“AAV are versatile tools used by neuroscientists for expression and manipulation of neurons. Many scientists have benefited from the high-quality, ready-to-use AAV prep service from Addgene, a nonprofit plasmid repository. However, it can be challenging to determine which AAV tool and techniques are best to use for an experiment. Scientists also may have questions about how much virus to inject or which serotype or promoter should be used to target the desired neuron or brain region. To help scientists answer these questions, Addgene launched an open platform called the AAV Data Hub (https://datahub.addgene.org/aav/) which allows researchers to easily share practical experimental details with the scientific community (AAV used, in vivo model used, injection site, injection volumes, etc.). The goal of this platform is to help scientists find the best AAV tool for their experiments by reviewing combined data from a broad range of research labs. The AAV Data Hub launched in late 2019 and over 100 experiments have since been contributed to this project. The dataset includes details and images from experiments conducted in six different species and several different expression sites….”
Category Archives: oa.addgene
Addgene: COVID-19 Resources
“The global research community is moving quicky to expand the knowledge and understanding of COVID-19 and related coronaviruses. To assist with this effort Addgene will maintain this plasmid collection page, which outlines various plasmids available and those coming soon. Additionally, we have linked to collections of open-access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists….”
Depositing and reporting of reagents: Accelerating open and reproducible science. | The Official PLOS Blog
“Centralized depositing of materials advances science in so many ways. It saves authors the time and burden of shipping requested materials. Researchers who request from repositories save time by not having to recreate reagents or wait months or years to receive samples. Many scientists have been on the receiving end of a request that was filled by an incorrect or degraded sample, which further delays research. Repositories like the ones recommended by PLOS handle the logistics of material requests, letting the scientists focus on what’s important: doing research….
By encouraging authors to deposit materials at the time of publication, journals will help accelerate research through timely distribution and accurate identification of reagents. Biological repositories exist to serve the scientific community. Take Addgene’s involvement in the explosive advancement of CRISPR research. Since 2012, over 8,400 CRISPR plasmids have been deposited and Addgene has distributed over 144,000 CRISPR plasmids worldwide, enabling researchers to share, modify, and improve this game-changing molecular tool. It is a prime example of the positive impact that biological repositories are making on research….”
Taking knowledge preservation to the next level: new partnership between protocols.io, Addgene, PLOS
“Digital information carries a significant risk of disappearing, as one of the “fathers of the Internet” Vint Cerf has been
. This is particularly problematic for research communication as vanishing records undermine the reproducibility and integrity of science. We have taken this concern seriously at protocols.io from day one, constantly aiming for better ways to ensure stability, preservation, and visibility of the methods and knowledge shared on our platform. Digital archiving solutions have been the center of our focus; however, today we are excited to share with you our new physical preservation initiative, guaranteeing zero loss, long into the future. We are thrilled to be joined by the Addgene plasmid repository and the Public Library of Science (PLOS) in this initiative.
Of course, for many years we at protocols.io have had public APIs and PDF export of all protocols. In 2016, we became a
of CLOCKSS (the digital preservation archive for scholarly content, started by Stanford librarians in 1999), sending a PDF copy of every new protocol to them, the second it is made public. More recently, we introduced integration with Dropbox and GoogleDrive, to facilitate individual backups.
While all of our efforts are reasonable and ensure preservation and accessibility for decades, they are not infallible solutions in the long run. This is because preservation and accessibility are not the same thing. How many people today can open a file from 1997 WordPerfect or 1999 PowerPoint, particularly if it has been saved on a floppy disk? How confident are we that PDFs of protocols will be accessible and readable in seventy years by the scientists of the future?
With the above concerns in mind, we have been exploring over the last year more reliable solutions that take advantage of modern technology. And so, we are excited to announce a partnership with
and
for low-cost physical preservation of protocols, using laser cutters. The PLOS editorial team will be in charge of selecting protocols that warrant physical preservation and Addgene, with their expertise in physical storage, will be handling the long-term archiving in their freezers….”
Addgene Depositors Get More Citations
“Professor Feng Zhang’s original 2013 gene editing paper on CRISPR/Cas amassed nearly 2,400 citations in its first four years (1). In addition to publishing in Science, Professor Zhang deposited the associated plasmids with Addgene. Since then, Addgene has filled over 6,500 requests for these plasmids. While clearly an outlier, this story had us wondering: is there a larger trend here? Do papers associated with Addgene deposits accumulate more citations than those without Addgene deposits? Even more interestingly, could we tell if depositing a plasmid with Addgene causes a paper to get cited more? …So what do we find [from Web of Science]? Lots more citations for the papers with plasmids deposited at Addgene – typically about four times as many as papers without plasmids deposited with Addgene….”