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NIF Webinar – February 7, 2012 at 11:00 PST

Lee Hornbrook — Tue, 31 Jan 2012 17:21:28 +0000

Hello everyone,

The next NIF Webinar will be held on Tuesday, February 7, 2012 at 11:00 am PST. Please join Carlo Quinonez as he discusses Open Hardware in Science: Benefits and Challenges.

The following is a description of the webinar:

The need for free and easy access to scientific data and other information essential to scientific experiments has been clearly recognized for decades. Developments such as open source software, open data, open access journals and open courseware rely on the easy and efficient transfer of information over the Internet. However, the dissemination and collaborative development of open hardware for the benefit of scientific progress poses unique challenges and opportunities. The widespread prevalence of scientist-developed tools has been driven by commercial instruments’ lack of flexibility and detailed engineering data vital for user-improvements. While these technologies are put to good use by their developers, practical issues such as poor documentation, difficulty of fabrication, and idiosyncratic operation typically limit the utility to broader research community. In this webinar we will discuss the open hardware toolset, Aquinas, that addresses some of these issues and provides a shared hardware platform for biological experimentation. Currently, several micro-fluidics designs are available for fabrication. The facile reproduction of scientist-developed tools improves the reproducibility and transparency of science overall. Furthermore, a shared hardware platform for biological experimentation would also propel large-scale collaborative efforts to significantly accelerate the discovery of cures and scientific breakthroughs.

Date and Time: Tuesday, February 7, 2011 • 11:00-12:00 PST
Topic: OpenHardware in Science: Benefits and Challenges
Presenter: Carlo Quinonez, Ph.D., IRACDA Fellow in the Department of Pharmacology, University of California, San Diego.
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

UCSD Researchers Induce Alzheimer’s Neurons from Stem Cells

Lee Hornbrook — Tue, 31 Jan 2012 16:41:32 +0000

Material taken from UCSD University Communications and Public Affairs News Center, January 25, 2012.

Led by researchers at the University of California, San Diego School of Medicine, scientists have, for the first time, created stem cell-derived, in vitro models of sporadic and hereditary Alzheimer’s disease (AD), using induced pluripotent stem cells from patients with the much-dreaded neurodegenerative disorder.

An account of this feat was published in the January 25 online edition of the journal Nature. It represents a new and much-needed method for studying the causes of AD, a progressive dementia that afflicts approximately 5.4 million Americans. More importantly, the living cells provide an unprecedented tool for developing and testing drugs to treat the disorder.

For the full story, please visit the UCSD News Center story at http://ucsdnews.ucsd.edu/pressreleases/researchers_induce_alzheimers_neurons_from_pluripotent_stem_cells/

Top 25 Accessed Databases at NIF for January 2012

Lee Hornbrook — Fri, 13 Jan 2012 23:34:09 +0000

Here are the top 25 accessed databases at NIF for January 2012:

1. Grants.gov/Opportunity
2. CCDB/All Information
3. SumsDB/Activation Foci
4. ResearchCrossroads/Grants
5. AntibodyRegistry/ABs
6. GENSAT/GENSAT
7. Drug Related Gene Database/DRG
8. BrainInfo/Brain Region
9. OneMind/BioBanks
10. RePORTER/CurrentNIHGrants
11. DrugBank/Drugs
12. ClinicalTrials/ClinTr
13. NIF Integrated Nervous System/Connectivity
14. NIF Integrated Video/Videos
15. ModelDB/Models
16. HumanBrainAtlas/Michigan
17. NIF Integrated Animals/Available
18. OMIM/Genes
19. NIHNeuro/Microarray Consortium
20. AllenInstitute/MouseBrainAtlas
21. NIF Integrated Software/Info
22. BrainMaps/Atlas
23. Gemma/Microarray
24. WikiPathways/ChemPathway
25. GeneNetwork/Info

NIF Top 25 Searches for January 2012

Lee Hornbrook — Fri, 13 Jan 2012 23:19:28 +0000

Here are the top 25 Searches at NIF for January 2012.

1. database
2. Images
3. antibodyregistry
4. Brain Regions
5. Brain Activation Foci
6. Cingulate Cortex
7. Drugs
8. Multimedia
9. Animals
10. Alzheimer’s
11. Antibodies
12. Cerebellum
13. Hippocampus
14. Mitral Cell
15. Amygdala
16. Cerebral Crus
17. Cerebral Peduncle
18. Flocculonodular Lobe
19. Forebrain
20. Basal Ganglia
21. Brainstem
22. Corpus Callosum
23. Frontal Lobe
24. hippocampus
25. Claustrum

Allen Brain Atlas training at UCSD – Jan. 23, 2012

Lee Hornbrook — Tue, 10 Jan 2012 18:35:38 +0000

Hello,

A training workshop is being offered at UCSD for the Allen Brain Atlas. “Using the Allen Brain Atlas Online Public Resources” will feature a training workshop on the Allen Brain Atlas online public resources for exploring gene expression in the nervous system. Basic data access, navigation and usability will be covered as well as more sophisticated search and visualization features.

