Video demonstrations for online scientific articles are now just one click away.
By Phil Meagher at JoVE (the Journal of Visualized Experiments)
Communicating scientific protocols is difficult. Word count limitations result in ambiguous protocols and techniques are becoming increasingly cross-disciplinary and complicated. As a result, reproducing experiments is frustrating. But there is a solution. What if instead of having to read protocols you could watch them first?
On January 17, the team at the Journal of Visualized Experiments, JoVE, released an application to help scientists at the bench do just that. The idea was simple: allow scientists to “visualize” all of the scientific articles available online by leveraging JoVE’s rapidly growing scientific methods video collection. (To date, JoVE’s published 2,966 methods-videos since the company launched in 2006.)
The application is called the AskJoVE button, and offers a novel opportunity for scientists looking to learn procedures from scientific articles. Functioning from within your internet browser’s bookmarks bar, this application, or “bookmarklet,” produces a collection of video-demonstrations of techniques mentioned in any given scientific articles—even for those published in the traditional, text-based format.
“We created this new feature because we want to visualize all the science literature in the world,” says Dr. Moshe Pritsker, JoVE’s CEO and co-founder, “For every science article you read, click on the Ask JoVE button and immediately see videos of experiments related to this article, filmed at the best university labs.”
With this in mind, try to now imagine yourself at the lab, reading through an article you’ll need to learn to replicate as part of your research. If a small, important part of the protocol suddenly becomes vague, getting help no longer must involve scheduling training with other scientists half way across the globe. Instead, simply click the AskJoVE button, and watch as the methods in that article are demonstrated on your screen.
The AskJoVE button is free to download, and it is easily set up via drag-and-drop installation.
Each technique featured by the button is demonstrated by its own original authors (filmed by JoVE) and accompanied by scientific animations produced by the JoVE video team. Once clicked, the AskJoVE button provides scientists with a concise and powerful tool that saves time and money.
Interested in introducing your lab’s technique to the world? Submit your abstract to JoVE via our publishing information page. For subscription information you may reach out via our website, or you can take a moment to recommend JoVE to your institution’s librarian.
J. Vis. Exp. (82) e51012, doi:10.3791/51012 (2013)
We’re pleased to have another guest post by the team at JoVE (The Journal of Visualized Experiments). This month’s featured article explores how the way that lab mice build their nests can provide a useful indication of their welfare. The video format is a great way to convey all the subtle behavioural nuances that might be lost in the traditional print-only journal format and again illustrates the great potential of using multimedia content in academic research. Let us know what you think in the comments section below!
By Kira M. Henderson, Ph.D.
Deputy Director of Journal Development Editor, JoVE
The JoVE video article, “Nest Building as an Indicator of Health and Welfare in Laboratory Mice,” offers an effective and simple solution for monitoring animal welfare of laboratory mice concurently with experimentation. Brianna N. Gaskill et al. document the two-part process of scoring nesting habits as representation of mouse behavior and overall health and wellbeing. The nesting and scoring process is fairly simple but includes numerous variables and subtle behavioral analysis. The method is presented with an additional layer of detail in a dynamic JoVE video article as opposed to a static text article.
Identifying pain is the first step in mitigating discomfort and addressing disease or injury. The field of pain management is highly coupled with pain identification through behavioral cues in laboratory animals, as animals cannot verbally describe when or where they have pain. Video articles allow researchers to precisely capture subtle differences in animal behavior as related to changes in wellbeing, which may be lost in standard methodology texts.
Advantages of the presented method over other pain and health monitoring techniques include the ease of use and ability to analyze results even if mice are inactive. The first part of the test examines and scores nest building according to the quality and complexity of the prepared nest. Considered variables include extent of material manipulation, size and shape of nest as well as height and depth of the overall nest dome. The second part of the test, “time to integrate to nest” or TINT, occurs after the mice complete their initial nest. The TINT test requires the addition of a single piece of new material into the mouse’s cage to determine if the mouse is actively integrating material into their nest. A cage where the mouse utilizes the new material is considered TINT positive, whereas a mouse that disregards the new material is TINT negative.
