Protect Yourself from Zombie Papers

Posted on April 25th, 2016 in Anita Bandrowski, Data Spotlight, NIFarious Ideas | No Comments »

Another fun flier to post around the department.

Zombification of papers: the inability to use or validate information in the paper.
How can we stop this terrible plague on the scientific literature? – RRIDs help get the Key biological reagents identified and authenticated.

Feel free to print this fun flier and post it on your office door!

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RRID: Improve your Impact Factor!

Posted on April 25th, 2016 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

Please feel free to take this fun flier and post it around your lab to help your lab-mates to remember how to get an RRID into your next methods section or grant application.

Screen Shot 2016-04-25 at 9.31.23 AM

What is the identity of your Cell Line?

Posted on April 12th, 2016 in Data Spotlight, Inside NIF, News & Events | No Comments »

The SciCrunch portals now contain a data source that will help people figure out if their cell lines have been reported to be contaminated and the Resource Identification Portal at scicrunch will start asking authors to check this source at the time of publication.

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Members of the International Cell Line Authentication Committee (ICLAC) have been working with ExPASy on Cellosaurus, a comprehensive data registry for cell lines and cell line information. Cellosaurus assigns a cell line identifier to each cell line, cross links these identifiers to products available at any of the ~20 cell lines stock centers which make them available and adds notes where concerns have been raised about a cell line.

NIH has recently announced a set of reproducibility principles that target cell line authentication as an important part of research reproducibility and expect that most grants, starting in May 2016, will include a new attachment that explains the authentication of key biological resources, including cell lines.

For these reasons, we are proud to announce that Resource Identification Portal will now include Cellosaurus the core database of annotated cell lines and hope that authors begin to identify their cell lines by the RRID in the coming months, helping to keep track of this key biological resource.

Do you have high performance computing needs for your computational work?

Posted on April 11th, 2016 in Data Spotlight | No Comments »

The Neuroscience Gateway (http://www.nsgportal.org) allows neuroscientists to use commonly available computational and imaging tools such as NEURON, NEST, Freesurfer etc on supercomputers free of charge. The online portal provides an easy to use interface to upload models or input files, run simulations and retrieve results. This NSF funded project is available for all researchers and the application form to access NSG is at

https://www.nsgportal.org/reg/reg.php

For any questions, please email nsghelp-at-sdsc.edu

Collaborative Cyberinfrastructure Environment – Survey

Posted on April 5th, 2016 in News & Events | No Comments »

Greetings NIF/SciCrunch Community!

Are you a researcher or educator? This survey needs your input!

“The aim of this survey is to understand how researchers and educators might need and use a cyberinfrastructure solution for data management, collaboration, computation and teaching.”

Please click here for a link to the survey!

Sincerely,

The NIF/SciCrunch Community

Human Brain Project Platform Release

Posted on April 4th, 2016 in News & Events | No Comments »

Greetings NIF/SciCrunch Community,

Please click the link below for a press release from the Human Brain Project regarding the release of their new platform. This platform will “Advance Collaborative Research in Neuroscience, Medicine, and Computing”!

Please click here for information on the Platform Release.

Sincerely,

The NIF/SciCrunch Team

Reproducibility in the Recipes of Science

Posted on March 31st, 2016 in Anita Bandrowski, Essays, Interoperability, News & Events | No Comments »

Hello SciCrunch/NIF Community! Please read below for Dr. Bandrowski’s post on “Reproducibility in the Recipes of Science”

Reproducibility in the Recipes of Science

Reproducibility in science is a very difficult question, with much that has been said about it from industry, government and researchers themselves, for a good summary please see [Nature Special](http://www.nature.com/news/reproducibility-1.17552) on reproducibility.

Many more things can and will be said about this complex issue, but I wanted to ask a different question: do we not already have a good exemplar of reproducibility when we look at our favorite recipe sites? There are list of ingredients, pictures of the finished product, and of course plenty of detailed instructions. There are even places for novice cooks to tell the recipe owner “hey this is hard to reproduce” or “it does not work with Indian saffron”.

Why doesn’t the **methods** section of our papers not look like that?

