Hello everyone,

The next NIF Webinar will be held on Tuesday, November 1, 2011 at 11:00 am PDT.   Please join Tal Yarkoni as he discusses the NeuroSynth framework.

The following is a description of the webinar:

The explosive growth of the human neuroimaging literature has led to major advances in understanding of human brain function, but has also made aggregation and synthesis of neuroimaging findings increasingly difficult. In this webinar, I will describe a highly automated brain mapping framework called NeuroSynth that uses text mining, meta-analysis and machine learning techniques to generate a large database of mappings between neural and cognitive states. The NeuroSynth framework can be used to automatically conduct large-scale, high-quality neuroimaging meta-analyses, address long-standing inferential problems in the neuroimaging literature (e.g., how to infer cognitive states from distributed activity patterns), and support accurate ‘decoding’ of broad cognitive states from brain activity in both entire studies and individual human subjects. This webinar will focus on (a) the methods used to extract the data, (b) the structure of the resulting (publicly available) datasets, and (c) some major limitations of the current implementation. If time allows, I’ll also provide a walk-through of the associated web interface (http://neurosynth.org) and will provide concrete examples of some potential applications of the framework.

Date and Time: Tuesday,November 1, 2011 • 11:00-12:00 PDT
Topic: Large-scale automated synthesis of functional neuroimaging data using the NeuroSynth framework
Presenter: Tal Yarkoni
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.

--
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

Hello everyone,

The next NIF Webinar will be held on Tuesday, October 25, 2011 at 11:00 am PDT.   Please join Jesse Brown as he discusses The UCLA Multimodal Connectivity Database.

The following is a description of the webinar:

The UCLA Multimodal Connectivity Database (UMCD; http://umcd.ccn.ucla.edu) is a new web-based effort to collect, categorize, and share connectivivty matrices that have been dervied from neuroimaging data. As the number of macroscopic brain connectivity studies has rapidly expanded and the number of publications has grown, the need for a repository for such data has become vital. The UMCD specifically caters to data from studies that have derived whole brain connectivity matrices to quantify the pairwise connection strength between any pair of regions in the brain. Connection strength can be determined using structural or functional measures of connection strength, such as diffusion tensory imaging tractography track density or functional MRI timeseries correlation. We designed the UMCD in order to make it easy to share connectivity matrices with sufficient meta information to make them searchable and visualizable by anyone who is interested. Any user can visit the site, browse all the publicly shared data, choose a network of interest based on a variety of criteria (age, disorder, imaging modality, etc.), and then analzye the network. This analysis is run on the fly in the cloud, quickly producing a report on the network’s global and local connectivity properties. Both interactive 3D and 2D visualizations are shown that depict the connection strengths and various regional properties. We hope that through data sharing on the UMCD, we will 1) enable large scale meta-analyses and classification efforts of connectivity matrix data, 2) provide prior probabilities for future experiments probing connectivity between specific regions, 3) sync up with other databases in an effort to synthesize brain connectivity data at the micro and macroscale. In this presentation I will demonstrate how to share data on the site, find specific data, and run an analysis of  publicly shared data.

Date and Time: Tuesday,October 25, 2011 • 11:00-12:00 PDT
Topic: The UCLA Multimodal Connectivity Database
Presenter: Jesse Brown
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.

--
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 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.

--
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 hereto 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>