The Bioinformatics Blog

There was an article on probiotics in the New York Times today. By Tara Parker-Pope it addresses some important issues rarely covered in the press about probiotics (see Well – Probiotics – Looking Underneath the Yogurt Label – NYTimes.com).

On the one hand, the article does a decent job of pointing out that there is great strain to strain variation among microbes labelled as probiotics. In this regard there is a great quote by Gregor Reid:

Lactobacillus is just the bacterium,” said Gregor Reid, director of the Canadian Research and Development Center for Probiotics. “To say a product contains Lactobacillus is like saying you’re bringing George Clooney to a party. It may be the actor, or it may be an 85-year-old guy from Atlanta who just happens to be named George Clooney. With probiotics, there are strain-to-strain differences.”

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Sure, James Watson has been known, especially recently, to say some outrageous things. But here is something I think everyone, scientists and the public should read – an opinoin piece in the NY Times today by Watson ( Op-Ed Contributor – To Fight Cancer, Know the Enemy – NYTimes.com)

This piece is worth reading because it contains some critical ideas and wisdom which has been missing in discussions of the fight against cancer.

First, Watson discusses the critical importance of basic science and says that when he expressed this importance to the National Cancer Institute advisory board many years ago, he was eventually booted off.

Second, he discusses how we have only recently begun to understand the basic biology of cancer (he also mentions how the human genome project has helped in this). The genome project will, he says, allow for the determination of most/all of the major genetic changes that occur in cancer cells.

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Previously I tried to get the word out on a change to the NIH policy for grant supported research that required researchers to transfer a copy of the final work to a repository (PMC) that provides free access to the article. My personally biased opinion is the policy was a great move, and that making scientific knowledge more highly available to everyone is a good thing.

Some publishers have already stepped up to embrace the new policy by transferring the paper to PMC for you, some well before the 1 year deadline. Others have no coherent plan and charge large fees for a paper to be transferred to PMC. For example, the American Psychological Society charges Wellcome Trust supported researchers $4,000 to send a copy of their paper to PubMed Central.

There already is controversy about the policy in Congress. House Bill HR 6845 was introduced (you can find it by querying ‘HR 6845′ here) as the Fair Copyright in Research Works Act. After glancing over it, it seems that the bill intends to reverse the NIH policy decision by making sure funding agencies can’t force the funded individuals to put their works in a public archive. While on the outset that may sound like it’s protecting the researcher by not ‘forcing’ them to make their work available, it seems to me it’s actually protection for publishers that don’t want to modify their business model. You publish with us, you transfer copyright to us, we get paid for others to view the work. That worked fine for a long time. But the world has changed. We now live in a world where information is instantly available. How about instead of reversing a policy that makes more information available to more people we try to work out a new publishing model?

Who knows where this whole thing will end up? I don’t have a clue. What I do know is that making scientific works available (even if after a waiting period) to a wider audience of researchers is a good thing that spurs more research and greater innovation. But that’s just my two cents.

If you have or want a career in academic biomedical or basic science research in areas that impact human health then your career depends on funding. For health related research the NIH is your bread and butter. You publish papers as a graduate student and post doc, get some expertise in a certain area, apply for funding, get funding, do research, publish more papers, apply for more grants; you get the picture.

Unfortunately for academic scientists the grant environment has become quite hostile lately. NIH appropriations have become flat in the face of a greater number of researchers, more expensive technologies, an economy that for all intents and purposes is in a recession, and ridiculous fuel costs (yes, that is germane as many suppliers now are applying a fuel surcharge to orders). Basically the same sum of money with decreased buying power is being split amongst a growing number of people doing more expensive research. Unfortunately this means fewer grants are being funded and fewer funded grants are being renewed. Every edge you can get in getting or maintaining a grant is important, which is why the new NIH public access policy is important.

