Tuesday, February 9, 2010

“IDBS Biomarker Discovery and Validation Solution Helps Lung Genomics ... - Market Wire” plus 3 more

“IDBS Biomarker Discovery and Validation Solution Helps Lung Genomics ... - Market Wire” plus 3 more

IDBS Biomarker Discovery and Validation Solution Helps Lung Genomics ... - Market Wire

Posted: 09 Feb 2010 12:58 AM PST

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SOURCE: IDBS

GUILDFORD, UK and BURLINGTON, MA--(Marketwire - February 9, 2010) - IDBS, the leading worldwide provider of research data management and analytics solutions to R&D organizations, today announced that its Biomarker Discovery and Validation Solution will be a key component in an $11 million National Heart, Lung and Blood Institute (NHLBI) award to create a molecular roadmap for chronic lung diseases. The project's infrastructure will be developed and hosted by the new Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute. The award was given to the Lung Genomics Research Consortium (LGRC), led by National Jewish Health and also includes Dana-Farber Cancer Institute, Boston University, University of Colorado Denver, and University of Pittsburgh.

The multi-center LGRC will use advanced genetic and molecular tools to characterize and better understand chronic obstructive pulmonary disease and pulmonary fibrosis, then share its discoveries with researchers around the world in a web-accessible data warehouse. Combining genetic, epigenetic, transcriptional, and phenotypic data will provide an unprecedented window into these diseases, improving diagnosis and future personalized treatments. Data will be generated from a biorepository of almost 1,300 well characterized tissue samples from patients with chronic obstructive pulmonary disease (COPD), pulmonary fibrosis and other chronic lung diseases.

The IDBS Biomarker Discovery and Validation Solution, based on the InforSense and E-WorkBook Suites, will provide the infrastructure to manage, analyze and visualize the phenotypic and genomic data generated in the project. IDBS will also provide ClinicalSense and VisualSense to deliver web interfaces, enabling researchers to leverage this new data source.

"The LGRC project aims to produce an invaluable resource to enable better characterization and treatment of these deadly and poorly served lung diseases. We created the Center for Cancer Computational Biology specifically to work on this type of research," said Professor John Quackenbush, Director of the Center for Cancer Computational Biology at Dana-Farber Cancer Institute. "We will be using the IDBS solution to help manage and analyze the phenotypic and genomic data generated as part of the project."

"We are delighted to be part of such a ground breaking research project and to be extending our relationship with Dana-Farber and the CCCB," said Neil Kipling, founder and CEO of IDBS. "Translational and biomarker research continues to be a primary focus at IDBS, with extensive investment being made in developing the InforSense and E-WorkBook Suites and applying our other world leading products in this field."

About IDBS

IDBS is a unique, global supplier of innovative data management and analytics solutions, which increase efficiency, reduce costs and improve business and scientific productivity of R&D organizations worldwide. Organizations such as Pfizer, GSK, Celera, MedImmune, Dana-Farber and Roche employ IDBS solutions as an integral part of their strategy to address the increasing pressures placed upon them by the need for the secure, compliant capture, integration and analysis of complex research data. IDBS is clearly differentiated from other software providers by its unique combination of deep domain knowledge and its ability to rapidly provide integrated business process and robust data analytics solutions along the entire R&D value chain. IDBS solutions secure organizations valuable R&D data assets and enable rapid decision-making through effective integration and analysis. They also support the protection of Intellectual Property (IP) and the requirements for data quality demanded under Good Laboratory Practice (GLP) and Good Manufacturing Practice (GMP) standards.

IDBS is a private company, founded in 1989 and headquartered in Guildford, UK. IDBS has worldwide consulting and support presence, with U.S. offices in California, New Jersey and Massachusetts, the EU, Australia and China. Find out more at www.idbs.com.

