In a recent article from Nature, and subsequent discussions (here and there), it is argued that a “growing chorus of scientists” would like to see more standardization of data so that sorting through that data would be a little easier. Indeed, biology in general is becoming more data intensive and less experimental, results of significant funding initiatives and advances in scientific methods that have brought the genome sequence down to about the price of an MRI. This means that the metadata or “things that I never cared about,” such as the vocabulary used to describe data, is becoming paramount for quick and easy data mining. I, for one, wish that this chorus would include some neuroscientists as we suffer, possibly much more than geneticists, from a near fatal disease called “multi-vocabularia.” This disease was brought about over the last 100 years by several disciplines, mainly anatomy and electrophysiology, essentially not talking to one another and became aggravated by molecular biologists trying to report gene expression in brain regions and really having no idea whether they should include the olfactory bulb in their reports of cortical gene expression (perhaps we could vote the olfactory bulb off the cortex island?). So, if geneticists lead the way, singing their way out of the data mess they created, perhaps we neuroscientists can at least take some lessons from them. Of course, geneticists as a group  named one gene stonin, and another one goaT (yes, it does tend to be difficult to find goat antibodies against it) and their favorite disease is an astrological sign, so our hopes may be way too high.

Hello everyone,

The next NIF Webinar will be held on Tuesday, October 11, 2011 at 11:00 am PDT.   Please join Bobby-Joe Breitkreutz as he discusses Search Engine Optimization (SEO).

The following is a description of the webinar:

The “tree falls in a forest” adage postulates that if no one is around to hear the sound, it may not exist at all. This translates perfectly to search engines and web content. Major search engines, such as Google, Bing, and Yahoo! do a great job of helping people find your content on the web. However, they can only do this if they know your website exists and more importantly can determine how to navigate it successfully. So, in order for humans to discover, react, comment and, most importantly for search engines, link to your website, you need to be sure the search engines can process your content completely and accurately. If someone makes a website and no one can find it, does it exist at all?

Date and Time: Tuesday,October 11, 2011 • 11:00-12:00 PDT
Topic: Search Engine Optimization (SEO)
Presenter: Bobby-Joe Breitkreutz
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

Mark your calendars! See you there.

The Neuroscience Information Framework (NIF) hosts a semi-regular Tuesday Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

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NIF Communications Team
UC San Diego
3rd Floor, Atkinson Hall
9500 Gilman Drive, MC 0446
La Jolla, California 92093

858-822-0755
http://www.neuinfo.org

In this challenge, a full stack of EM slices will be used to train machine learning algorithms for the purpose of automatic segmentation of neural structures.

Anybody can participate in the challenge. The only requirement consists of filling up the registration form here to get a user name and password to download the data and upload the results.

The best ranked methods will be presented a the workshop previous to the IEEE International Symposium on Biomedical Imaging (ISBI) 2012

Please Visit the website for full details about the challenge>

President Barack Obama will soon honor University of California, San Diego Bioengineering Professor Shu Chien in a White House ceremony for the seven eminent researchers to receive the National Medal of Science, the highest honor bestowed by the United States government on scientists and engineers. Chien is the only engineer among the seven medalists announced last week.

Shu Chien, a professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering, is a world leader in the study of how blood flow and pressure affect blood vessels. Chien’s research has led to the development of better diagnostic tests and treatments for atherosclerosis, which refers to the hardening of the arteries, and other diseases.

Biologists at the University of California, San Diego have identified more than 70 genes that play a role in regenerating nerves after injury, providing biomedical researchers with a valuable set of genetic leads for use in developing therapies to repair spinal cord injuries and other common kinds of nerve damage such as stroke. 

While scientists in recent decades have gained a good understanding of how nerve cells, or neurons, develop their connections in the developing embryo, much less is known about how adult animals and humans repair or fail to repair those connections when axons are damaged. 

