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.


Have you ever wondered what is the longest gestation period for a bird, or what is the maximum age for a squirrel?

Posted on July 15th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Well wonder no more! NIF is here to help answer these burning questions.

This week we have a couple of new sources from the aging community: AnAge and the Lifespan Observations Database.

The AnAge data set contains data based on the phylogenetic tree and users can select or search for individual species or groups of organisms from kingdom or phylum to class like rodents or birds.

Screen Shot 2014-07-15 at 10.13.14 AM

I have often wondered which rodent reaches female sexual maturity latest. Finally my curiosity is satisfied!

Screen Shot 2014-07-15 at 10.14.32 AM

 

Can you find the answer to the question: What is the largest rodent?

Let us know what you have wondered about that can now be answered using this data.

 

New in NIF – Neuroscience Gateway

Posted on June 9th, 2014 in Anita Bandrowski, News & Events | No Comments »

New in NIF this week we have upgraded our view of ModelDB. Now little green or red dots appear next to each model.

What does it mean if there is a green dot?
– Green dots indicate that the model runs “as-is” on the NSG cluster (tresteles usually).
Red dot?
– Does not mean that the model is necessarily broken, but it does not run “as-is” on the cluster. You may have to extract code, or update it.

For all green dots, output files are available on our servers for download, so don’t be afraid to click on the dot, or the column entitled “output files”.

The good folks at the Neuroscience Gateway (NSG) portal are ready to run your models on a supercomputer without asking for your first-born child, or your justification of why you want to run your model. All you need to do is create an account, download or create your model code and go. For models that have been deposited in the ModelDB public repository, we had several summer students attempting running code. Some ran fine, other code needed some attention before creating output files. Our students did not have the expertise to fix the models so they just gave them a red dot. If you would like to change the red dot to green for a model that you know and love, we will be happy to talk to you info-at-neuinfo.org and figure out why the model does not run. You can also update code at ModelDB.

To run any Neuron or Genesis code on the NSG, just pick up the model code and get an account on http://www.nsgportal.org/ and submit.

Happy Modeling!

Have you ever wondered what dragonfly neurons look like?

Posted on June 5th, 2014 in Anita Bandrowski, News & Events | No Comments »

Wonder no more!!!

Version 5.7 of NeuroMorpho.Org was released on 30 May, 2014.

The release included 29 new data sets (1341 reconstructions), including from three new animal species (dragonfly, moth, and sheep). The database now contains 11,335 reconstructions from 144 contributing labs. More than 3.2 million reconstructions were downloaded in over 130,000 unique visits from 146 countries.

Please visit the What’s new page for details on data included in this release, including new species strains, brain regions, cell types, and experimental conditions. The Acknowledgements include details on contributing labs, and the About page provides an updated overview of the repository content.

A new user-friendly functionality, OntoSearch, was introduced in this release, enabling more powerful searches of species and strains with automated synonym translation, taxonomical relations, and keyword auto-completion. The literature coverage database was also updated to include publications through March 2014.

We are continuously grateful to all the data owners who freely share their data with the community.

We always appreciate any and all feedback and comments.

Sincerely,

The NeuroMorpho.Org team

MCCSCourse, registration open

Posted on May 15th, 2014 in Anita Bandrowski, News & Events | No Comments »

The course will discuss principles, approaches and resources that neuroscientists can use to navigate the literature and develop future research paths.

Specifically. the course will introduce a new set of practical tools that neuroscientists can use in their work, including the Neuroscience Information Framework and ResearchMaps designed to address the ever growing complexity of neuroscience studies. The course will emphasize a hands on approach to these key tools guided by the people that had a central role in developing them.

The Neuroscience Information Framework (NIF) is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.

Researchmaps are simplified, interactive and unbiased representations of previous findings that are invaluable in preparing research surveys, in guiding experiment planning, and in evaluating research plans. They are a graphical approach to summarizing large amounts of complex experimental findings in causal weighted networks. Although research maps can be derived with nothing more than pen and paper, the course will introduce a new completely free and open source web app (ResearchMaps) that can be used to facilitate the generation and use of these maps.

Although primarily intended for graduate students and post-docs, all neuroscientists are welcome to participate in the course. The course is free, but registration is needed because there is limited seating.

NITRC can host your data!

Posted on May 15th, 2014 in Anita Bandrowski, Data Spotlight, News & Events | No Comments »

Dear NIF community;

Many of you are aware of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC – nitrc.org) for finding and hosting software. What is somewhat less well known is that NITRC can host your data for public sharing as well. As part of NITRC’s three broad classes of functionality (resource hosting; image repository; and virtualized computational environments) broad support for data sharing is provided. Use NITRC data sharing to satisfy your funders and publishers data sharing requirements.  Contact the Moderator at moderator@nitrc.org for detailed information and assistance.

Thank you.
-The NITRC Management Team