Register for ReproNim Training Workshop

Posted on September 21st, 2017 in Anita Bandrowski, News & Events | No Comments »

The ReproNim Training Workshop is now open for registration. Register and information at:https://tinyurl.com/repronim-sfn17Purpose:
The issue of lack of reproducibility has been described in several scientific domains for several years, raising concerns specifically in the life science community. ReproNim has developed a curriculum
(http://www.reproducibleimaging.org/#trai…) that will give the students the
information, tools and practices to perform repeatable and efficient research.

This training workshop will introduce material on the critical aspects of reproducible brain imaging and will orient attendees using a hands on and practical experience to conduct neuroimaging analyses with the next generation of tools.

By the end of this course, the student will be aware of training materials and concepts necessary to perform reproducible research in neuroimaging. The student will be able to reuse these materials to conduct local workshops and training and be able to customize the training for their specific scenario.

Prerequisites:
If you are a student, postdoc or researcher in life science who directly works with neuroimaging data – or wish to work with these data, and you have some basic computational background, this training workshop is for you. For instance, you should have already done either some R, or Python, or Matlab or Shell scripting, or have used standard neuroimaging tools (SPM, FSL, Afni, FreeSurfer, etc) and be engaged in neuroimaging research projects. You should have already completed a neuroimaging analysis or know how to do one.

Logistics:
Location: George Washington University, Marvin Center, Room 402-404
https://events-venues.gwu.edu/meeting-ro…
Dates: November 10-11, 2017.
Costs: Free – but space is limited – please apply for approval.
Schedule:
Friday November 10th:
8:30-9am: Introduction to the course and participants “setup”
9am-10:45: Reproducibility Basics (Module 0)
10:45-11am : Coffee break
11am-12:45 : FAIR data (Module 1)
12:45-2pm : Lunch+coffee
2pm-3:45: Data Processing (Module 2)
3:45-4pm: coffee break
4pm-5:45pm: Statistics for reproducible analyses (Module 3)
5:45-6:15: Questions and answers and feedback session
Saturday November 11th:
9am-12pm: The Re-executable Micro Publication Challenge

During this time, we will propose a small challenge around producing
an entirely re-executable neuroimaging analysis from fetching data to
producing statistical results. This will also be a time with close
interactions with neuroimaging experts in data handling and analysis.

12pm-12:30: Closing session: feedback and future: “become a trainer”.

Weekly online office hours will be held prior to the workshop. Registered attendees will receive information via email.

Modules:
Module 0 – Reproducibility Basics: Friday Nov. 10. 9am-10:45am.
This module guides through three somewhat independent topics, which are in the heart of establishing and efficiently using common generic resources: command line shell, version control systems (for code and data), and distribution package managers. Gaining additional skills in any of those topics could help you to not only become more efficient in your day-to-day research activities, but also would lay foundation in establishing habits to make your work actually more reproducible.

Module 1 – FAIR Data: Friday Nov. 10. 11am-12:45.
This module provides an overview of strategies for making research outputs available through the web, with an emphasis on data. It introduces concepts such persistent identifiers, linked data, the semantic web and the FAIR principles. It is designed for those with little to no familiarity with these concepts. More technical
discussions can be found in the reference materials.

Module 2 – Data Processing: Friday Nov. 10. 2pm-3:45pm.
This module teaches you to perform reproducible analysis, how to preserve the
information, and how to share data and code with others. We will show an example framework for reproducible analysis, how to annotate, harmonize, clean, and version brain imaging data, how to create and maintain reproducible computational environments for analysis and use dataflow tools to capture provenance and perform efficient analyses (docker) and other tools.

Module 3 – Statistics: Friday 4am-5:45
The goal of this module is to teach brain imagers about the statistical aspects of reproducibility. This module should give you a critical eye on most of the current literature and the knowledge to do solid work, understand exactly what is a p-value and its limitation to represent evidence for results, practical notion of power and associated tools, etc.

