NIF now pleased to serve more electrophysiology data

Posted on September 30th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

For years, physiology has been lagging far behind anatomy as data sharing is still in infancy in that community as opposed to being fairly standard now in neuro-anatomy.

We are pleased to announce that the Physiobank registry resource from MIT, containing data from a set of physiology experiments has been added to the NIF Data Federation.

 

This brings us to 6 sources of data (anatomy is still winning, but perhaps we can change that)

CRCNS, a repository of e-phys data (patch clamp mostly)

NeuroElectro, a rather large listing of cellular properties mined from e-phys papers

NeuronDB, a curated set of e-phys properties of known cell types including currents, receptors and transmitters

EEG-base, a repository of EEG data

Neurodatabase, a repository of extracellular data sets.

 

Note, this list may be incomplete because it does not include Model data, so please see Integrated Models, a virtual database currently indexing computational models from:ModelDBOpen Source BrainSimTK and  CellML.

 

New in NIF! Find your MRI images in NeuroVault

Posted on September 29th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

New to NIF this week is NeuroVault.

NeuroVault is a public repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies. Many of the data are also accessible from OpenfMRI.

There are currently 369 images, and we anticipate many more in the coming months.

If you wish to share your data via NeuroVault click here.

Obama wants to hear your 2 cents!

Posted on September 5th, 2014 in Anita Bandrowski, General information, News & Events | 2 Comments »

The White House OSTP is requesting comments on a number of issues, one of which is how the federal government can improve reproducibility in the science it funds: https://www.federalregister.gov/articles/2014/07/29/2014-17761/strategy-for-american-innovation

The overwhelmingly important thing is that the White House receive LOTS of individual comments. A ton of comments is how something like this gets attention, and turns into a White House initiative that has some teeth. That is exactly how the White House came to require that federally-funded research be made publicly accessible — they got 300+ comments, and on a technical issue, that’s a lot.

As a way of furthering issues like open data, open code, pre-registration, etc., do think about sending something to the White House, and telling all of your likeminded colleagues to do so as well. Doesn’t matter if it’s only a one-paragraph email — that still counts.

How to do so: Email: innovationstrategy@ostp.gov. Include [Strategy for American Innovation] in the subject line of the message.

Olympus competition

Posted on September 2nd, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

Olympus would like to invite you to submit several of your images and/or digital video clips to the 2014 Olympus BioScapes Digital Imaging Competition, which will honor extraordinary microscope images of life science subjects. Up to five images or videos can be entered via the Internet. Entries for the contest can be uploaded through a web browser directly to the Olympus servers at the following URL:

http://www.olympusbioscapes.com/enter.asp

The deadline for new entries is September 30, 2014.

The winners of the competition are tentatively scheduled to be published in Scientific American.

A note about the contest: First prize will be Olympus microscope or Camera equipment valued at $5,000. Nine additional winners will also receive valuable prizes from Olympus. Each person entering can submit up to five movies, images, or image sequences. It is not necessary for people entering the competition to be users of Olympus equipment. Winners will be notified in late October, and publicly announced in December, 2014.

Comment requested: Academic credit for reviewing

Posted on August 22nd, 2014 in General information, News & Events | No Comments »

This seems a very interesting blog written by Rebecca Lawrence. The link is below.
I am re-posting it for the NIF community.


Link to original blog: http://blog.f1000research.com/2014/08/22/peer-review-service-recognition-orcid-casrai-recommendations-need-your-feedback/


Laura Paglione (Technical Director, ORCID) and I (Rebecca Lawrence) have been co-chairing the CASRAI Peer Review Services Working Group to look at the best way to recognise referee reports as a formal output in for example an ORCID profile. This project has looked at the peer review of a wide range of outputs from articles (open, closed, pre- and post-publication peer review), to grants, conference abstracts, and the review ofuniversities/faculties/departments.