The most important highlights of the new policy is that any NIH supported research published in a peer-reviewed journal must have the final accepted manuscript deposited in PubMed Central with in 12 months of publication. The up side is an increased in accessibility to people that don’t have the advantage of being at an institution with a million different site licenses for journals. The downside is, of course, more work for the researcher.  The following types of papers are subject to the new policy per the faq:

The Policy applies to any manuscript that:

• Is peer-reviewed;
• And, is accepted for publication in a journal on or after April 7, 2008;
• And, arises from:
  • Any direct funding ¹ from an NIH grant or cooperative agreement active in Fiscal Year 2008, or;
  • Any direct funding from an NIH contract signed on or after April 7, 2008, or;
  • Any direct funding from the NIH Intramural Program, or;
  • An NIH employee

Complying with the new access policy is part of the terms of agreement for any NIH award from now on, so be sure before you sign any copyright agreements to have papers published that the agreement wouldn’t prevent you from depositing the work in PubMed Central within the timelimit. Furthermore, references to your own published works in NIH grant proposals must include a PubMed Central ID (PMCID).

Don’t forget to stay in compliance with this policy, or the big bad NIH administrators may sneak out of your closet in the night and freeze your funding.

 

The helix graphic is reproduced from Dr. Lincoln Stein’s article “How Perl Saved the Human Genome Project” as published in the September 1996 issue of The Perl Journal.

Reprinted courtesy of the Perl Journal, http://www.tpj.com Archive.

Lincoln Stein’s website is http://stein.cshl.org

DATE: Early February, 1996

LOCATION: Cambridge, England, in the conference room of the largest DNA sequencing center in Europe.

OCCASION: A high level meeting between the computer scientists of this center and the largest DNA sequencing center in the United States.

THE PROBLEM: Although the two centers use almost identical laboratory techniques, almost identical databases, and almost identical data analysis tools, they still can’t interchange data or meaningfully compare results.

THE SOLUTION: Perl.

The human genome project was inaugurated at the beginning of the decade as an ambitious international effort to determine the complete DNA sequence of human beings and several experimental animals. The justification for this undertaking is both scientific and medical. By understanding the genetic makeup of an organism in excruciating detail, it is hoped that we will be better able to understand how organisms develop from single eggs into complex multicellular beings, how food is metabolized and transformed into the constituents of the body, how the nervous system assembles itself into a smoothly functioning ensemble. From the medical point of view, the wealth of knowledge that will come from knowing the complete DNA sequence will greatly accelerate the process of finding the causes of (and potential cures for) human diseases.

Six years after its birth, the genome project is ahead of schedule. Detailed maps of the human and all the experimental animals have been completed (mapping out the DNA using a series of landmarks is an obligatory first step before determining the complete DNA sequence). The sequence of the smallest model organism, yeast, is nearly completed, and the sequence of the next smallest, a tiny soil-dwelling worm, isn’t far behind. Large scale sequencing efforts for human DNA started at several centers a number of months ago and will be in full swing within the year.

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ioPuppy OS is an electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners. BioPuppy is available as a live CD cum installation CD (and in USB Pen drive) and containing all the required software to boot the computer with ready to use bio-informatics tools. BioPuppy is based of the Puppy Linux. The another objective of this BioPuppy is small in size. Our estimated size of BioPuppy is ~150MB. BioPuppy derived from Puppy-3.01-seamonkey Linux. 

INCLUDES: 
- Sequence Analysis Tools: Sim-4, Tigr-Glimmer 2, Genewise, Muscle, Sigma, HMMER, Clustal-W, mafft 
- Structure Prediction Tools: mfold, gibbs 
- Protein Structure Analysis Tools: Garlic, Rasmol 
- Phylogenetic Analysis tools: Fast DNA, Phylip, Phylodraw 
- Protein Modeling: Modeller 
- Docking: MGL Tools (Autodock tools, Python Molecular Viewer (PMV), Vision) 
- System Biology: Copasi 
- On-line tools: BLAST, EMBOSS 

FOR MORE INFORMATION: 
To download and for more details visit http://biopuppy.org/ 

An article by Erica Ogg: 

“Fun fact: the fastest supercomputer in the world–used to monitor the U.S. nuclear weapons stockpile–is really just a PlayStation 3 on steroids. Roadrunner is based on the IBM QS22 blades, which are built using advanced versions of the Cell processor in Sony’s PS3. It also runs using x86 chips from Advanced Micro Devices, making it the world’s first hybrid supercomputer. 

“In total, Roadrunner takes up 278 refrigerator-size server racks, and connects 6,562 dual-core AMD Opteron and 12,240 Cell chips.” 

Full story: 
[link]