Biosharing Standards Registry Survey

Posted on January 25th, 2016 in News & Events | No Comments »

Hello, NIF/SciCrunch Community,

Please take a moment to fill out the survey listed and described in the link below.

“The Biosharing team is conducting a survey on standards with and for 2 major/research infrastructure programmes/ in the life, environmental and biomedical sciences, namely the *ELIXIR* and *NIH Big Data to Knowledge Initiative*.”
https://bd2kccc.org/2016/01/15/biosharing-standards-registry-survey

Sincerely,

The NIF/SciCrunch Team

iNeuro Project Workshop Report

Posted on January 8th, 2016 in News & Events, Uncategorized | No Comments »

Hello NIF/SciCrunch users!

Please take a moment to view the iNeuro Project Workshop Report.

The report outlines necessary steps for preparation and production in regards to accomplishing two main objectives regarding big-data in the Neuroscience Community:

1. Preparing a workforce to meet the challenges of large-scale neuroscience data.

2. Producing curricula and resources for large-scale neuroscience data analysis.

Click the link below for access to the report.

iNeuro Conference Report

Sincerely,

The NIF/SciCrunch Community

bioCADDIE External Monthly Webinar

Posted on December 9th, 2015 in News & Events, Uncategorized | No Comments »

bioCADDIE External Monthly Webinar

Hypothes.is

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

Presenters
Maryann Martone, PhD
University of California, San Diego

Abstract
Hypothes.is: Creating a light-weight, open, portable knowledge layer over biomedicine

The Internet has transformed society, and science with it. But only now are we developing a key component, long imagined by early web pioneers: the ability, as users, to contribute to and connect online resources.

Hypothes.is (http://hypothes.is) has developed the capability to add interactive and machine-searchable annotations to any web resource. Annotation is an ancient and ubiquitous practice in scholarship; for as long as we’ve had scholarly works, we’ve had notes and information attached to them. Annotation, particularly scholarly annotation, is distinct from current commenting systems in that it is anchored to a specific portion of a research object, i.e., a statement, an object in an image, a gene sequence and located according to the physical particulars of the target, i.e., the margin, image coordinates.

With Hypothes.is, any content on the web can be turned into an interactive forum for on-line discussions or annotated with additional information. Because Hypothes.is is engineered for the web, annotations can be replied to, shared and searched across contexts. But annotation need not be restricted to narrative works. We are actively exploring incorporation of annotation tools into data repositories and other research objects.

The implications of this technology are profound for collaborative creation of knowledge across many domains, including journalism, government, education and research. In biomedicine, Hypothes.is provides an independent communication channel on top of the scientific research objects where additional information can be added to otherwise static artifacts. It provides a lightweight interactive tool for peer review, education and post-publication mark-up.

For this reason, Hypothesis was founded as a non-profit, so that the annotation layer will remain open and available to everyone. Because it is built on open software, annotations can be shared and ported across people and tools, without being locked into proprietary software. Hypothes.is has launched a growing coalition with publishers, societies, libraries and other technology providers to commit to providing an open annotation layer for all scholarly works (https://hypothes.is/annotating-all-knowledge/).

In this presentation, I provide an overview of the technology and show how Hypothes.is is providing a lightweight, portable web-enabled knowledge layer across the biomedical workflow.

Biographies
Dr. Martone received her BA from Wellesley College in biological psychology and her PhD in neuroscience in 1990 from the University of California, San Diego, where she just retired as a Professor in the Department of Neuroscience. Her background is in neuroanatomy, particularly light and electron microscopy, but she spends most of her time now in the field of neuroinformatics. Dr. Martone is the principal investigator of the Neuroinformatics Framework project, a national project to establish a uniform resource description framework for neuroscience. Her recent work has focused on building ontologies for neuroscience for data integration. She just completed her tenure as the US scientific representative to the International Neuroinformatics Coordinating Facility (INCF), where she still heads the program on ontologies. She is finishing up her tenure as president of FORCE11, an organization dedicated to advancing scholarly communication and e-scholarship, on December 31, 2015. Dr. Martone remains a professor emeritus at UCSD and has recently joined Hypothes.is, a non-profit dedicated to developing an annotation layer over the web, as Director of Biosciences.

Details on how to join the webinar:
Must use Web and Audio
Please include name and institution when joining meeting.
Web: http://www.readytalk.com/ (Join meeting with access code 2201876)
Audio: 1-866-740-1260 (access code 2201876)
International call in numbers are available here (access code 2201876)
Click here to test your computer’s compatibility before the meeting.

