronics.
Findings he helped research were published in prominent journals such as Science, Nature and Applied Physics Letters. "

They are removing is doctorate credentials. It should be really hard to go from possible Nobel winner to losing everything ... but if he did fake all the work, he deserves it.

Directory of open access
journals

A service created to cover free, full text journals. The project is funded by Open Society Institute - Budapest and also supported by SPARC (The Scholarly Publishing and Academic Resources Coalition).
http://www.osi.hu/infoprogram/
http://www.arl.org/sparc/

Journals that has an embargo period will not be added.
This is a pity. They should also include papers released after the embargo period.

Gene regulation: A reason for reading nonsense


The process of transcribing DNA can itself regulate gene expression in yeast: in the case concerned it is the very act of reading the DNA, not the message produced, that carries out the regulatory job.
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A simple example where the RNA polymerase disrupts the expression of a gene by production of a upstream non-coding sequence. The message is not important only the actual reading trough the downstream promoter.

Double check casts doubt on statistics in published papers


A study highlighting statistical gaffes in scientific literature has brought renewed calls for vigilance among mathematically challenged researchers and journal editors.
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Maths in Biology .. still not up to it.

Synthetic Biology: "The First International Meeting on Synthetic Biology"

The MIT ppl are marking territory :). The buzzword seems to be catching up fast. I think at least in the next couple of years it is a safe bet to go for Synthetic Biology

Bioinformatics.Org: PRESS RELEASE: Lincoln D. Stein to be presented the 2004 Benjamin Franklin Award in Bioinformatics

"Bioinformatics.Org is proud to present the 2004 Benjamin Franklin Award in Bioinformatics to Lincoln D. Stein of Cold Spring Harbor Laboratory, New York. As expressed by his nominators, Stein is being presented this award for his creation of a great number of open-source bioinformatics programs and for championing open-source principals in many venues, including published reviews, lectures, seminars, funding-review panels, and advisory board meetings. "

The Scientist :: Scientists Abandon their Software, Feb. 16, 2004: "Good biology programs abound in universities, but academia offers little incentive to keep them current "

The problems with bioinformatics these days. What happens to developed software after the PhD and post docs move one ? It seems a complicated matter. How to maintain update and debug academic useful code.

Yahoo! News - Perl Gets Extreme Makeover: "Perl Gets Extreme Makeover"

The title says it all .. they are planning a big change in PERL syntax for the next release - "Although Perl 5's expressions are the most sophisticated available and aspired to by other programming languages, "no one pretends for a moment that they're anything but hideously ugly," said Damian Conway" :) righ on

The Scientist :: Fraud spurs Cell paper retraction: "Postdoc fabricated data, leaving his career in tatters and embarrassing his boss "

So people actually get to a point where they are so frustrated that they fake their results just to get a publication. In the process they get other groups of track and make them spend 1 or 2 years proving them wrong.
Science is not an easy thing to work on...

A news on The Scientist about a new network of excellence on bioinformatics. It is called BioSapiens Network of Excellence in Bioinformatics and it involves 24 bioinformatics groups in 14 countries. Janet Thornton (current director of EBI) is coordinating the network. They received 12 million euros for building up this network for genome annotation for a period of 5 years but they say that BioSapiens should be here to stay for a while.
This type of integration was indeed lacking.


The info at EBI

The Scientist :: Unleashing the Power of Genomics: Understanding the Environment and Biological Diversity , Dec. 1, 2003

An older story I didn't catch. Craig Venture talks about environmental genomics. They are sequencing several new ocean bacteria. In the next ten years this type of effort will lead help build up the possible "lego" blocks to use in organism engineering.

The Scientist :: Nanotech is Novel; the Ethical Issues Are Not, Feb. 16, 2004

Another article on the ethical concerns on nanotechnology. If this picks up there will be a considerable slow down of the research on the subject. This means that the field is still growing strong. So much that it attracted the attention and concern of the general public.

Programming from the Ground Up > Programming and Technical Books > Bartlett Publishing | CafePress

This sounds like a good book to improve my programing skills. Linux assembly language :D.

IBM advancing on its search engine project
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"Search is trying to find the best page on a topic. WebFountain wants to find the trend,"
It's based on text mining, or what's called natural language processing (NLP). While it indexes Web pages, it tags all the words on a page, examines their inherent structure, and analyzes their relationship to one another. The process is much like diagramming a sentence in fifth grade, but on a massive scale. Text mining extracts blocks of data, nouns-verb-nouns, and analyzes them to show causal relationships.
"The Web has become just a huge bulletin board, and if you can look at that over time and see how things have changed, it answers the question, 'Tell me what's going on?'" said Sue Feldman, analyst at market research firm IDC. "This looks for the predicable structure in text, and uses that just the way people do, to do some analysis, categorize information and to understand it."
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This is going to be massive ! Doing web crawling and NLP at the same time. The same idea I thougt about for the research papers (trying to define science's trends) but applied to the internet.

All systems go

Short article talking about Systems Biology. It still looks like a good area to be, it is still expanding with jobs postings and funding on the rise. Specially in Europe and Japan who have been lagging as usually.

Bioperl Release 1.4

I missed this release . I think I just was not using much PERL this past months will all the Java3D stuff I have been doing. I have to get around to installing the new version sometime this week :D

Curious additions include a siRNA object :), SeqIO formats for kegg and tigr. A lot to play with if I had the time.

The HUPO PSI's Molecular Interaction format[mdash]a community standard for the representation of protein interaction data

A new standard for molecular interaction data. A step in the right direction finally. Following this it would be nice to see a global "universal" repository for the interactions build from all the interaction databases.

PNAS -- Cozzarelli et al. 101 (5): 1111(Sub only)

PNAS is considering moving to an open access model charging more for the publications. This editorial is about a survey they did to the publishing authors. The result was a 50% in favor of an open access model but the authors would only accept to pay 500 dollars for the paper. This price, according to the editor, is a quarter of the the real price.
I guess the move is not for soon , but they are considering it.

Slashdot | Google v. Microsoft:
A slashdot posting about the possible search engine war coming up if Microsoft decides to take a bite at the this market. Here is quote from a posting that seems to me exacly what is going to happen:

"If Microsoft makes typing in 'www.google.com' a chore, no one will use it and M$ will have won. All they have to do is use some strategy in placing their search links. Put a search link on every Microsoft web page. Put one on the taskbar in Windows. Put one on the start menu. Put one on the IE menu, and lastly, redirect all entries in the URL bar to MSN search if it isn't a valid URL."

The only thing to add to this will be the lawsuit by Google and another anti-competition trial.

For Science, Nanotech Poses Big Unknowns (TechNews.com)

I haven't actually tough about this very much but this article makes same good points on how nanothech as advanced uncheck by safety regulation.