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.

One week left to apply INCF seed funding projects!!

Posted on November 23rd, 2016 in News & Events | No Comments »

One week left to apply INCF seed funding projects. Submit your application no later than November 30, 2016. Read below for more information on the grants.

“INCF* invites applications for seed funding of collaborative brain research projects. The deadline for submission is no later than November 30, 2016. Projects must be completed within 2017.

Seed funding grants should facilitate community work in collaborative brain research, promote the use of neuroinformatics solutions, and accelerate advances in understanding the brain and treating its illnesses.There are two types of funding available, project funding and travel grants.

Travel grants will be used to support collaborative work. One of the collaborators (traveller or host) must be based in one of the 17 INCF network countries. The proposed travel should support one or more of the following:
- exchange of information relevant to neuroinformatics between parties based in different countries
- progression of work relevant to neuroinformatics requiring the participant to travel to another location, usually another country, for collaboration
- participation in neuroinformatics training or education as a lecturer or participant (but not general attendance at scientific meetings)
Project funding supports projects that will deliver tools, data, research, education, training or community development, for example:
- driving forward delivery of a product that addresses a neuroscience use case
- enable a project to develop to the stage of attracting larger-scale external funding, for example initial consortium meetings or pilot data collection
- organisation and hosting of a scientific workshop
- development of training or educational content
The funding could facilitate, for example: initial consortia formation for the creation of a competitive funding proposal; work to demonstrate a proof of concept; tool development or integration; hosting of a workshop to explore and develop an area; or development of education and training content. The leader of a funded proposal must be based in one of the 17 countries in the INCF network.

All participants of a funded proposal must commit to sharing all reports, data, code, and training/education materials from the final project, subject to any limitations imposed by any subsequent funder. Projects must be completed within 2017.

More information and FAQ: https://www.incf.org/resources/funding-support

*INCF is an international organization launched in 2005, following a proposal from the Global Science Forum of the OECD to establish international coordination and collaborative informatics infrastructure for neuroscience. The INCF international network currently spans North America, Europe, Australia and Asia. INCF fosters the global digital interconnectivity of data, methods and people engaged in brain research to catalyze insights into brain function in health and disease.”

Neuronify the first neuroscience app on my phone

Posted on November 23rd, 2016 in Anita Bandrowski, Inside NIF | No Comments »

So I never ever put apps on my phone because they are a waste of space, also I have an old sad phone so a couple of apps just decimate up my memory.

This all changed at the 2016 SfN meeting last week when I talked to some lovely grad students from Norway, who showed me Neuronify. Ok I know what you are thinking, how can an app for something neuroscience-related actually be useful? I was certainly a skeptic, but no longer.

You have got to try it!

I am an electrophysiologist, by training, and always wondered why anyone in their right mind would ever simulate data. Isn’t that like making things up?
Then I started simulating data on some nice Cray supercomputers, because it was fun, but it is a little inconvenient to lug one of those to class or a dinner date.

Neuronify solves this problem, at least for relatively simple simulations, allowing students to quickly see how neurons behave in a network while doing what they do all day anyway, i.e., play with their phones.

I can’t say enough about how much fun I am having with my phone, now that I can simulate Tritonia swimming central pattern generator circuits, without having to find snails!

http://cinpla.org/neuronify/

Neuronify RRID:SCR_014755

INCF Applications for Seed Funding! Project and Travel Grants available!

Posted on October 26th, 2016 in News & Events, Uncategorized | No Comments »

Hello NIF/SciCrunch Community!

Our partners at INCF are inviting applications for “seed funding of collaborative brain research projects.” Please click the link for more details!

https://www.incf.org/resources/funding-support

Sincerely,

The NIF/SciCrunch team

seed-funding-image

 

Registration is now open for Brainhack Los Angeles

Posted on October 10th, 2016 in General information, News & Events | No Comments »

Hello SciCrunch/NIF Community!

Please read below for information on registering for Brainhack Los Angeles!

“Registration is now open for Brainhack Los Angeles – Big Data Tools for Connectomics (http://events.brainhack.org/LA2016/)! This 3-day workshop will be held November 10-12 in Los Angeles, California just before the 2016 Society for Neuroscience (SFN) Annual Meeting. Brainhack events (http://brainhack.org) bring researchers from disparate backgrounds together to collaborate on problems in neuroscience. Brainhack Los Angeles is supported by and brings together the incredible expertise of two NIH BD2K Centers, ENIGMA [http://enigma.ini.usc.edu/] and Big Data for Discovery Science [http://bd2k.ini.usc.edu/]), and a NIH P41 Center, ReproNim: Center for Reproducible Neuroimaging Computation [http://www.reproducibleimaging.org/]). Email info@brainhack.org for more information.”

Sincerely,

The SciCrunch/NIF team