This webinar is open to all.
More information about this webinar, future webinars, and events may be found at:
https://biocaddie.org/events/webinars.

Force2016 Conference

Posted on December 1st, 2015 in News & Events, Uncategorized | No Comments »

Hello NIF/SciCrunch Community! See below for important information on the upcoming Force 11 Conference.

“Force2016 Conference
Dates: Preconference: April 17, 201; Main conference: April 18-19, 2016
Venue: Portland, Oregon
Hashtag: #Force2016
Site: www.force2016.org
Chair: Melissa Haendel
Program Chairs: Susanna Sansone and Nicole Vasilevsky

The FORCE2016 Research Communication and e-Scholarship Conference brings together a diverse group of people interested in changing the way scholarly and scientific information is communicated and shared. Join us in Portland if you are passionate about transforming research processes and scholarly communication in support of maximizing accessibility and efficiency. Keynote speakers include John Brownstein (Harvard Medical School), Cassidy Sugimoto (Indiana University), Phil Bourne (NIH) and the Alan Alda Institute for Communicating Science.

Who is it for? Scholars, researchers, librarians, data managers, grant administrators, funders, publishers, editors, societies and anyone else interested in scholarly communications

What is Force11? FORCE11 is a grass-roots organization that aims to improve knowledge creation and sharing by encouraging better use of new technologies by working across disciplines, roles and sectors. Everyone is welcome to join Force11 and participate in a variety of working groups, task teams and pilot projects.

SUBMIT ABSTRACTS: Posters, Demos, Sessions at this form here.

Sessions descriptions:
No see, no touch traps: still struggling to escape or free at last? – Open Access let the world first see (access), and then use (license) research content. But access doesn’t stop at the point of reading.
Starting off on the right foot with data management – Calling for participants to argue positions on data sharing
Data by the people, for the people – Ethical considerations for human subjects research and patient data sharing
Pitch it: innovation challenge – Give us your great ideas on how to change scholarship!
Travel Fellowship Funding – Apply Today Travel Fellowships are available for up to $1,200 for travelers within the US and Canada, and up to $2,000 for international travelers. While applications will be accepted from anyone who wishes to attend the conference and demonstrates a need for support, we especially encourage applications from student/young scholars and those from beyond North America and Europe.

SUBMIT TO HOST: Pre-conference Workshops and Meetings Sunday, 17 April 2016, is available for groups who want to meet in conjunction with the FORCE2016 conference, whether for workshops, informal or formal collaborations, or business meetings. Meetings should be related to the goals and mission of FORCE11. If you are interested in hosting a meeting at the FORCE2016 venue, please submit this form.

New SPARC Other Transaction (OT) Funding Opportunity Announcements!

Posted on November 30th, 2015 in News & Events | No Comments »

Check out these funding opportunity announcements from our colleagues at SPARC!

“Dear Colleague,

The NIH Common Fund Program on Stimulating Peripheral Activity to Relieve Conditions (SPARC) has released four new funding opportunity announcements. These RFAs solicit applications that address two separate but interrelated research foci:

Comprehensive Functional Mapping of Neuroanatomy and Neurobiology of Organs – Projects that support a full, multi-expertise approach to understanding both afferent and efferent components of nervous system control of major organ function. These large projects will comprehensively provide data for the detailed, predictive functional and anatomical neural circuit map for neural control of medically relevant functions of a specific organ and its functionally-associated structures (for example, the bladder and associated sphincter).
Pre-application: Stimulating Peripheral Activity to Relieve Conditions (SPARC): Comprehensive Functional Mapping of Neuroanatomy and Neurobiology of Organs (OT1)
(RFA-RM-15-003)
Application Receipt Date(s): Applications are accepted bimonthly on or around the 15th of the month: January 15, 2016 January 17, 2017 January 15, 2018 March 15, 2016 March 15, 2017 May 16, 2016 May 15, 2017 July 15, 2016 July 14, 2017 September 15, 2016 September 15, 2017 November 15, 2016 November 15, 2017
Limited Competition – Stimulating Peripheral Activity to Relieve Conditions (SPARC): Comprehensive Functional Mapping of Neuroanatomy and Neurobiology of Organs (OT2)
(RFA-RM-15-018)
Application Receipt Date(s): Not Applicable. New and Resubmission applications are accepted on the date specified in the Invitation to Submit after successful competition of the corresponding OT1 (RFA-RM-15-003) application.