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A Conversation With Samuel Wang - New York Times

Posted: 09 Feb 2010 12:00 AM PST

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At his Princeton laboratory, Samuel Wang is searching for basic information on how the brains of humans and dogs work. Dr. Wang, 42, an associate professor at the university, also spends time popularizing breakthroughs in his specialty — neuroscience. His book, "Welcome to Your Brain," was named 2009 Young Adult Science Book of the Year by the American Association for the Advancement of Science. Next semester, he will offer a first for Princeton: an undergraduate course called "Neuroscience and Everyday Life." Here is an edited version of a four-hour conversation.

Q. YOU'RE ALMOST EVANGELICAL ABOUT YOUR WORK. WHY DID YOU BECOME A NEUROSCIENTIST?

A. I was at Caltech in 1985, and I took a class in classical mechanics and another in introductory cell biology. And I remember asking this physics instructor about second order corrections in Lagrangian dynamics. He said, "Oh yes, that's been thought of," while spewing out a bunch of equations on the blackboard. I then asked my biology instructor a question about neurotransmission. He kind of smirked at me and said, "Nobody knows the answer to that."

That felt great! It was great to ask a basic question and learn the answer wasn't known. So neuroscience seemed like the way to go.

Q. AND NOW IS MORE KNOWN?

A. Much more. In the 1980s, we knew some things about how individual neurons, synapses and the brain — or at least regions of it — worked. Today, we have the means to see how they work as a system, together. What has changed is advances in molecular biology, genetics and also technology.

In the 1980s, the best tool for looking at neurocircuitry was to take a piece of removed tissue and look at single neurons. We now can see multiple neurons, and we can actually see how the cells talk to one another. Functional magnetic resonance imaging, F.M.R.I., lets you see what's happening on the whole brain level. In the last three years, we've gotten connectomics, where people are taking a bit of tissue and mapping every connection in it. And there's optogenetics — I'm doing a lot of that — where you express some fluorescent protein in some tissue that allows us to see individual cells and watch the change.

The other day, I went to a psychology lecture and I could see how I could turn what I'd just heard into an experiment. This colleague was working on decision-making and he'd theorized that it is guided, in part, by the release of dopamine. So I told him, "We can make dopamine go up very suddenly in the neurocircuitry — we can emulate that little release of chemicals in the dish." So that means it's possible to work out these theoretical ideas in the lab. People 30 years ago in neuroscience were smart, but they didn't have the instrumentation to test their ideas. That's only become possible in the last 10 years. And it's a very different feeling.

Q. IS YOUR LAB DEVELOPING ANY OF THIS NEW TECHNOLOGY?

A. Yes. We are developing ways to look into brain tissue while it is thinking. The tools are optical, like the microscopes I build to observe and manipulate synapse function. In my lab, we can tickle different parts of a circuit tens of thousands of times a second. That's close to emulating real brain function.

Q. YOU ARE STUDYING THE STRUCTURE OF DOG BRAINS. HOW DID THAT PROJECT BEGIN?

A. My wife and I took our pet pug for spinal surgery. At the vet's office, there were all these M.R.I.'s sitting around, hundreds of them, and it struck me: "Hey, dogs aren't covered by Hipaa! Their records aren't confidential!"

It was like discovering a goldmine of data. We've since gotten all these veterinarians on Long Island and in Maryland to donate M.R.I.'s, and we have this huge database. We're looking for relationships between dog brain size and dog breed characteristics. Australian sheep dogs and poodles can do fairly complex tasks. My pug, he's very sweet, but he's not the brightest.

There's actually a lot of scientific literature on breed characteristics, intelligence and temperament. So we check all these M.R.I.'s against these studies, and we're trying to find structural correlates. This is a huge opportunity to look at the relationship between brain structure and behavior. We're asking, Do we find a larger cortex — the part of the brain that's involved in problem solving and intelligence — in those breeds that are good in problem solving? Or, Could we find a larger amygdala, which is related to emotional responses, in dogs that are known to be high strung or nasty?

Q. ARE THERE IMPLICATIONS FOR HUMANS IN THIS?

A. That's not clear yet. Dogs are much more variable than we are. Dogs can vary by a factor of 60 in body mass and a factor of 3 in brain size. This kind of variation is not something you commonly run across in humans. Compared with dogs, we're all alike. There's no striking difference between Einstein's brain compared to that of non-Einsteins.

