Archive for the ‘Webinar Announcement’ Category

Webinar from BioCaddie (aka DDI): Jeff Grethe presents NIF

Posted on February 9th, 2015 in Anita Bandrowski, News & Events, Webinar Announcement | No Comments »

Cooperative and collaborative data and resource discovery platforms for scientific communities – The Neuroscience Information Framework (NIF) and SciCrunch


Date: Thursday, February 12, 2015
Time: 10:00 AM – 11:00 AM (PST); 1:00 PM – 2:00 PM (EST)



Jeffrey S. Grethe, Ph.D.
Associate Director, Center for Research in Biological Systems
University of California, San Diego


Data and information on research resources are everywhere, in numerous repositories and download sites, and more floods in every day. What’s a researcher to do? In order to be able to use shared data, the first fundamental rule is that you have to be able to find it. We have search engines like Google for web documents, PubMed and Google Scholar for articles, NCBI for selected genomics resources. The Neuroscience Information Framework (NIF; was instantiated in 2006 in response to a Broad Agency Announcement from the NIH Blueprint for Neuroscience Research citing an overwhelming need for an ”information framework for identifying, locating, and characterizing neuroscience information”. NIF was tasked with surveying the neuroscience resource landscape and developing a resource description framework and search strategy for locating, accessing and utilizing research resources, defined here as data, databases, tools, materials, literature, networks, terminologies, or information that can accelerate the pace of neuroscience research and discovery. NIF adds value to these existing biomedical resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without the need for extensive redesign of their components or information models. Unlike more general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, provides search strategies tailored to neuroscience, and also provides access to content that is traditionally “hidden” from web search engines. To accomplish this, NIF has deployed an infrastructure allowing a wide variety of resources to be searched and discovered at multiple levels of integration, from superficial discovery based on a limited description of the resource (NIF Registry), to deep content query (NIF Data Federation). It is currently one of the largest sources of biomedical information on the web, currently searching over 13,000 research resources in its Registry, and the contents of 250+ data resources comprising more than 800 million records in its Data Federation.

Building on the NIF infrastructure, SciCrunch was designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. A data portal that searches across hundreds of databases can be created in minutes. Communities can choose from our existing SciCrunch data sources and also add their own. SciCrunch was designed to break down the traditional types of portal silos created by different communities, so that communities can take advantage of work done by others and share their expertise as well. SciCrunch currently supports a diverse collection of communities in addition to NIF, each with their own data needs: CINERGI – focuses on constructing a community inventory and knowledge base on geoscience information resources; NIDDK Information Network (dkNET) – serves the needs of basic and clinical investigators by providing seamless access to large pools of data relevant to the mission of The National Institute of Diabetes, Digestive and Kidney Disease (NIDDK); Research Identification Initiative (RII) – aims to promote research resource identification, discovery, and reuse.


Dr. Jeffrey S. Grethe, Ph.D. is a Principal Investigator (MPI) for the Neuroscience Information Framework (NIF; and the NIDDK Information Network (dkNET; in the Center for Research in Biological Systems (CRBS; at the University of California, San Diego. Following a B.S. in Applied Mathematics from the University of California, Irvine, he received a doctorate in neurosciences with a focus on neuroinformatics and computational modeling from the University of Southern California. Throughout his career, he has been involved in enabling collaborative research, data sharing and discovery through the application of advanced informatics approaches. This started at USC with his involvement in the Human Brain Project and continues today with his work on NIF, dkNET and with standards bodies such as the International Neuroinformatics Coordinating Facility.

Details on how to join Webinar:

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This webinar is open to all.
More information about this webinar, future webinars and events can be found at:

Please join us for a webinar discussing Neurostars: A Q&A platform for neuroscience

Posted on October 20th, 2014 in Anita Bandrowski, Author, News & Events, Webinar Announcement | No Comments »

Next week we kick off the fall webinar series, with Dr. Satrajit Ghosh from the Massachusetts Institute of Technology. Dr. Ghosh is a research scientist at the mcgovern institute for brain research and an assistant professor at harvard medical school. He will talk about Neurostars and Biostars.

Neurostars ( and Biostars ( are sibling question and answer platforms for neuroscience and bioinformatics communities. Based on the successful StackOverflow model, these platforms provide a voting mechanism, a modern user-interface, integrated search, and personalization characteristics that are typically not available in traditional mailing lists or forums. It also supports facilities for data discovery links and discussion using the bittorrent mechanism, and is now part of the mozilla science lab ( Neurostars is maintained and run by the International Neuroinformatics Coordinating Facilities (INCF) with community input and support.