Instructors: J. Bates, S. Ghosh, J. Grethe, Y. Halchenko, C. Haselgrove, S.
Hodge, D. Jarecka, D. Keator, D. Kennedy, M. Martone, N. Nichols, S. Padhy,
JB Poline, N. Preuss, M. Travers

This workshop is brought to you by ReproNim: A center for Reproducible Neuroimaging Computation NIH-NIBIB P41 EB019936

Organization for Human Brain Mapping (OHBM)
5841 Cedar Lake Road, Suite 204
Minneapolis, MN 55416 USA
Phone: 1 952-646-2029 | Fax: 1 952-545-6073
info@humanbrainmapping.org
www.humanbrainmapping.org

They’re Back!! NIF Webinars re-launching this Friday!

Posted on September 12th, 2017 in General information, News & Events, Webinar Announcement | 1 Comment »

Exciting News! Straight from the brain into the press!

The NIF team is proud and excited to announce the Neuro-Tools Webinar Series! The Series will focus on online tools, resources, gateways, curated inventories, and labs that are creating a dynamic and accessible place for research, conversation, and publication in the neuroscience community and, more broadly, the scientific community.

The series begins this Friday, September 15th, with Drs. Bandrowski and Martone discussing RRIDs.

Title: RRIDs, What Are They Good For And How Do I Use Them

Synopsis: The Resource Identification Portal was created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) – persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in our system where more than one identifier exists for a single resource.

To Join: At the time of the conference click this link https://ucsd.zoom.us/j/713924977

Note: for other options on joining , click here. 

For biographies, and future webinars click here.

JNeurosci and eNeuro are now hyperlinking #RRID in their articles!

Posted on August 15th, 2017 in General information, News & Events | No Comments »

The reproducibility bug is spreading! Have you and your research been infected yet? The latest journals to join are JNeurosci and eNeuro. These journals are used by the Society for Neuroscience for sharing strong science. Check it out! http://www.eneuro.org/content/4/4/ENEURO.0051-17.2017

en-brain-cover_0

Sincerely,

The NIF/SciCrunch Team

 

NeuroMorpho.Org v7.2

Posted on August 9th, 2017 in Data Spotlight, General information | No Comments »

A new version of NeuroMorpho is out now! Check out the message from the NeuroMorpho.Org team.

Dear colleagues,

We’re pleased to announce the July 19, 2017 release of Version 7.2 of NeuroMorpho.Org, adding 7721 reconstructions from 83 new datasets. The repository now provides access to 70,025 cells and passed 7 million downloads in 163 countries. Please visit the What’s new page for details on the added data and other updates. The literature coverage was also updated to include publications through June 2017. We are continuously grateful to all the data contributors who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing.

Sincerely,

The NeuroMorpho.Org team

scicrunch_data_386459422

The computing of biology or the biology of computing?

Posted on March 6th, 2017 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

So there is a new story out that is fascinating to me as a ‘recovering’ biologist.

It appears that sequencing has become so cheap and deadly accurate that we have a new storage mechanism for our data. DNA. Yes you read that correctly. Those living organisms and viruses can’t have all the fun.

A company in San Francisco can synthesize DNA and this can be shipped and read back by using traditional sequencing by a different company. Ok some of the basic tricks of data storage and a decoder had to be built in, but the amount of information that was stored per unit area was much higher than conventional devices.

The cost of $3,500/Mbyte is also a bit higher than the $300 physical drives, but the data in the test was 100% accurate, or at much better fidelity than traditional computational systems. Chew on that IBM!

By the way, apparently the data that was coded was: a movie, a full computer operating system, and several scientific articles. When the information was retrieved, the OS installed researchers celebrated by playing minesweeper, which may be the first game to be encoded in DNA.

The other cool thing about this is while this is very new technology and very expensive, now we can imagine all over again the world of the Diamond Age by Stephenson, where espionage involves the cells in our bodies and the data can be destroyed by activating an enzyme.