We have now reviewed options for linking peer review service activities with a person identifier such as ORCID, and developed recommendations for data fields, descriptors, persistence, resolution and citation. We now need your feedback!  We are inviting interested subject experts from all these areas to review and comment on the draft outputs of this working group; the deadline for comments is Friday, September 12th 2014. In order to participate, please follow the instructions below.


1) Access the “Document Details” page here, which will provide information about the document as well as a link to download the file.
2) On the “Document Details” page click the link in the “Name” row to download the document.
3) Once you have reviewed the document, return to the “Document Details” page. Click on “add a comment” on the upper left hand side of the “Document Details” table to open the comment form.
4) Please complete one comment form for each term about which you wish to provide feedback. Commenting follows the steps below:
a) In the “Subject” line, reference the term number to which you are referring in your comment. (Example: D04)
b) Complete the comment box with your first comment.
c) Please ignore the items “Section” and “Item” as you have already addressed these by providing the term number in the Subject line.
d) If you would like to expand upon your comment by providing a proposed solution, please do so in the “Proposed Solution” field. This field is optional.
e) For security reasons, please slide the lock button at the bottom of the form to the right.
f) If you have no other comments to add click “Save” at the bottom of the form. Please note that we strongly prefer for each comment to address only one term at a time.
g) If you are commenting on multiple terms click “Save and add another” at the bottom of the form. Please note that you will not be required to re-enter your contact information for each added comment.

 


We really hope you will take this opportunity to provide your feedback on these recommendations so that we can ensure that the final output successfully achieves the goals of this project: proper recognition of the huge amount of unpaid and often invisible effort researchers put in throughout their careers to the essential task of reviewing the work of others.


I have been co-chairing the CASRAI Peer Review Services Working Group together with Laura Paglione (Technical Director, ORCID) to look at the best way to recognise referee reports as a formal output in for example an ORCID profile. This project has looked at the peer review of a wide range of outputs from articles (open, closed, pre- and post-publication peer review), to grants, conference abstracts, and the review of universities/faculties/departments.


We have now reviewed options for linking peer review service activities with a person identifier such as ORCID, and developed recommendations for data fields, descriptors, persistence, resolution and citation. We now need your feedback! We are inviting interested subject experts from all these areas to review and comment on the draft outputs of this working group; the deadline for comments isFriday, September 12th 2014. In order to participate, please follow the instructions below.

  1. Access the “Document Details” page here, which will provide information about the document as well as a link to download the file.
  2. On the “Document Details” page click the link in the “Name” row to download the document.
  3. Once you have reviewed the document, return to the “Document Details” page. Click on “add a comment” on the upper left hand side of the “Document Details” table to open the comment form.
  4. Please complete one comment form for each term about which you wish to provide feedback. Commenting follows the steps below:
  • In the “Subject” line, reference the term number to which you are referring in your comment. (Example: D04)

Neurodata Without Borders needs your imput!

Posted on August 12th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Dear Colleague,

The Neurodata Without Borders (NWB) project has just started. The project goal is to build a common data format for neurophysiology data from Allen Brain Institute, Janelia Farms and two labs from NYU and Caltech.  Although focusing on a limited set of use cases, the project also aims to develop products that will serve the broader community.

At this point we would like to solicit community input about ideas/approaches for designing a generalizable neurophysiology data format. If you are interested in contributing to this project, please review the project description at:
https://crcns.org/NWB
and fill out the questionnaire:
https://docs.google.com/forms/d/1CNTd4M-8kQ_WhEZc7n7WxpTa0LOupt_q3z21E1fRxjM/viewform

On the basis of the questionnaire responses and ensuing communication, we will organize the first hackathon meeting of the project, to be held November 20 – 22, 2014 (just after SfN) at Janelia Farm, in Ashburn, Virginia.  At this hackathon we will discuss in detail the requirements for a common format based on the project use cases and also discuss, compare and evaluate alternative techniques for implementing the common format.

