Archive for the ‘Anita Bandrowski’ Category

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.

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.

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

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.

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!