The link to this story: http://science.sciencemag.org/content/355/6328/950.full

FORCE11 Scholarly Communication Institute

Posted on February 10th, 2017 in Anita Bandrowski, Force11, News & Events | No Comments »

ANNOUNCING THE LAUNCH OF THE NEW

FORCE11 Scholarly Communication Institute

July 30 – August 4, 2017
University of California, San Diego
La Jolla, CA   USA


FORCE11 (Future of Research Communications and E-Scholarship)—a global community of researchers, students, librarians, publishers, funders and scholars interested in the future of scholarship—is pleased to announce the launch of its new annual Summer Institute in Scholarly Communications: the Force 11 Scholarly Communications Institute at the University of California, San Diego (FSCI@UCSD), July 30-August 4, 2017.

FSCI@UCSD is a week-long program that offers participants training, networking and skills development in new modes of research communication.

The UC San Diego Library is hosting the event that will take place at the Institute of the Americas on the UC San Diego Campus.

“The research community lacks a forum for coordinated access to training, skills development, and expert knowledge on new modes of research communication,” says Cameron Neylon, President of Force 11, “even as funders are mandating change and the wider world has embraced new forms of communication.”

Based on proven models in other disciplines, FSCI@UCSD will bring world-leading experts in different aspects of scholarly communication to San Diego to design and deliver courses that will help participants to navigate this new world. Courses will be established for all levels, from absolute beginners to experts. They will also be aimed at different audiences, including students, researchers, administrators, funders, and information professionals, including librarians and publishers.

Typical topics to be covered at the annual event will include:

Introductory Level

  • Open Access, Open Source, Open Data, What Does this All Mean?
  • Building a Digital Presence: Social Media, Repositories, and the Researcher
  • Research Communications 101: Tools for Improving Scholarly Communication
  • Data and Other Forms of Non-narrative Publication
  • Understanding Research Metrics
  • Open Peer Review: How to give and Receive Criticism

Advanced

  • Copyright, Open Access and Open Data
  • New Metrics and How to Use Them to Build a Research Portfolio
  • Introduction to Open Data Management
  • Implications of OA on Research Publications
  • Making it Work: Knowledge Mobilization, Knowledge Translation, and Popularization

Specialised/Topic Focussed

  • Implementing Successful Open Access, and Open Data Mandates
  • Supporting the Research Lifecycle  for Researchers and Administrators
  • Evaluating New Forms of Research Publication
  • Implications of OA on Publication and Collection Building
  • Data Ownership and Copyright Issues
  • Data-informed Strategy for Institutional Leaders
  • Maximizing Impact Across Disciplines
  • Increasing Transparency and Reproducibility in Research Communications

“Scholarly Communication is in a disruptive phase at the moment. Students know the rules that governed their supervisors’ early careers are changing” said Maryann Martone, past president of Force 11 and UCSD professor emerita. “Libraries know the current publishing and data repository system is unsustainable; researchers know the systems within which they have worked are changing rapidly,” adds Brian Schottlaender, UCSD’s Audrey Geisel University Librarian. “Administrators know government, industry, funders, and the general public are expecting research to be performed, communicated, and measured in new ways. But knowing that things are changing is not the same as understanding what those changes are or how individuals and institutions can navigate them. This is what FSCI@UCSD will provide.”

For more information or to sign up to receive further information about the FSCI@UCSD, visit www.force11.org/fsci

Comment on Location

Given the uncertainty regarding travel to the US and the recent FORCE11 Statement on travel restrictions, there may be questions regarding the location of the Institute in San Diego. The Institute has been in planning with UCSD for some time and UCSD has committed to providing long-term and substantial financial, administrative, and intellectual support. This support allows us to focus our fundraising on supporting travel for those who who would otherwise be unable to attend, which has been a feature of our work in planning FORCE11 meetings for some years. While the current situation makes this harder, we elected to move forward with the planned location. We remain committed to working to mitigate the effects of restrictions to travel across the full set of FORCE11 events.