I would like to introduce the members of the Society for Neuroscience to an initiative that has been trying to move the methods to look a little more like your favorite recipe site, by asking authors to do a little more thorough job when listing their key ingredients, such as antibodies.

It has been going on for a couple of years years as an agreement between several of the key journals in neuroscience, which ask authors to provide an RRID, or a unique identifier for key biological reagents in their methods sections. Currently these RRIDs are generated for antibodies, organisms and software tools.

We are very pleased that [eNeuro](http://eneuro.org/content/3/2/ENEURO.0046-16.2016) has recently joined the charge as has [Neuron](http://www.cell.com/neuron/rrid), so you may be seeing some of these RRIDs in the papers that you read.

However, we know that many journals will allow authors to add the RRIDs to their papers even if the journals are not officially pushing authors themselves, so we hope that you will join the charge with your next paper. Please go to [scicrunch.org/resources](https://scicrunch.org/resources) and search for your key biological resources, open the “cite this” box and copy the citation into your methods. This way, tracking down the ingredients used in any paper becomes much easier and that is of course the first step in experimental reproducibility.

OHBM Hackathon 2016 – Stipends Application

Posted on March 28th, 2016 in News & Events, Uncategorized | No Comments »

Hello NIF/SciCrunch community!

Please take a moment to read this message from the Organization for Human Brain Mapping:

“OHBM Hackathon 2016 – Stipends Application

The registration for the fourth OHBM Hackathon is now open! Thanks to the generous support of our sponsors, the OHBM special interest group in open science will award a limited number of stipends to students attending the OHBM Hackathon 2016, including free registration and 500 USD for travel and accommodations. If you would like to apply for one of the stipends, please email the following material to info@brainhack.org by Friday April 15th, 2016 11:59PM EST:

(1) A one page Brainhack project proposal

(2) A one page biosketch.

(3) Proof that you are a graduate student or post-doc (typically a letter from your supervisor).

The organizing committee will determine the winners based on the merits of the submitted materials, as well as geographical, expertise and gender diversity. The winners will be encouraged to develop their project during the hackathon, notably using the brainhack slack ahead of the event. All hackathon participants will have the opportunity to submit a report on their project for publication in the 2016 Brainhack Proceedings (see the 2015 call for reference). Awards will be announced by email by May 1st.

The “Open Science” SIG would like to acknowledge the generous support of the Organization for Human Brain Mapping, the Ludmer Center for NeuroInformatics and Mental Health, the Wellcome Trust and OpenfMRI.”

SPARC Funding Opportunities: Informational Webinar – March 24, 2016 from 12pm-1pm

Posted on March 21st, 2016 in News & Events, Uncategorized | No Comments »

Hello NIF/SciCrunch Community!

The SPARC Program will be hosting an Informational Webinar about its three FOA’s on March 24, from 12 – 1 PM. Please read below for more information.

“Dear Colleague,

The NIH Common Fund Program on Stimulating Peripheral Activity to Relieve Conditions (SPARC) currently has three funding opportunity announcements (FOAs) receiving applications. We are hosting an Informational Webinar on March 24, 2016 from 12pm-1pm which is open to all. Please click on the image below for more information.
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Component 1: Anatomical and Functional Mapping of the Innervation of Major Internal Organs – now in Phase 1

(RFA-RM-15-003) Pre-application: Comprehensive Functional Mapping of Neuroanatomy and Neurobiology of Organs (OT1) – due every other month,Next due date is May 16, 2016

Component 2: Next Generation Tools and Technologies – now in Phase 2

(RFA-RM-16-002) Pre-application: Technologies to Understand the Control of Organ Function by the Peripheral Nervous System (OT1) – Due May 16, 2016

Component 3: Use of Existing Market-Approved Technology for New Market Indications – now in Phase 1, visit the New Market Indications – Device Portal for information about the device(s) and support provided by SPARC’s industry partners

(RFA-RM-16-009) Pre-clinical Development of Existing Market-approved Devices to Support New Market Indications (U18) – Due May 2, 2016
Please contact NIH-CF_SPARC@mail.nih.gov if you have any questions regarding this webinar. In addition, please feel free to share this announcement with your colleagues.

