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.

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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

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/

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

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

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!

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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

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!

The NIF Top 10 Categories for December 2011 are….

1. Nervous System Level:Multi-Level
2. Nervous System Level:Brain Regions
3. literature
4. Data Type:Images
5. Data Type:Antibodies
6. Data Type:Animals
7. registry
8. Data Type:Drugs
9. Data Type:Connectivity
10. Data Type:Disease

Here are the Top 10 Searches at NIF for December 2011

1. cerebellum
2. “Purkinje Cell”
3. “Diencephalon”
4. antibodyregistry
5. hippocampus
6. “Brainstem”
7. s100b
8. sert
9. “Frontal Lobe”
10. “Oligodendrocyte Precursor Cell”

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

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