This webinar will go over some of the basic operations, some features that are only available on these platforms, and finish with a near term roadmap of new features under consideration.


Available here:

When: Anytime!

Scientific Data Reproducibility, a conversation – July 23, 2014, 1 pm EST

Posted on July 16th, 2014 in Anita Bandrowski, Author, Data Spotlight, Webinar Announcement | 2 Comments »

Drs. Martone of NIF and Iorns of Science Exchange among others address important issues around reproducibility of data.

A video recording of this event is available here. Note you have to register to see it.

Title: Improving Scientific Reproducibility In The Life Sciences: Considerations for Researchers, Publishers and Life Science Tool Providers
Date: July 23, 2014     * completed * video available  
Time: 1:00 PM Eastern (10:00 AM Pacific)         
Duration: 90-minutes

In recent years scientific reproducibility has been a topic of much debate.  This debate has been sparked in part by the now infamous “Amgen Study” conducted by Glenn Begley and team that found fewer than 7 of 53 landmark pre-clinical studies published between 2002 and 2012 could be reproduced as described in the initial publication.

The factors that contribute to poor reproducibility in pre-clinical research are complex; some relate to systemic problems in how research is conducted and funded while others relate to how research is documented and published. Recently the role that scientific suppliers, publishers and researchers can play in improving research reproducibility has come into sharp focus. Improving reagent traceability and documentation in literature have been identified as areas that can make a significant contribution to increased reproducibility.

This webinar will bring together thought leaders that are behind some of these efforts and explore how their projects are contributing to the goal of improving scientific reproducibility.

Neuronal Computation Series – NIF Webinars

Posted on September 24th, 2013 in Jonathan Cachat, Webinar Announcement | No Comments »

October will kick off a NIF webinar series around the topic of Neuronal Computation. What is that you ask?

Three rather remarkable and ambitious projects will be highlighted:

On October 1st, Stephen Larson will be discussing the Open Worm Project

Open Worm Project


October 15th, Kenneth Yoshimoto will be presenting on the Neuroscience Gateway Portal


and October 29th, Padraig Gleeson will be presenting on the Open Source Brain initiative.


 check out the full details and descriptions here

We look forward to seeing you there. Also please feel free to contact us – or @neuinfo - with any feedback, comments or webinar suggestions.

BAMS Webinar Recording Available

Posted on March 27th, 2013 in Data Spotlight, News & Events, Webinar Announcement | 1 Comment »

Topic: BAMS – a workspace for macro-connectomes construction
Date/Time: March 26, 2013, 11 am PDT (2:00 Eastern Time)
Presenter: Mihail Bota
The Brain Architecture Management System is one of the most populated public resources of neuroanatomical connectivity reports, collated from the literature or inserted by researchers. As a new addition, BAMS includes a complex interface for construction and representation of connections matrices (connectomes).

This presentation will focus on our methodology to extract connectivity information from published references, and present the connectomes construction interface with emphasis on the rat cerebral cortex.

Webinar: Partha Mitra talks about mouse brain connectivity, this Tuesday!

Posted on March 4th, 2013 in Data Spotlight, News & Events, Webinar Announcement | No Comments »

Topic: The Mouse Brain Architecture Project
Date/Time: March 5, 2013; 11 am PDT (2:00 Eastern Time) – Recording is available at link below
Presenter: Partha Mitra

The basic premise of the Mouse Brain Architecture Project is that, while great advances have been made at the individual neuron and microcircuit levels, there is a large gap at the whole-brain level of analysis of neural circuitry. The project seeks to fill this gap experimentally, by systematically mapping the meso-circuit of the whole mouse brain, and simultaneously addressing the computational and theoretical questions that arise.

The project utilizes a shotgun-like approach, covering the brain with a grid, with each grid point receiving two anterograde and two retrograde tracer injections. An individual mouse is injected with a single tracer substance at a single grid location. Each brain is subsequently sectioned and digitally imaged. The resulting data volumes will be subsequently co-registered in order to obtain the brain-wide meso-circuit.

NIF Webinar: Feb 19th 11 am PDT: Sage Bionetworks discusses ClearScience

Posted on February 12th, 2013 in Force11, News & Events, Webinar Announcement | No Comments »

Please join us to discuss the future of scientific communication as seen by SAGE Bionetworks.

