Sandia National Laboratories has two positions open in Computational Neuroscience

Posted on July 10th, 2015 in News & Events | No Comments »

Hello NIF Community!

Sandia National Laboratories has two positions open in Computational Neuroscience.  Details below.  Please share with your colleagues.

Sincerely,

The NIF/SciCrunch Team

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Postdoc position:

We are seeking postdoctoral researchers to join an interdisciplinary research program focused on understanding neural computation at the circuit level.  Example research topics of interest include computational models of visual cortex, neural circuitry underlying perception, and the neural basis of decision-making.

Candidates should have a strong background in neuroscience, and an interest in understanding of relations between neuroscience, cognitive science, and computation. Experience or familiarity with related machine-learning fields is also desired. Our department is part of a highly interdisciplinary community of researchers with interests spanning systems neuroscience and brain-inspired computing, engineering, and computer science.  Successful applicants will be expected to conduct high-quality research, maintain a successful publication record in peer-reviewed journals, and develop collaborations with this vibrant and growing community.  This position is located at Sandia’s Albuquerque, NM, USA site.

To view the full job advertisement and to apply, visit http://www.sandia.gov/careers/ and click “View All Jobs”.  Go to the Advanced Search, then search for Job Opening ID 650197.

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Permanent Staff position:

We are seeking computational neuroscientists to join an interdisciplinary research program focused on understanding neural computation at the circuit level.  Preference will be given to candidates using computational approaches, broadly defined, to understand visual cortex and perception, but we welcome applicants from all areas of computational neuroscience.  Example research topics of interest include computational models of visual cortex, neural circuitry underlying perception, and the neural basis of decision-making.

Candidates should have a strong background in neuroscience, and an understanding of relations between neuroscience, cognitive science, and computation. Experience or familiarity with related machine-learning fields is also desired. Our department is part of a highly interdisciplinary community of researchers with interests spanning systems neuroscience and brain-inspired computing, engineering, and computer science.  Successful applicants will be expected to conduct high-quality research, maintain a successful publication record in peer-reviewed journals, and develop collaborations with this vibrant and growing community.  Staff members at Sandia are expected both to contribute to ongoing projects and to develop new lines of research with potential for application in solving complex problems. This position is located at Sandia’s Albuquerque, NM, USA site.

Multiple positions for varying levels of experience are available.  For more information and to apply, visit http://www.sandia.gov/careers/ and click “View All Jobs”.  Go to the Advanced Search, then search for Job Opening ID 650198.

Eating my own Dog Food!

Posted on July 4th, 2015 in Anita Bandrowski, Curation, Interoperability, News & Events | No Comments »

While not all of you have been fortunate enough to attend the first Beyond the PDF meeting, I will say this; it was eye opening for this scientist. To me, the most memorable statement from the meeting was when Geoffrey Bilder argued from the back of the room that we should all Eat Our Own Dog Food! What he meant was that anyone building tools should actually use them or proclaiming any broad “thou shalt-s” should himself live up to the particular proclamation.

Easier said than done, Geoffrey!

In the years since this historic meeting, these statements have been eating away at my psyche.

I lead the Resource Identification Initiative, a project to add unique identifiers to all papers that use: antibodies, model organisms, software tools or databases. Basically I am telling authors to do “my bidding” and make their papers better to search and give academic credit to developers of software tools like R or ImageJ. I am asking these authors to help others selflessly and do something different than they have done before.

When submitting a paper to Frontiers in NeuroInformatics, as a middle author at the very beginning of the RII project, I felt very reluctant to add RRIDs to the paper. Who was I to suggest such a thing? I waited for the editor to remind us to add the identifers, I waited and no question came. Before final submission, I overcame my very uncharacteristic muteness and asked my collaborators to add the RRIDs to a table where I felt they were appropriate. It turned out that my colleagues did not object and the journal editor, also didn’t say anything about including them. His journal was not yet on board, something that has been remedied since.

Why did I feel so strongly that I should not include an identifier for tools while telling others to do it?
What was I afraid of?
Change is hard!

I am really not sure now what I was so afraid of because after overcoming this initial scientific recalcitrance I simply put RRIDs in the next paper without a second thought and continued to put them in since.