Foundational Functional Mapping of Neuroanatomy and Neurobiology of Organs – Projects that focus on filling current knowledge gaps in order to provide the foundational functional neuroanatomy and neurobiology data for major organs, potentially leading to a subsequent large Comprehensive Functional Mapping project.
Pre-application: Stimulating Peripheral Activity to Relieve Conditions (SPARC): Foundational Functional Mapping of Neuroanatomy and Neurobiology of Organs (OT1)
(RFA-RM-15-019)
Application Receipt Date(s): January 15, 2016

Limited Competition – Stimulating Peripheral Activity to Relieve Conditions (SPARC): Foundational Functional Mapping of Neuroanatomy and Neurobiology of Organs (OT2)
(RFA-RM-15-020)
Application Receipt Date(s): Not Applicable. New applications are accepted on the date specified in the Invitation to Submit after successful competition of the corresponding OT1 (RFA-RM-15-019) application.

SPARC is uniquely positioned to serve as a community resource that provides the broader public and private research communities with the scientific foundation necessary to pilot new and/or improved closed-loop neuromodulation devices and stimulation protocols to treat diseases and conditions through precise neural control of peripheral end-organ system function. The SPARC program is comprised of four interrelated research components with joint aims to support multidisciplinary teams of investigators to deliver detailed, predictive, functional and anatomical neural circuit maps of the innervation of multiple major internal organs in humans. These FOAs serve as part of the SPARC program’s first phase by focusing on anatomical and functional mapping using current state-of-the-art technologies. It is anticipated that the resulting projects will enable later competitive high resolution mapping projects and pre-clinical testing for new therapies.

Detailed in the FOAs, the Other Transaction (OT) mechanisms will afford the program the agility necessary to make rapid progress toward program goals. In addition, the OT mechanisms will enable the SPARC Program Manager and funded awardees to quickly and fluidly incorporate relevant breakthroughs and discoveries, engage non-funded pioneers, and establish SPARC awardee collaborations and partnerships. For more detail on the management of SPARC Other Transaction awards visit our SPARC Other Transaction Authority page. Guidelines for these OT processes are listed within the NIH Other Transaction Award Policy Guide for the SPARC Program. This document describes the various laws, regulations, guidelines and polices to which the SPARC program will adhere.

Please contact SPARC_Biology@mail.nih.gov if you have any questions regarding these funding opportunities. In addition, please feel free to share this announcement with your colleagues.”

Sincerely,

The NIF/SciCrunch Team

The NIH Common Fund Program on Stimulating Peripheral Activity to Relieve Conditions (SPARC) has released new funding opportunity announcements.

Posted on November 19th, 2015 in Uncategorized | No Comments »

Hello NIF/SciCrunch Community! Please read this message from our colleagues at the NIH Common Fund SPARC Program staff regarding new funding opportunities!
“The NIH Common Fund Program on Stimulating Peripheral Activity to Relieve Conditions (SPARC) has released new funding opportunity announcements. These RFAs solicit applications that address two separate but interrelated research foci:
Comprehensive Functional Mapping of Neuroanatomy and Neurobiology of Organs – Projects that support a full, multi-expertise approach to understanding both afferent and efferent components of nervous system control of major organ function.  These large projects will comprehensively provide data for the detailed, predictive functional and anatomical neural circuit map for neural control of medically relevant functions of a specific organ and its functionally-associated structures (for example, the bladder and associated sphincter).
January 17, 2017; March 15, 2017; May 15, 2017; July 14, 2017; September 15, 2017; November 15, 2017; January 15, 2018.
Foundational Functional Mapping of Neuroanatomy and Neurobiology of Organs – Projects that focus on filling current knowledge gaps in order to provide the foundational functional neuroanatomy and neurobiology data for major organs, potentially leading to a subsequent large Comprehensive Functional Mapping project.
SPARC is uniquely positioned to serve as a community resource that provides the broader public and private research communities with the scientific foundation necessary to pilot new and/or improved closed-loop neuromodulation devices and stimulation protocols to treat diseases and conditions through precise neural control of peripheral end-organ system function. The SPARC program is comprised of four interrelated research components with joint aims to support multidisciplinary teams of investigators to deliver detailed, predictive, functional and anatomical neural circuit maps of the innervation of multiple major internal organs in humans. These FOAs serve as part of the SPARC program’s first phase by focusing on anatomical and functional mapping using current state-of-the-art technologies. It is anticipated that the resulting projects will enable later competitive high resolution mapping projects and pre-clinical testing for new therapies.
Detailed in the FOAs, the Other Transaction (OT) mechanisms will afford the program the agility necessary to make rapid progress toward program goals. In addition, the OT mechanisms will enable the SPARC Program Manager and funded awardees to quickly and fluidly incorporate relevant breakthroughs and discoveries, engage non-funded pioneers, and establish SPARC awardee collaborations and partnerships. For more detail on the management of SPARC Other Transaction awards visit our SPARC Other Transaction page. Guidelines for these OT processes are listed within the NIH Other Transaction Award Policy Guide for the SPARC Program. This document describes the various laws, regulations, guidelines and polices to which the SPARC program will adhere.
Please contact SPARC_Biology@mail.nih.gov if you have any questions regarding these funding opportunities. In addition, please feel free to share this announcement with your colleagues.”