Title: clearScience: Dragging Scientific Communication into the Information Age
Presenter: Erich Huang & Brian Bot (Sage Bionetworks)
Date: February 19th, 2013; 11 am PDT

Abstract: Scientific communication must be re-engineered. Complex analyses from biomedical research are outpacing the means to convey them effectively. Imprisoning insights gleaned from these data to a few two-dimensional representations is wholly inadequate for transmitting the complexity of “big science” to our peers and the public. Numerous editorials and papers, as well as the cancer genomics scandal at Duke University highlight the need for infrastructure that supports reproducible and transparent science. When only 11% of landmark cancer studies can be independently confirmed, it is clear that serving our patients requires a new standard of openness and reproducibility. If scientific progress depends on our being able to effectively communicate our science so that the community can build upon it, evidence shows that we need to improve.

As a not-for-profit research organization, Sage Bionetworks is charged with exploring open models in the practice of biomedical science and enhancing the value of medical research to the community. The foundation for this exploration is Synapse, a cloud-based platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services. While typical scientific publications are a minor elaboration on a 15th century technology, we propose that ‘publication’ of data-intensive science should not just be a representation of science, but the science itself.

We will present clearScience, a pilot project in building infrastructure for effective scientific communication. By leveraging Synapse services, we demonstrate how scientists can easily transition from exploring data—executing science—and providing the scientific community all the resources to recreate analyses. By capturing the complete lifecycle of a project, reproducibility becomes a byproduct rather than a burden of publication. Further, we provide for “forking an analysis”, allowing anyone to explore and elaborate on ‘published’ work. If the goal of biomedical research is to deliver results that will ultimately alleviate suffering and minimize harm to patients, being able to transparently share, reproduce, and build off of one another’s work is critical to scientific progress. clearScience represents one compelling model for facilitating this progress.

NIF Webinar: NIF 5.0 New Features for the user and developer-POSTPONED

Posted on February 7th, 2013 in Force11, News & Events, Webinar Announcement | No Comments »

Screen Shot 2013-02-07 at 10.24.22 AM


The next NIF webinar will highlight the features of NIF 5.0, the new light-weight interface, that allows users to visually subset and customize data. We will focus on user features in the beginning, but will also address some of the new and improved features for developers, including services for autocomplete on neuroscience terms, text processing, and data services. With the release of MyNIF, users can quickly build portals into just the data sets they want.

Please join us!

Date: TBD
Time: 11 am PDT

NIF Webinar: Dr. Hongwei Dong on Macroconnectomes Feb 5th 11 am PDT

Posted on January 29th, 2013 in News & Events, Uncategorized, Webinar Announcement | No Comments »

Please join NIF for the next webinar at the crossroads of neuroscience and informatics.

Topic: The state of Macroconnectomes: what can these tell us about the nervous system?

Date/Time: February 5, 2013 – 11:00 am PDT (2:00 Eastern Time)

Presenter: Hongwei Dong


URL: Recording available

Macro-connectomes (connectivity matrices at the brain regions level) are essential for understanding the structure-functional relationships of different parts of the mammalian central nervous system. They are also the starting point in construction of functionally relevant networks with different levels of complexity.

The construction of macroconnectomes is a complex and time consuming task involving combined efforts from experimental neuroanatomists and neuroinformaticians. There is no completed macroconnectome of any species to date, but a substantial amount of rat and macaque connectivity data is already collated by several neuroinformatics groups. The advent of more sophisticated axonal tracing techniques promises rapid production of high quality experimental connectivity data in (rodent) animal models. Moreover, improved tools for visualization, sharing, and analysis of tract tracing data, will expectedly facilitate extraction of knowledge and assembly of connectome matrices from such data.

Please join us for the NIF Webinar – Dataverse Nov 27th, 11 am PDT

Posted on November 20th, 2012 in Force11, News & Events, Uncategorized, Webinar Announcement | No Comments »

Topic: The Dataverse Network
Date/Time: November 27, 2012 – 11:00 am PDT (2:00 Eastern Time)
Presenter: Merce Crosas
The Dataverse Network is an open-source repository for sharing, citing and analyzing research data developed at the Institute for Quantitative Social Science (IQSS) at Harvard University. It provides a platform for replicating previous work and helping validate science. It generates a formal persistent data citation to allow referencing a data set (and its version) from a publication. Each Dataverse in a Dataverse Network is customized and managed by a researcher or research group, while the data sets are archived in a central repository. Harvard University currently hosts a Dataverse Network fo social science data and another one for astronomy data.