To read the full news> 

Technology Conference and Society will be held at University of California, Los Angeles, USA from 16-18 January. This Conference will address a range of critically important themes in the various fields that address the complex and subtle relationships between technology, knowledge and society. Plenary speakers include some of the leading thinkers in these areas, as well as numerous paper, colloquium and workshop presentations.

A written paper can be submitted to The International Journal of Technology, Knowledge and Society, a fully refereed academic Journal. Virtual participants may also submit papers for consideration by the Journal. All Conference participants who have finalized their registration will receive a complimentary online subscription to the Journal. This subscription is valid until one year after the Conference end date.

To submit a paper

Hello everyone,

The next NIF Webinar will be held on Tuesday, October 4, 2011 at 11:00 am PDT.   Please join Brian Canada as he discusses  Crowdsourcing the Zebrafish Phenome Project .

The following is a description of the webinar:

One of the key objectives of the Zebrafish Phenome Project is to systematically annotate the cellular-level morphological phenotypes associated with each gene in the zebrafish genome. During this webinar, I will offer a demonstration of CABERNET, our proposed crowdsourcing application for the scoring of zebrafish histological abnormalities of varying degrees of severity. Inspired by crowdsourcing “games” and other tools for annotating digital content, CABERNET is designed to promote the generation of high-quality, ontology-compliant “consensus annotations” of phenotypes that are independently contributed by multiple domain experts. Potential mechanisms for “incentivizing” the crowdsourcing of the Zebrafish Phenome Project—or indeed, any large-scale biological data collection project—will also be discussed.

Date and Time: Tuesday,October 4, 2011 • 11:00-12:00 PDT
Topic: Crowdsourcing the Zebrafish Phenome Project
Presenter: Brian Canada
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

Mark your calendars! See you there.

The Neuroscience Information Framework (NIF) hosts a semi-regular Tuesday Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

DSC Host Largest Academic Cloud

Sep 26, 2011

The San Diego Supercomputer Center at the University of California, San Diego, has launched what it claims is thelargest academic-based cloud storage system in the country. The system is capable of an initial raw 5.5 petabyte of storage and is 100 percent disk-based with high-speed 10 gigabit Ethernet network interconnections. 

SDSC’s Cloud uses two Arista Networks 7,508 switches, providing 768 total 10 gigabit Ethernet ports for more than 10Tbit/s of non-blocking, IP-based connectivity.  Users can store their data in the cloud for as low as $3.25 per Month for 100GB or $32.50 per Terabyte per Month with no transfer costs. 

To read the full article> 

Stampede Charges Computational Science Forward in Tackling Complex Societal Challenges

Sep 26, 2011

The Texas Advanced Computing Center (TACC) at the University of Texas at Austin announced on September 22nd, 2011 that it will deploy and support a world-class supercomputer with comprehensive computing and visualization capabilities for the national open science community. Made possible by a $27.5 million grant from the National Science Foundation (NSF), this new deployment is part of the NSF “eXtreme Digital” (XD) program, an integrating system for the majority of NSF’s high end computational resources made widely available to U.S. researchers. 

The new system, “Stampede,” will be built by TACC in partnership with Dell and Intel to support the nation’s scientists in addressing the most complex scientific and engineering problems. Stampede is anticipated to go into full production in January 2013 and will be available to researchers for four years. 

To read the full press release> 

The Journal of Librarianship and Scholarly Communication (ISSN 2162-3309), a quarterly, peer-reviewed, open-access publication for original articles, reviews and case studies that analyze or describe the strategies, partnerships and impact of library-led digital projects, online publishing and scholarly communication initiatives, is looking for papers to go on its inaugural issue.

The editors are seeking papers that expertly discuss and represent these core dimensions of scholarly communication: author rights advocacy, repository management, traditional and non-traditional publishing models, citation metrics, copyright management, digital collection development, and the impact of any of the above on the system of scholarly exchange and reward (e.g. tenure and promotion).

For more information, visit the submission page>