Funding Opportunity for Identification of Genetic and Genomic Variants by Next-Gen Sequencing in Non-human Animal Models (U01)

Posted on November 16th, 2015 in News & Events | No Comments »

Greetings NIF/SciCrunch Community!

Check out this funding opportunity from the National Institute on Drug Abuse, NIH.

“Identification of Genetic and Genomic Variants by Next-Gen Sequencing in Non-human Animal Models (U01) – See more at: http://grants.nih.gov/grants/guide/pa-files/PAR-15-120.html#sthash.5RXMqC9J.dpuf ?

The next deadline is March 1, 2016

Research Scope and Objectives
This announcement encourages applications for projects aimed at the discovery of gene variants in outbred or selectively bred non-human animals through the use of Next-Gen Sequencing technologies. The proposed projects should be based on data demonstrating the relevance of the traits to drug abuse behaviors and processes of addiction. Investigators may employ previously selectively bred animals, re-derived strains, strains selected for some specific new phenotypes, beginning with a novel progenitor population, or an outbred population. Vulnerability phenotypes, for purposes of this FOA, are defined as individual differences that convey increased propensity to acquire, maintain or escalate to uncontrollable, compulsive drug intake, or increased vulnerability to relapse to drug seeking and drug-taking following a period of abstinence. Vulnerability phenotypes may be defined behaviorally or neurobiologically, must have demonstrated heritability, and be suitable for mapping in outbred or selectively bred strains. The following are examples of vulnerability phenotypes that have been characterized behaviorally which would be appropriate for study; however, this is not an inclusive listing and there may be others:

· High drug sensitivity, reactivity or preference

· Preference or sensitivity for non-drug rewards

· Somatic and affective drug withdrawal

· Novelty preference or novelty seeking

· Increased incentive motivation for reward-related stimuli

· Sensitivity to develop escalation of drug taking

· Impulsivity

· Poor cognitive flexibility (e.g., reversal learning, set shifting, etc.)

· Resistance to punishment during drug-seeking

· Persistent responding in the absence of drug

· Heightened relapse and reinstatement

· Enhanced stress reactivity

· Disrupted circadian rhythms

Vulnerability phenotypes that have been identified by individual differences in neurobiological substrate or mechanisms (structural, functional, chemical) that can be genetically mapped are also appropriate.

Mapping of genetic modifiers of vulnerability phenotypes in knockout or knock-in animals, i.e. identification of gene variants that modify a drug abuse associated phenotype when a knockout or knock-in animal or defined mutation is bred into a different genetic background, is also responsive to this FOA.

If you are interested in submitting an application for the March 1, 2016 deadline.”

Click below to apply!

http://grants.nih.gov/grants/guide/pa-files/PAR-15-120.html#sthash.5RXMqC9J.dpuf ?

Sincerely,

The SciCrunch/NIF Team

 

[EZID] Practical Hacking On Identifiers at BiOSphere 2 (PHOIBOS2), Feb. 17-19, 2015, Oracle, Arizona, USA

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

Greetings NIF/SciCrunch Community! Please check out this announcement below in regards to a three day PHOIBOS2 workshop at Biosphere 2 which will be located in Oracle, Arizona.