Q. YOU SAY THAT FUNCTIONAL MAGNETIC RESONANCE IMAGING HAS CHANGED BRAIN RESEARCH. DO YOU FIND THAT SOME RESEARCHERS ARE OVERINTERPRETING IT?

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PBS Kids' teaches biology in an online game - AZCentral.com

Posted: 04 Feb 2010 07:04 PM PST

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Parents and teachers looking for a way to make learning biology fun for kids can find it in an outstanding free online game called "Lifeboat to Mars" at www.pbskidsgo.org/lifeboat.

"Lifeboat to Mars" is a simulation game that kids play while connected to the Internet. The game was produced by Red Hill Studios for PBS Kids Go with support by a grant from the National Science Foundation.

Once you register by creating an online persona (which is not your real name) and a password, you join Ort, a robot on a spaceship mission to Mars. Unfortunately, an explosion has wiped out part of your cargo of microbes, plants and animals. Your mission is to help rebuild the on-board ecosystems before you reach Mars.

To accomplish this mission, you will need to play two kinds of simulations: one set in a microscopic world called Microbe Games and the other in an ecosystem with animals and plants called Ecoland Games. To familiarize you with how to play both of these simulations, the game has you go through two sets of starter games, which act as the game's tutorials.

Once you finish each set of starter games, other more difficult games become available. In this manner, "Lifeboat to Mars" very cleverly leads kids through progressively more difficult material, which builds on the lessons learned in the starter games.

For example, in the Ecoland Starter Games, you will be asked to figure out which two plants grow best in moist soil. You will be given several plants to try, but some will simply die because the soil is too wet. Likewise, in the Microbe Starter Games, you will be asked to direct a microbe through a tank to a Finish point. But there is no food in this water, just pockets of light. You will learn to add chloroplasts to your microbe so that it can make its own food from photosynthesis by stopping in the patches of light.

Later on in the harder games, you will use what you learned about plants to help set up an ecosystem that can support herbivores and, later, carnivores. And when playing the harder Microbe games, you will use your knowledge of chloroplasts to race through more crowded microscopic environments.

Another exciting aspect of "Lifeboat to Mars" is the ability to create your own simulations to share with others. After working through the starter games and playing a few of the other more sophisticated scenarios, a new area opens up called "Modding." In the Modding sections for both Microbes and Ecoland, you can design your own scenarios. You can establish the goal of the scenario, and how hard it is to win. After you finish creating a mod and test it out by winning it, your mod is then uploaded to the game's servers for others to play.

In addition to the 48 simulations, the game also has a culminating Lifeboat simulation game. By playing the earlier simulations, you earn points to help you complete the Lifeboat simulation. In all, "Lifeboat to Mars" offers kids hours of fascinating, interactive learning.

What makes this free online game so good is that it lets kids learn by trial and error. Each simulation sets forth clear learning objectives and goals, and then provides the means to accomplish the goals. The key to making a good simulation for kids is to find the balance between making the achievement too easy and making it too hard. For the most part, "Lifeboat to Mars" finds that sweet spot; however, several of the simulations will take several tries before success is achieved. This is particularly true with the Microbe games where kids' success is hampered by rather rudimentary controls of using the arrow keys to move your microbe.

For teachers wanting to incorporate this game into their science curriculum, a teacher's guide will be available on the PBS Kids Go Web site in early March.

Rating 4 stars (out of 4)

Best for ages 8 to 12

From PBS Kids Go, www.pbskidsgo.org/lifeboat, free using an Internet browser that supports Flash.

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Biology counts in loving relationships - Newsday

Posted: 05 Feb 2010 12:22 PM PST

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February 5, 2010 By DRS. MICHAEL ROIZEN AND MEHMET OZ. King Features  

When it comes to a healthy relationship, some biological facts can help you build one. Here's what to know before you dive fully into a relationship:

1. Love is all chemicals. When in love, your brain pumps out the love-potion ingredient dopamine (the addictive substance that sugar, sleep and tobacco also release) and increases the release of serotonin, the euphoria hormone. You also get...

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