Sincerely,
NIH Common Fund SPARC Program staff”

NIF Supports the release of Findable, Accessible, Interoperable, and Reusable (FAIR) Data.

Posted on March 15th, 2016 in News & Events, Uncategorized | No Comments »

Hello NIF Community!

Below is a press release in regards to FAIR Guiding Principles formal publication. NIF fully supports the release and publication of Findable, Accessible, Interoperable, and Reusable (FAIR) Data and its future incorporation in the scientific community.

“Press release: FAIR guiding principles published in journal of the Nature Publishing Group family

Today, March 15 2016, the FAIR Guiding Principles for scientific data management and stewardship were formally published in the Nature Publishing Group journal Scientific Data. The problem the FAIR Principles address is the lack of widely shared, clearly articulated, and broadly applicable best practices around the publication of scientific data. While the history of scholarly publication in journals is long and well established, the same cannot be said of formal data publication. Yet, data could be considered the primary output of scientific research, and its publication and reuse is necessary to ensure validity, reproducibility, and to drive further discoveries. The FAIR Principles address these needs by providing a precise and measurable set of qualities a good data publication should exhibit – qualities that ensure that the data is Findable, Accessible, Interoperable, and Reusable (FAIR).

The principles were formulated after a Lorentz Center workshop in January 2014 where a diverse group of stakeholders, sharing an interest in scientific data publication and reuse, met to discuss the features required of contemporary scientific data publishing environments. The first-draft FAIR Principles were published on the Force11 website for evaluation and comment by the wider community – a process that lasted almost two years.  This resulted in the clear, concise, broadly supported principles that were published today. The principles support a wide range of new international initiatives, such as the European Open Science Cloud and the NIH Big Data to Knowledge (BD2K), by providing clear guidelines that help ensure all data and associated services in the emergent ‘Internet of Data’ will be Findable, Accessible, Interoperable and Reusable, not only by people, but notably also by machines.

The recognition that computers must be capable of accessing a data publication autonomously, unaided by their human operators, is core to the FAIR Principles. Computers are now an inseparable companion in every research endeavor. Contemporary scientific datasets are large, complex, and globally distributed, making it almost impossible for humans to manually discover, integrate, inspect and interpret them. This (re)usability barrier has, until now, prevented us from maximizing the return-on-investment from the massive global financial support of big data research and development projects, especially in the life and health sciences. This wasteful barrier has not gone unnoticed by key agencies and regulatory bodies. As a result, rigorous data management stewardship – applicable to both human and computational “users” – will soon become a funded, core activity within modern research projects. In fact, FAIR-oriented data management activities will increasingly be made mandatory by public funding bodies.

The high level of abstraction of the FAIR Principles, sidestepping controversial issues such as the technology or approach used in the implementation, has already made them acceptable to a variety of research funding bodies and policymakers. Examples include FAIR Data workshops from EU-ELIXIR, inclusion of FAIR in the future plans of Horizon 2020, and advocacy from the American National Institutes for Health. As such, it seems assured that these principles will rapidly become a key basis for innovation in the global move towards Open Science environments. Therefore, the timing of the Principles publication is aligned with the Open Science Conference under the Netherlands EU Presidency in April 2016.

With respect to Open Science, the FAIR Principles advocate being “intelligently open”, rather than “religiously open”. The Principles do not propose that all data should be freely available – in particular with respect to privacy-sensitive data. Rather, they propose that all data should be made available for reuse under clearly defined conditions and licenses, available through a well-defined process, and with proper and complete acknowledgement and citation. This will allow much wider participation of players from, for instance, the biomedical domain and industry where rigorous and transparent data usage conditions are a core requirement for data reuse.

“I am very proud that the FAIR Principles were published, just over two years after the Lorentz meeting where we came up with the early principles. They play such an important role in many forward looking policy documents around the world and the authors on this paper are also in positions that allow them to follow these Principles. I sincerely hope that FAIR data will become a ‘given’ in the future of Open Science, in the Netherlands and globally”, says Barend Mons, Professor in Biosemantics at the Leiden University Medical Center, Head of Node ELIXIR-NL at the Dutch Techcentre for Life Sciences, Integrator Life Sciences at the Netherlands eScience Center, and board member of the Leiden Centre of Data Science.