Click on the links below if you wish to participate.

Have a course idea?
Is there a particular topic you wish would be presented?
Want to present a class, a course, a workshop, a seminar, or a keynote talk?
Want to join the planning committee?

Have questions?

Want more information when available?

If at first you do succeed: Publish a Replication Report with #RRIDs anyway!

Posted on January 30th, 2017 in Anita Bandrowski, Data Spotlight, Force11, News & Events, NIFarious Ideas | No Comments »

Science is the act of trying and trying again, whether or not we confirm what we think should be happening.

Begely and Ellis in their 2012 paper from Amgen stated that only about 11% of cancer studies were replicable sending shockwaves through the scientific community for years. However, the authors did not give the scientific community all of the data that showed the replicates.

This week in eLife, the Center for Open Science and a cohort of great ‘re-do-ers’ have just published the first batch of studies that are replicates of influential cancer studies, attempting to confirm or deny what the original study claimed. We at the RRID initiative have noted that the original studies often lacked identifying information in the reagents they used, as is alluded to by some of the replication attempts. These simple omissions make replication much more difficult, something that the ‘re-do-ers’ struggled with.

This is really a monumental step and we will wait for the final publications to determine whether these rigorous and fully transparent attempts also fall in the 11% replication level as claimed by Begely and Ellis, but so far some of the replicates show trends in the same direction reported by the original study authors, though no replication attempt has panned out exactly the same way as the original paper. We certainly need to wait and see for the rest of the reports, but I am personally heartened that the original authors are engaged in the replication, commenting on these reports attempting to understand their own data and the new data.

The immortal Aristotle was once reported to say “Quality is not an act, it is a habit.” I think that if he were alive today he would be very interested in these developments and would implore us to look at ourselves and if we did not like what we see, he would call on us to change for the better. While none of my papers will likely be the target of this kind of scrutiny, I do hope that the methods and results will stand up in the long term. This is a call to action for all of us, to be more precise and to do better delivering on the promise of science for the patients who deserve our very best attention and very best methodology.

Funding Opportunity Announcement: KIBM IRG Program 2017-18

Posted on January 10th, 2017 in General information, News & Events | No Comments »

Hello NIF/SciCrunch Community!

Please read below for a funding opportunity from the Kavli Institute for Brain and Mind.

“Dear KIBM Community,

The Kavli Institute for Brain and Mind is now inviting applications for Innovative Research Grants (IRGs) to support novel and interdisciplinary brain-mind research in 2017-18.

Please review the attached file and the following website for program details:
http://kibm.ucsd.edu/research/innovative-research-grants

The deadline for proposals will be Friday, March 31, 2017.
This grant program was made possible by generous support from The Kavli Foundation.

Nick Spitzer and Rusty Gage
Co-Directors, Kavli Institute for Brain and Mind”

Follow the link above for more information on the application procedure!

Sincerely,

The NIF/SciCrunch team

Happy Holidays!

Posted on December 20th, 2016 in News & Events | No Comments »

Dear readers,

On behalf of all of us at the Neuroscience Information Framework and the SciCrunch Community, we would like to wish you the most splendid of holiday seasons. We hope your vacation season is relaxed and safe. As we enter through the new year be sure to stay updated with our partner sites on Facebook and Twitter (@scicrunch @neuinfo @dk_net) so that we can keep you updated on all of the exciting developments in the world of Neuroscience in 2017.

Sincerely,

The Neuroscience Information Framework Team

joy-1823937_1280

Rigor and Transparency in Reproducibility on BioLegend’s Podcast!

Posted on December 12th, 2016 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

download

Come one come all, listen to a podcast on reproducibility on your way home today.
“Talkin’ Immunology” hosts a conversation about Rigor and Transparency.