So as I was drafting this blog, a colleague asked me to contribute to a table in her paper, I will be one of those middle authors (huge paper with tons of authors), but this time as with my own papers I have asked her to include the RRIDs without being afraid; it took me about 8 minutes to pull all relevant RRIDs from scicrunch.org/resources and the paper was just submitted. I do not care if the journal is participating in the initiative officially or not.

I guess that what I have learned from all of this, is that once you accept change it becomes the new normal and RRIDs are a great new normal. Thanks Geoffrey for nagging me, I am very glad to say that I have Eaten My Own Dog Food!

Apply for the position of Program Manager of SPARC at NIH

Posted on June 11th, 2015 in News & Events, Uncategorized | No Comments »

Hello NIF Family!

The position for Program Manager of the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program at the National Institute of Health (NIH) is available. If you think you might qualify for this position and would be interested in applying, please read the letter of notice below:

Common Fund Program Manager 
Are you a top-level Scientific Researcher seeking a career at one of the preeminent biomedical research institutes in the Nation and the world? The Program Manager (PM) of the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program will use her/his research expertise to lead SPARC awardees to develop integrated functional/anatomical neural circuit map(s) in multiple organ systems, create next generation tools to accelerate research, and cultivate and maintain ongoing partnerships between the NIH, FDA, and industry.  The goal of the SPARC program is to develop proof of concept for a new class of neural control devices to precisely treat a wide variety of diseases and conditions.
 
We are looking for applicants with a commitment to scientific excellence and the energy, enthusiasm, and innovative thinking necessary to lead within a dynamic and diverse organization.  The ideal candidate would have expertise in neuroscience and/or any field of biomedical research focused on the peripheral nervous system; medical device development and associated FDA policies; fostering and working with interdisciplinary research teams; and managing and overseeing large collaborative networks involving academia, industry and/or federal government.  For the full list of qualifications, please see the official position announcement.
 
Applications will be reviewed starting July 1, 2015 and the search will be closed when a suitable candidate is identified.  More information can be found at http://www.jobs.nih.gov/vacancies/executive/oer.htm
Sincerely,
NIH Common Fund SPARC Program staff

“The Resource Identification Initiative: A cultural shift in publishing”

Posted on June 5th, 2015 in News & Events | No Comments »

The NIF community is very excited about a recently released research article, “The Resource Identification Initiative: A cultural shift in publishing” (Anita Bandrowski, Matthew Brush, Jeffery S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena Tan, Nicole Washington, Elena Zudilova-Seinstra, Nicole Vasilevsky) The research article focuses primarily on the Research Resource IDentifier (RRID). NIF is excited about RRIDs because they could play a major role in redefining the way that scientists communicate about and receive credit for the data, software tools, antibodies and model organisms that they produce. For more information regarding the article as well as a direct link to the article please visit the following link: https://pascophronesis.wordpress.com/2015/05/31/rrid-shows-promise-in-meta-identification/

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Version 6.1 of NeuroMorpho.Org

Posted on May 27th, 2015 in News & Events | No Comments »

NIF/SciCrunch is very pleased to hear that NeuroMorpho.org has released two new datasets to its collection. This means there are 4597 new reconstructions for your accessing pleasure! To view these reconstructions at NIF/SciCrunch please follow this link (https://neuinfo.org/mynif/search.php?list=cover&q=neuromorpho&t=indexable&nif=nif-0000-00006-1). Please look below for the detailed release from NeuroMorpho. NOTE(5/29): The above link will be fully updated with the new resources on Monday morning (June 1, 2015).
Thanks and Crunch on!

“Version 6.1 of NeuroMorpho.Org was released on 13 May, 2015.

This release included two new data sets of 4597 reconstructions. NeuroMorpho.Org now contains 31,982 reconstructions from 147 contributing labs. More than 3 million reconstructions were downloaded in over 150,000 unique visits from 150 countries.

Please visit the What’s new page for details on the added data and other updates including updated Metadata Form, inclusion of publication DOIs in the Literature Coverage, and an unabridged collection of tools and resources. The literature coverage database was also updated to include publications through March 2015

We are continuously grateful to all the data owners who freely share their data with the community. We appreciate any and all feedback and comments.

