Archive for the ‘NIFarious Ideas’ 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

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.

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.

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!

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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!

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:

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If not, then leave a comment!

Protect Yourself from Zombie Papers

Posted on April 25th, 2016 in Anita Bandrowski, Data Spotlight, NIFarious Ideas | No Comments »

Another fun flier to post around the department.

Zombification of papers: the inability to use or validate information in the paper.
How can we stop this terrible plague on the scientific literature? – RRIDs help get the Key biological reagents identified and authenticated.

Feel free to print this fun flier and post it on your office door!

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RRID: Improve your Impact Factor!

Posted on April 25th, 2016 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

Please feel free to take this fun flier and post it around your lab to help your lab-mates to remember how to get an RRID into your next methods section or grant application.

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Brain Health Registry

Posted on March 3rd, 2014 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

The Brain Health Registry — led by researchers at UCSF — is a groundbreaking, web-based project designed to speed up cures for Alzheimer’s, Parkinson’s and other brain disorders.  It uses online questionnaires and online neuropsychological tests (which are very much like online brain games). It can make clinical trials — which are needed to develop cures — faster, better and less expensive.

 

The project is scheduled for a public launch in the spring, but we’re inviting you to be among the first to participate and provide feedback.

 

Click here to see our website and get more information about the Brain Health Registry.

  • It’s easy. It takes a few minutes to sign up and less than 3 hours per year. And it’s all done online, so you can do it from home — or anywhere you have Internet access.
  • It offers a breakthrough. 85% of clinical trials have trouble recruiting enough participants. By creating a large online database of pre-qualified recruits, The Brain Health Registry can dramatically cut the cost and time of conducting clinical trials. This is the first neuroscience project to leverage online possibilities in this way and on this scale.
  • It’s meaningful. With every click of the mouse, you help researchers get closer to a cure for Alzheimer’s and other brain diseases. If Alzheimer’s runs in your family, this may be an important gift to your loved ones.
  • It’s safe. Top scientists from some of the most respected institutions in medicine are leading the Brain Health Registry. They understand your need for privacy, and they will protect it at every step of the way.

We’re currently in our pre-launch phase.  Try it out!  If you offer feedback – and we hope you do – we will read it, consider it carefully, and respond to you directly.

 

As an early adopter, you can help us in two ways.  You can help in the way all members can help — by answering the questionnaires and taking the online brain tests, you strengthen the database that the scientific community needs.  You can also help us improve our new website – we’ll be making many changes, based on your feedback, before our public launch.

 

Please take the time to visit our sight, sign up and offer your feedback.

Resource Identification Initiative – AntibodiesOnline is giving away “nerd mugs” to help identify antibodies in your paper.

Posted on December 16th, 2013 in Anita Bandrowski, News & Events, NIFarious Ideas | No Comments »

Dear NIF Community members;

Our partners in crime, FORCE11, are hosting a working group, the Resource Identification Initiative, that is working with journals to make it easier to identify research resources used in the materials and methods of biomedical research through the use of unique identifiers.  For the pilot project, we are concentrating on antibodies, genetically modified organisms and software.  Our goal is to make identification of research resources:  1)  machine-processable;  2)  available outside any paywall;  3)  uniform across journals.  More information can be found at:  http://www.force11.org/Resource_identification_initiative

Our colleagues at Antibodies On Line have set up a beta testing site specifically for antibodies: http://www.antibodies-online.com/resource-identification-initiative/

If you use antibodies in your research, or know those that do, please help us test the tools and provide feedback.  Antibodies Online is generously providing nerd mugs and shirts to those who participate (they make great Holiday gifts!).