Participation is free.
Advanced registration is required.

To register: Email info@alleninstitute.org and indicate “UCSD Training Workshop” in the subject line. Capacity is limited.

The workshop will be held:

Monday, January 23, 2012
1:30 pm – 4:30 pm
UCSD
CNCB Auditorium
La Jolla, CA

This workshop will touch on the full spectrum of resources available via the Allen Brain Atlas data portal (www.brain-map.org), but will focus primarily on navigation and search features of the following data sets:

> Adult human brain
> Adult mouse brain
> Non-human primate brain

For a hands-on experience, attendees are encourages to bring a laptop with Internet/Wi-Fi connectivity so that they can follow along.

Thank you!

--
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

NIF v4.0 – Release Comments

jcachat — Thu, 15 Dec 2011 00:00:12 +0000

We are pleased to announce the release of NIF v4.0, which went live during the week of December 5th, 2011. NIF v4.0 has a number of features that improve overall performance of the Neuroscience Information Framework, as well as user focused features to improve navigation in the search results.

On the backend, we now have Solr serving our Lucene indices. With Solr, we can access advanced search functionality while processing queries to NIF. Also, our system has been upgraded to solid-state drives (SSD) to improve retrieval performance.

For the end-user, there have been a few features that are highlighted with the release of NIF v4.0 that we would like to expand on. Many users familiar with NIF know that we have a mountain of neuroscience-related data – some 336 million records. While searching for data, users often are looking for a smaller subset than a simple search result can provide. To achieve this, users are now able to “Filter” on each column within the Data Federation. The filtering functionality limits the search result set to records containing the filtered string. For example, in the NIF Integrated Animals view, results are retrieved across the Rat Genome Database (RGD), International Mouse Strain Resource (IMSR), Caenorhabditis Genetic Center (CGC), and Zebrafish International Resouce Center (ZIRC). If a researcher is only looking for potential zebrafish animal models, they are now able to use “zebrafish” as a filter on the “Organism” column. A video tutorial for the Filtering feature is available at NIF 4.0 – Advanced Search Filtering Functions.

NIF users also desired a way to save search results or at least a snapshot of them while they try out different searches. One way to achieve this, is to “Load in a new window”, which is available on all data sources in NIF v4.0. Clicking this button will, as it suggests, loads the current result set into a new window useful for data comparisons. Additionally, users are able to use the “Export” feature, which is not new to NIF v4.0, but permits more through massaging of search results using popular spreadsheet or data analysis software. Lastly, the “View in Pivot” option desires some mention. Pivot is an exploratory interface available for most Image data type resources. This interface allows users to dynamically organize and sort images into various categories provided by the resource. A video tutorial highlighting each of these features is available at NIF 4.0 – Advanced Search Results Features – New Window, Pivot and Export.

Lastly, NIF Literature has received some noteworthy improvements. The literature indices, gathered from PubMed and PubMed Central (open-access), have been collapsed into a single tab with the release of NIF v4.0. Additionally, we have provided “facets” for the user. Facets are produced from the top result count across Year, Authors and Journals. This way, users are able to quickly reduce search results to a particular area of interest, as well as gather a quick overview of the top authors or journals related to their search string. A video tutorial highlighting these features is available at NIF 4.0 – Scientific Literature Search & Faceting

If you have any questions or comments please feel free to visit the NIF Forum to post and become engaged in the discussion!

NIF Top 10 Categories for December 2011

Lee Hornbrook — Mon, 12 Dec 2011 23:05:36 +0000

What are people looking for at NIF? As the year draws to a close, we bring you the NIF Top 10.

The NIF Top 10 Categories for December 2011 are….

Nervous System Level:Multi-Level
Nervous System Level:Brain Regions
literature
Data Type:Images
Data Type:Antibodies
Data Type:Animals
registry
Data Type:Drugs
Data Type:Connectivity
Data Type:Disease

NIF Top 10 Searches for December 2011

Lee Hornbrook — Mon, 12 Dec 2011 22:59:02 +0000

As the year ends, we begin a new series of posts, the NIF Top 10.

Here are the Top 10 Searches at NIF for December 2011

cerebellum
“Purkinje Cell”
“Diencephalon”
antibodyregistry
hippocampus
“Brainstem”
s100b
sert
“Frontal Lobe”
“Oligodendrocyte Precursor Cell”

Standardization of DNA Collection and DNA Databases

Lee Hornbrook — Fri, 07 Oct 2011 21:21:35 +0000

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.

NIF Webinar – Tuesday, Oct. 11, 2011 at 11:00 am PDT

Lee Hornbrook — Thu, 06 Oct 2011 21:58:05 +0000

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.

--
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