“In the era of big data and informatics, there is growing awareness among scientists and scientific data managers of the need for permanent, globally unique identifiers for both physical specimens and digital data, leading to the development of new systems for minting, tracking, resolving, and querying identifiers. However, existing identifier systems have not yet been put to the test with the types of very large, multidisciplinary datasets that loom on the horizon, and developing an identifier infrastructure for really big data (pre- and post-publication) is crucial next step.

During the three day PHOIBOS2 workshop at the world-renowned Biosphere 2 in Oracle, Arizona, identifier practitioners and data generators will come together to summarize the current state of the field, identify and elucidate the technical issues, and develop solutions. PHOIBOS2 will incorporate elements of a hackathon, but outputs may also include non-technical products like a draft proposal, a survey, or educational materials. The agenda for the meeting is modeled after the successful MIT Hacking Medicine, in which groups of participants are asked to identify a problem and articulate what a system that solved the problem would look like, including technologies, support material, and a business model. We aim to develop a vision of an identifier infrastructure that spans the entire data lifecycle in the context of very large, complex, multi-disciplinary, research-oriented datasets.

If you are a scientist, or user or developer of identifier systems, and would like to take part in this innovative experience, please complete the online application available here by November 30, 2015. The meeting is open to all, with room and board covered for up to 30 participants, and limited funding available to support travel costs, particularly for early career or under-represented participants. Funding requests will be considered in early December, after all applications are received.

This workshop is funded by the U.S. National Science Foundation, with logistical support provided by the iPlant Collaborative.”
——————————————————
Ramona L. Walls, Ph.D.
Senior Scientific Analyst
The iPlant Collaborative
Thomas J. Keating Bioresearch Building

Training Activity – Human Brain Project – Call for Applications

Posted on October 28th, 2015 in News & Events | No Comments »

Hello NIF/SciCrunch Community!

Check out the Call for Applications that has recently been released by the Human Brain Project!

HBP_3rdWorkshopManchester_Call for Applications_V3

“This is the third and final workshop organised by the Human Brain Project Education Programme during its first phase, and will present thoughts on the emerging trends and directions we may expect in the next five to ten years. Amongst other topics, we will have presentations on:

- Future Developments in Theoretical Neurosicence!

- Gaute Einevoll (UMB)

- Future Developments in Supercomputer Technology! Thomas Lippert (FZ Jülich)

- Future Developments in Informatics Technology!

- Sean Hill (EPFL)

- Future Developments in Medical Informatics Technology! Richard Frackowiak (CHUV)

- Future Developments in Neuromorphic Technology! Karlheinz Meier (UHEI)

- Future Developments in Microprocessor Design! Steve Furber (UMAN)

- Future Developments in Neurorobotic Technology!

- Alois Knoll (TUM)#

- Future Developments in Brain Simulation!

- Felix Schürmann (EPFL)”

Click on the link above for more information!

Sincerely,

The NIF/SciCrunch Team

NIF Events at SfN

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

NIF Events:

Monday:

BANTER (it’s a party): NIF is one of the co-sponsors of the Banter event at SfN. Don’t miss it! @sfnbanter #sfnbanter

Location: Frontier, 1072 N. Milwaukee (Blue Line to Division)

Event Time: 9:30 PM

Tuesday:

Poster Presentation: “Bringing knowledge to data: Visualizing coverage of the neuroscience data space in the Neuroscience Information Framework” *T. GILLESPIE, A. E. BANDROWSKI, J. S. GRETHE, M. E. MARTONE

Location: Poster 544.01 at DD37, Hall A

Presentation time: 8:00 AM – 12:00 PM

Presentation and Demo: “Research Resource ID’s and Annotating the Web” by Maryann Martone

Location: INCF Booth

Presentation and Demo Time: 1:30 PM – 3:15 PM

Related Events:

Friday

Using NEURON to Model Cells and Networks 9 a.m.–5 p.m.
Saturday

Using the Neuroscience Gateway Portal (NSG) for 9–10:30 a.m.

Big Data Opportunities Using the NIMH Data Archive (NDA) 6:30–10 p.m.

 

Sunday, October 18

Neuroinformatics Social 6:45–8:45 p.m.

The NWB Neurophysiology Data Format (Alpha Version) 6:30–7:30 p.m.

 

Tuesday, October 20

Computational Neuroscience Social 6:45–8:45 p.m.

The BRAIN Initiative in 2015: Updates and Outreach Town Hall and Reception 6:30–8:30 p.m.