eLife partnership with Hypothes.is will lead to some serious waves in open scholarly annotation

Posted on September 20th, 2016 in General information, News & Events | No Comments »

Hello NIF/SciCrunch Community!

Been craving some good news for open annotation? Well this recent news press should cheer you up!

“eLife, a non-profit initiative inspired by research funders and led by scientists, is working with Hypothes.is to bring publishers and researchers an open annotation platform for important online discussions.”

Click here for the full press release.

Sincerely,

The NIF/SciCrunch (and hypothes.is) team

Perfect storm to fix antibody problems?

Posted on September 9th, 2016 in Anita Bandrowski, General information, NIFarious Ideas | No Comments »

This article comes from the GBSI folks, reporting on antibody validation solutions:

Well, the prefect storm has converged, and a proposal for validation of antibodies continues the year-long effort by many in the research community to fix a widely-known problem in research and reproducibility – poorly characterized antibodies. This first of many efforts to come to a head is led by Mathias Uhlen and the ad-hoc International Working Group on Antibody Validation, and outlines five conceptual pillars for antibody validation to be used in an application-specific manner. Several of the co-authors will present their paper at HUPO 2016 later this month in Taipei. Additional efforts include the 2nd International Antibody Validation Meeting on September 15th in the UK, and one by GBSI that you may have heard about. An online community has emerged to help crowdsource potential standards and will continue to drive the conversation. Still not convinced this is a big deal? Thermo Fisher Scientific has pledged to verify the specificity of their antibodies in line with these new recommendations. Pair these and other activities with Cell’s STARMethods and the future is looking brighter for research reproducibility.

NSG Satellite Symposium at SFN Annual Meeting 2016, San Diego – November 12th, 9am-12pm

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

Dear NIF/SciCrunch Community,

Please read the message below from NSG regarding their Satellite Symposium which will take place at SFN 2016!

Dear NSG user,

We will be hosting a Satellite Symposium as a part of the SFN Annual Meeting in San Diego this November. The date of the NSG symposium is November 12th, Saturday and it will be hosted from 9am till 12pm Pacific Time. If you are interested to attend please register (deadline Friday, October 28th, 2016). We would appreciate very much if you would let your colleagues know about the workshop.

Information about the workshop and how to register are available here: http://www.nsgportal.org/workshop.html
Agenda of the workshop is available from here: http://www.nsgportal.org/2016_sfn.pdf

Brief overview of the workshop:

Using the Neuroscience Gateway Portal for Parallel Simulations
Satellite Symposium, Society for Neuroscience Annaul Meeting

9 AM – Noon on Saturday, November 12th, 2016
Location: downtown San Diego near the Convention Center where SFN Annual Meeting will take place

Brief agenda:

Introduction to NSG – Hands on Demo
Amit Majumdar, Subha Sivagnanam, Kenneth Yoshimoto San Diego Supercomputer Center, UCSD; Ted Carnevale, Yale School of Medicine

Using the NSG for community modeling with the Human Brain Project
M Migliore1, A Romani2, CA Rössert2, R Migliore1, CA Lupascu1, LL Bologna1, F. Franchina, S Saray3, J-D Courcol2, W Van Geit2, S Kali3, and E Muller2

1Institute of Biophysics, National Research Council, Palermo, Italy

2Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland

3Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary

Optimization of multiscale brain models via parallel evolutionary algorithms on supercomputers
Salvador Dura-Bernal, Samuel A Neymotin, William W Lytton
SUNY Downstate Medical Center, NY

Application of automated brain tissue segmentation in radiation oncology
Roshan Karunamuni, Nate S White, Carrie R McDonald, Vitali Moiseenko, Anders M Dale, Jona A Hattangadi-Gluth
Department of Radiation Medicine and Applied Sciences and the Center for Multimodal Imaging and Genetics (CMIG), UCSD

NeuroMorpho announces 10 years and 50K Neuron Reconstructions

Posted on September 6th, 2016 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

We are excited to announce that almost exactly 10 years after the original launch, NeuroMorpho.Org passed the milestone of 50,000 reconstructions in the September 1, 2016 release of Version 7.0.

Screen Shot 2016-09-06 at 9.51.48 AM

This major update includes 12,693 additional reconstructions from 35 new datasets. The new data added in these last 6 months equal the total amount accumulated in the first seven years.

This release also introduce several new functionalities, including
(1) bibliography documenting data re-use from nearly 500 citations;
(2) ontology-smart searches by species, brain regions, neuron types, and experimental conditions;
(3) DOI minting capability for each article-associated dataset; and
(4) API enabling object-oriented access to data and metadata.

The literature coverage database was also updated to include publications through August 2016. Please visit the What’s new page for details on the added data and other updates. We appreciate any and all feedback and comments.

We are continuously grateful to all the data contributors who freely share their hard-won tracings with the community.

Sincerely,
The NeuroMorpho.Org team

A STAR is Born, Indeed

Posted on August 26th, 2016 in Anita Bandrowski, Data Spotlight, News & Events, NIFarious Ideas | No Comments »

News on the RRID front is encouraging!

Screen Shot 2016-08-26 at 4.37.49 PM

We have been very busy adding new journals over the last year. It is wonderful whenever we see a new journal with and RRID, especially when the instructions to authors are updated and you know that this is a serious effort from the editors.

More recently RRIDs are being type-set into journals by groups such as BMC, eLife (structured methods), Elsevier and Cell Press journals improving the syntax of the identifiers and allowing journals to link to databases from articles if they chose to do so.

However a step further has just been undertaken by an entire journal group. Cell Press has just restructured their methods section to make it “STAR: Structured Transparent Accessible Reporting”-compliant. This of course includes RRIDs!

http://dx.doi.org/10.1016/j.cell.2016.08.021

The idea is that authors create a list of research resources in a table helping to keep track of all the “ingredients one needs to replicate the study” and echoes the NIH language of Rigor and Transparency. This will be a real boon for reproducible science!

Some papers using the new format are already out from Cell:

http://www.sciencedirect.com/science/article/pii/S009286741631011X

http://www.sciencedirect.com/science/article/pii/S0092867416309953

http://www.sciencedirect.com/science/article/pii/S0092867416309321

We LOVE structured methods!

Nice example for the new Authentication of Key Biological Resources document

Posted on July 15th, 2016 in Anita Bandrowski, General information, News & Events | No Comments »

The UCSD libraries in collaboration with NIF have put together an example of an authentication document that you may work with for your next NIH grant.
This addresses the new announcements by NIH for better transparency and rigor:

NOT-OD-16-081
NOT-OD-16-058
NOT-OD-16-034
NOT-OD-16-011
NOT-OD-16-031
NOT-OD-16-012
NOT-OD-16-005
NOT-OD-16-004
NOT-OD-15-103
NOT-OD-15-102

The example document is here: http://libraries.ucsd.edu/services/data-curation/data-management/write-dmp/ExampleAuthenticationKeyBiologicalChemicalResources.pdf

This example uses the RRID system to identify and some emerging standards from the HUPO group and ICLAC (iclac.org) for an authentication rubric.

Your grandmother is much better at open reproducible science than you!

Posted on July 15th, 2016 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

Yes you read it correctly, I am calling you out on your ability to do open reproducible science.

This 3 minute video should convince you:

Screen Shot 2016-04-26 at 10.03.08 AM

If not, then leave a comment!

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!

Screen Shot 2016-04-25 at 9.31.23 AM

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.

Screen Shot 2016-04-11 at 11.00.21 AM

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.