Scientific Data Reproducibility, a conversation – July 23, 2014, 1 pm EST

Posted on July 16th, 2014 in Anita Bandrowski, Author, Data Spotlight, Webinar Announcement | No Comments »

Drs. Martone of NIF and Iorns of Science Exchange among others will be addressing important issues around reproducibility of data.
Please join us for this webinar.

Free Registration click here.

Title: Improving Scientific Reproducibility In The Life Sciences: Considerations for Researchers, Publishers and Life Science Tool Providers
Date: July 23, 2014        
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.

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

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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

NSF Workshop on Noninvasive imaging of brain function

Posted on May 1st, 2014 in Anita Bandrowski, News & Events | 1 Comment »

The National Science Foundation (NSF) – Directorate for Engineering (ENG) in cooperation with the DARPA and National Institutes of Health (NIH) announces a workshop to explore the scientific and technological grand challenges, strategies, opportunities, and breakthrough ideas for innovation in Noninvasive imaging of brain function. The goal of the workshop is to identify research directions and opportunities that, if pursued, can initiate new developments in brain imaging instrumentation and technologies. The workshop will result in a comprehensive publishable document that will be widely distributed.
http://tinyurl.com/NSF-Brain

The 2014 Hackathon registration is open! – Hack the Brain

Posted on April 28th, 2014 in Anita Bandrowski, News & Events | No Comments »

The 2014 Hackathon registration is open! This unique 3-day event (June 5-7) will be held prior to annual meeting of the Organization for Human Brain Mapping (OHBM) at the legendary c-base, a decked-out collaborative art and technology space at the heart of the Berlin hacker community. In keeping with the spirit of prior neuroimaging hackathons such as OHBM 2013 and Brainhack 2012 and 2013, participants will have the opportunity to propose collaborative projects and engage in a number of open challenges.

For updated information on the developing Hackathon content, and to contribute your own ideas, check out www.brainhack.org. Current projects include the Sage Alzheimer’s Disease Challenge, cloud computing tutorials with NITRC-CE and Amazon Web Services, workshops on data-sharing and meta-analysis, and many others initiated by scientists from the brain imaging community (see http://brainhack.org/categories/hackathon2014/).

Participants engaged in the Alzheimer’s Disease Challenge will have the unique opportunity to set an initial benchmark for a multi-phase effort to identify early accurate predictive biomarkers that can inform the scientific, industrial and regulatory communities about the disease.

Join this vibrant community and help build open neuroscience initiatives in one of the most unique tech venues in Berlin. To keep the collaborations flowing, meals and refreshments are all included in the registration costs and will be provided on-site, as well as $100+ in Amazon Web Service credits for your computational needs. Participation is limited, so we encourage you to register now.

The spirit of the Hackathon will also be continuing into the OHBM meeting in Hamburg from June 8-12, where a collaboration space will be available in the conference venue. This space will be open to all OHBM attendees to discuss, present, and continue working on hackathon projects.

OHBM Hackathon website: https://www.humanbrainmapping.org/hackathon

Registration: https://www.humanbrainmapping.org/i4a/ams/conference/conference.cfm?conferenceID=98

Projects: http://www.brainhack.org/

Cesar A. Berrios-Otero of F1000Research: lecture Tuesday April 29th, 2 pm.

Posted on April 24th, 2014 in Anita Bandrowski, News & Events | No Comments »

Tuesday April 29th

2pm

CNCB Large Conference Room

 

Cesar A. Berrios-Otero, Ph.D.

F1000Research

 

Sharing data, reducing bias and enhancing research papers

Unavailability of data and research results can have pernicious effects on scientific evidence. This bias is particularly harmful in medicine, where drugs may be prescribed based on misleading evidence. Sharing data increases the reliability and reproducibility of research, leading to more efficient ways to do science. It also increases the amount of credit researchers receive for their work (e.g. more citations). It is now easier than ever to share scientific data and results. Small datasets can be published as supplementary material; larger datasets can be deposited databases, e-notebooks, and repositories — and linked back to papers. F1000Research takes this further by publishing all data supporting a paper, and integrating and visualizing those data in line with published papers.

RRID’s are in the wild! Thanks to JCN and PeerJ

Posted on April 9th, 2014 in Anita Bandrowski, Curation, Essays, News & Events | 1 Comment »

We believe that reproducing science starts with being able to know what “materials” were used in generating the results.

Along with a truly dedicated group of volunteers from academia, government and non-government institutes, publishers and commercial antibody companies we have been running the Resource Identification Initiative (RII).

This initiative is meant to accomplish the following lofty goal: Ask authors to uniquely identify their antibodies (no easy task), organisms (an even harder task), and the databases and software tools that they used in their paper.

In order to ask them at the appropriate time, we gathered a group of journal chief editors to help us ask this question when authors are most interested in answering the question during the process of publication. We created many things to help them identify these things such as a database that stores information for 5 of the most common species used in experiments, antibody catalogs from over 200 vendors, and a database and tool catalog that contains over 3000 software tools and over 2500 academic databases, the largest of its’ kind.

We have been granted 3 months to determine if authors would actually do this. It has been two months, we fielded requests from about 30 users who could not find their resources, there have been more than 40 new software tools or databases registered to our tools registry, and more than 100 antibodies, but we kept waiting for RRIDs to show up in the literature.

Today our wait is over thanks to two papers, Khalil and Levitt in the Journal of Comparative Neurology and Joshi et al in PeerJ.

These authors apparently were able to correctly identify resources such as Matlab, NeuroLucida, ProteinDataBank and antibodies including anti-cholera toxin antibody from List Bio.

What does this tell us?

Well to start that this process is not impossible! That identifiers do exist for many things or the process of obtaining new ones is not so difficult that people can’t do this. It also tells us that when asked at the right time, authors are willing to go the extra step, find and provide identifiers to their reagents or software tools!

Great, but why do I care about a single paper that uses an antibody or Matlab?

Well, it turns out that for many years JCN and NIF staff have been working diligently to link papers through that same identifier so in the case of this cholera toxin antibody we have marked 23 other papers that have used it since 2006.

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