More information about the project is available in a recent press release: http://www.kavlifoundation.org/kavli-news/prominent-us-research-institutions-announce-collaboration-toward-sharing-and

Please forward this email to anyone you know with relevant expertise who may be interested in contributing to this project.

Thank you,
Fritz Sommer and Jeff Teeters
Redwood Center for Theoretical Neuroscience
UC Berkeley

Have a great idea for a company? Check out the Brain Start Up Challenge

Posted on August 6th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

Overview
The National Institutes of Health (NIH) has a significant portfolio of inventions available for licensing. The Center for Advancing Innovation (CAI) has evaluated many of them to identify those with the strongest commercial viability
The Heritage Provider Network, the NIH, and CAI are launching a start-up Challenge to exploit these opportunities

 

Phases
Phase 0: Enter Challenge: Teams provide information regarding the invention they have chosen to develop their business plan around, details and backgrounds of the members of their team, and how team members meet eligibility requirements. Teams also outline their intent to participate in the Challenge

Phase 1: Elevator Speech: Teams develop a two minute elevator speech via recorded video; a 350 word executive summary outlining potential commercial product(s) and company vision. Winners of this phase will move on to Phase 2: Business Plan

Phase 2: Business Plan: Teams develop a 10-page business plan with a detailed financial plan; a 20 minute “live” pitch presented to the challenge judges. The winners of this phase will receive a $2500 award per team that is provided by CAI and The Heritage Provider Network as well as move on to Phase 3: Start-up

Phase 3: Start-up: Teams launch their start-ups, including incorporation, license negotiation, and executing other regulatory/developmental needs

For more information check out the
http://www.brainstartupchallenge.org/overview.html

Validation problem with antibodies – get free samples, report back, help community

Posted on July 29th, 2014 in Anita Bandrowski, News & Events | No Comments »

Antibodyresource.com is running an interesting validation program over in the UK.
They are providing free samples of antibodies, the catch is that they would like to see if the antibody validates.

If this is something you are interested in, please contact Christian at christian.booty@antibodyresource.com

From Christian:
“The antibody comparison program, is designed to greatly reduce the time (and money) which neuroscientists spend identifying the best antibodies for their research, by testing antibodies from multiple vendors using identical experimental protocols, thus enabling a quick and easy comparison to identify the most appropriate one(s).

We have determined that the best people to test the antibodies are the labs conducting research on the specific proteins which the antibodies recognize, as they have intimate knowledge and experience of antibody-based experiments with those proteins, including an optimized protocol.

We have already procured many suppliers’ antibodies. All we need now are the scientists! So, we want to recruit labs as quickly as possible, and are hoping that members of the Neuroscience Information Framework community might be able to help either by publicizing this program or by participating directly.

If you are working on one of these antibody targets, we would love to talk to you:
Akt
Caspase-3
CD117
CD14
CD31
CD34
CD4
CD44
CD45
c-Myc
EGFR
ERBB2
GAPDH
GFAP
Insulin receptor
Interleukin-6
ki-67
LGR5
NALP3
p53
Podoplanin
TAU
TNF-alpha
Ubiquitin
Vimentin

Don’t like to go searching for gut viruses? Use a computer instead, they are much cleaner

Posted on July 26th, 2014 in Anita Bandrowski, General information, News & Events | No Comments »

The Neuroscience Information Framework often gets questions about what types of things can be found in the data about brains presumably because people would rather poke in brains than data.

However, some of our bioinformatics colleagues from the other side of town (at SDSU) that really didn’t want to go searching though their gut contents did it virtually and discovered a new highly prevalent virus.

Actually this is a bacteriophage that was found in samples from about half of gut microbiomes sampled and cleanly deposited as data in various databases.

Now there is a whole new reason to look at databases that I never thought of. They are just a lot less messy!!!

See more about the phage here: http://newscenter.sdsu.edu/sdsu_newscenter/news.aspx?s=75082

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.