Sincerely,

The NeuroMorpho.Org team”

The re3data.org – Registry of Research Data Repositories is moving forward

Posted on May 12th, 2015 in News & Events | No Comments »

NIF / SciCrunch is very excited about a couple of upcoming collaborations with re3data. Please take a look below for their new announcement about the DataCite (from Harvard) collaboration. Re3data’s goals align with one of the main goals at NIF / SciCrunch, to avoid silos of user interface that interfere with the user finding content relevant to their research. We list many of re3data’s registries through our registry (check out the re3data repositories here: https://scicrunch.org/browse/resources?query=re3data.org&filter=). Happy Crunching!

The DataCite General Assembly met at the British Library last week and approved the inclusion of the re3data.org – Registry of Research Data Repositories into the portfolio of services that are managed by the DataCite organization.

Scince 2012 re3data.org offers researchers, funding organisations, libraries and publishers a comprehensive overview of the heterogeneous landscape of research data repositories.

 In May 2015 re3data.org lists more than 1,200 research data repositories from around the world covering all academic disciplines.  The databases, repositories and data infrastructures are described following a detailed schema (Vierkant et al. 2014). Besides the detailed description, re3data.org summarises the properties of a repository into a user friendly icon system helping researchers to easily identify an adequate  repository for the storage of their data sets (Pampel, et al. 2013).  More than 5,000 unique visitors are using the registry  per month. An average of 10 repositories are added to the registry every week.

The registry offers two search possibilities: (1) free text search through a simple search box, and (2) filters for more specific searches. In the list of results each record includes the name of the repository, the subjects covered, a brief description of the content and a set of icons visualizing key properties of the repository. A comprehensive view of the descriptive record of the repository can be obtained by clicking on the name of the repository in the search results.  It is also possible to simply browse through the list of indexed data repositories.

A REST-API is currently being beta tested that provides the full list of repositories and enables retrieval of full, structured records describing individual repositories. The interface aims to implement a RESTful application architecture. In line with the HATEOAS concept, the data can be discovered automatically and retrieved in XML by following hypermedia links. The interface, currently being beta, supports versioning and will be extended with future requirements.

The re3data.org registry cooperates with other Open Science initiatives like BioSharing and OpenAIRE. Project partners in re3data.org include the GFZ German Research Centre for Geosciences, Humboldt-Universität zu Berlin, Purdue University, and KIT. The work of re3data.org has been funded by the German Research Foundation (DFG) in Germany and the Institute of Museum and Library Services (IMLS) in the United States.

 

GBSI Antibody Survey

Posted on April 23rd, 2015 in News & Events | No Comments »

Hello NIF family!

The GBSI (Global Biological Standards Institute) has created a survey in order to gather valuable information in regards to how researchers view the best practices in Cell Culture Authentication and Research Antibodies. The survey aims to address challenges and barriers researchers face in implementing these practices. The Survey is available through the following link http://surveys.mckinley-advisors.com/s3/LC.

At the beginning of the survey (question #3), there is a simple way to take one or both surveys. Each survey should only take about 10 minutes to complete.

Please note when taking the survey: http://antibodyregistry.org/ is a great source for validated antibodies and it would be excellent to add this to the survey.

Thank you!
The NIF Team

 

NIH Plan for Increasing Access to Scientific Publications and Digital Scientific Data

Posted on March 4th, 2015 in Anita Bandrowski, Interoperability, News & Events | No Comments »

The NIH put out a plan to increase access to scientific data.

What do they really mean and what does this mean to researchers?

Researchers have been asked to provide PubMed Central PMC identifiers in grant applications and this single requirement has pushed authors to submit their papers to PMC and many journals do this as a matter of fact leading to a large corpus of publications that are fully searchable texts. I think that researchers are now familiar with this process and see the benefit, as I do when I am at home and need to look up a piece of information from my old paper that a publisher tries to charge me $36 to find.

What happens to data and what is meant by data?
Will authors need to submit all of their supplementary data files to PMC?

Perhaps not, some wording in the document from the NIH shows that they know that data is not homogeneous. They recognize that they can’t handle the diversity in a good way without working with existing repositories.

They point out that data should be FAIR:
Findable
Accessible
Interoperable
Reusable
This is known as the FAIR standard.

They also state:
“A strategy for leveraging existing archives, where appropriate, and fostering public- private partnerships with scientific journals relevant to the agency’s research; Encourage public-private collaboration; Encourage public-private collaboration to … otherwise assist with implementation of the agency plan; Ensure that publications and metadata are stored in an archival solution that… uses standards, widely available and, to the extent possible, nonproprietary archival formats for text and associated content (e.g., images, video, supporting data).”

So will there be a set of repositories that are “approved” community standards? Will the NIH have a box for grantees to put in their community repository IDs?
Seems like a good direction!

For now, NIF has a very large list of repositories that will house your data.
Try this registry search.
There are over 1000 that respond to the query, but which one or which ones can you use?
It does not seem that the NIH is willing to be proscriptive, so it will be left to individual communities to rally around repositories that best serve them.
For now, NIF just aggregates the information around these and attempts to make them findable (the F in FAIR).

Integrated Annotation just added the 7-million-th record

Posted on February 27th, 2015 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Yes we do have annotations!

What can we do with these annotations?

* When you are reading a paper, would you like to know if the data you are looking at has been stored somewhere?

* Would you like to know if someone figured out what antibody the authors used?

* What about the mouse described in the paper, is there additional information in MGI?

The integrated annotation view is an aggregate of any database included in NIF that contains the PubMed Identifier.

In over 50 databases there are citations containing PubMed Identifiers, a reference for a particular data record. While each database is different, there are some themes. Records may include reagents used in the paper like AddGene plasmids, data that is stored somewhere like ModelDB computational models, or they may include a set of values that were extracted from the paper like BioNumbers.

Through a software tool called the LinkOut Broker, we submit these data to PubMed (unless the database does this already), an annotation that says this paper is referenced in a particular database. However, these citations are not searchable in PubMed and so we have made the integrated annotation view to allow NIF users to search these same annotations.

However, we know that people read papers in many places, pdf readers and on line so we have started working with several groups including a team at Science Direct to push the data into the places where the readers are. We are proud to work with the Elsevier Antibody App team, who created an application visible in Science Direct in all Elsevier papers that have an antibody annotated in the antibodyregistry.org.

An example paper from Experimental Neurology can be viewed here http://www.sciencedirect.com/science/article/pii/S0014488614003896

The NIA Butler-Williams Scholars Program

Posted on February 27th, 2015 in Anita Bandrowski, News & Events | No Comments »

The NIA Butler-Williams Scholars Program (formerly Summer Institute on Aging Research) is accepting applications for an intensive introduction to aging research. This program for investigators that are new to aging research is focused on the breadth of research supported by the National Institute on Aging, including basic biology, neuroscience, behavioral and social research, geriatrics and clinical gerontology. As an offering through the NIA Office of Special Populations, program content will include a focus on health disparities, research methodologies, and funding opportunities. The Butler-Williams Scholars Program (B-W Scholars) is one of the premier, short-term training opportunities for new investigators. New researchers are defined as those who have recently received the M.D., Ph.D. or other doctoral level degree. The B-W Scholars Program provides participants with unparalleled access to NIA and NIH staff in an informal setting.

The 2015 B-W Scholars Program will be held July 27-31, 2015 in Bethesda, Maryland. Support in most cases is available for travel and living expenses.  The B-W Scholars Program is sponsored by NIA with support from the National Hartford Centers of Gerontological Nursing Excellence.

***Applications are due Friday, March 27, 2015***

Researchers with an interest in health disparities research are encouraged to apply. Applicants from diverse backgrounds, including individuals from underrepresented racial and ethnic groups, individuals with disabilities and women are always encouraged to apply for NIH support. Applicants must be U.S. citizens, non-citizen nationals, or permanent residents.
Please view more information on the NIA web site:  www.nia.nih.gov/about/events/2014/butler-williams-scholars-program-2015

For more information, please contact:
Ms. Andrea Griffin-Mann
Office of Special Populations
National Institute on Aging
National Institutes of Health

griffinmanna@mail.nih.gov