Proper nest building can signify mouse health and stability. High nest building scores and TINT positive outcomes suggest normal or healthy mouse behavior, while low nest building scores and TINT negative could be a sign of disease or behavioral defects requiring veterinary attention. Sick or wounded mice could compromise the results of a research study as well as cause general discomfort for the animal.
This publication in JoVE provides other researchers with a clear and visual demonstration of how to test nest building behavior in lab mice as an indicator of animal health. JoVE is further exploring the field of pain monitoring in an upcoming Special Issue titled, “Chronic Pain Modeling and Analysis”. This Special Issue is currently accepting abstracts for consideration at www.jove.com/publish/special-issues.
Last month we saw another edition of the global extravaganza that is Social Media Week. This time around there were over 1000 events and 25,000 attendees in 8 cities around the globe. The theme for this year was “Open & Connected” which is pretty much a perfect fit for the Mendeley philosophy. So we thought it would be great to host an event in the London SMW Hub about how technology is changing the way we conduct and fund research, how researchers interact, discover content and share their findings, as well as how the non-academic public can get involved and make a real different through citizen science initiatives.
Our Masterclass was streamed live and proved to be one of the most popular events of the week, with hundreds of people tuning in and sending their own questions.
Mendeley Co-founder and President Jan Reichelt kicked off the series of lightning presentations by explaining how Mendeley can help researchers organise their papers, but also how it went far beyond that. “Research is an inherently social activity, and Mendeley is an environment starting with productivity going over into collaboration, and that also crucially captures the social context going on around that research.”
Rachel Greene from JoVE challenged researchers to “stop reading and start watching,” explaining how the majority of the time scientists failed to accurately replicate the findings of key studies. She believes that technologies such as the one used in their peer-reviewed Journal of Visualized Experiments are much more suited for that purpose than traditional print, and can therefore dramatically increase reproducibility and the pace of scientific discovery.
“In the past everything was recorded on paper, but current science is very digital,” says IJsbrand Jan Aalbersberg from Elsevier’s Article of the Future project, which aims to improve scientific communication in all its rich facets. “All the records are digital, all the capturing of scientific data is digital, and the communication of that information of course is also digital. However the traditional publishers have not yet adapted to that, what they usually do is flatten the multidimensional, rich research that an author has created into a two-dimensional paper of text and images.” He gave insight into some tantalizing possibilities, including the ability to run variations of some experiments – in computer science for example – within the parameters of the article itself, making it a living, evolving piece of collaborative research.
Nicolai Humphreys from The Lancet told of how the meaning of the journal’s name came from the fact that “A lancet can be an arched window to let light in and can also be a sharp surgical instrument to cut out the dross” and upon founding the journal in 1823 Thomas Wakley stated his intention that the publication should serve both those functions. Fast-forward nearly 200 years and Nicolai is part of the team that is using technology to cut out the dross and make academic publishing more dynamic and cutting edge.
Emma Cooper described the journey that took their digital amusements company Team Cooper to developing a Facebook game in conjunction with The Sainsbury Laboratory to help harness the brainpower of citizen scientists to tackle Ash Dieback disease. Quoting Dr Dan MacLean, who approached them about building the game with their data, “humans are smart and humorous, and we love games.” The key to the success of Fraxinus is the human ability to recognise patterns, and this proved really addictive with players (over 38,000 in the first month), who spend 20 minutes on average playing the game, where the average tends to be around 5-10 minutes.
That is what Robert Simpson from citizen science web portal Zooniverse calls “cognitive surplus,” which describes the vast amount of time that we collectively spend on activities such as watching TV. “The human race spends 16 years every hour playing Angry Birds every hour. There’s a lot of brainpower out there and what we try to do is take that brainpower and make it more useful to researchers.” The team at Zooniverse works with researchers to design sites that take their data and presents it into a format that will let the crowd help them to achieve their objectives. In the case of Snapshot Serengeti, for example, this meant classifying the millions of pictures taken over 2 years by camera traps in Tanzania to provide new insight into wildlife dynamics.
“These days with modern technology Citizen Science is becoming a fresh new hot subject in science,” says Margaret Gold of Citizen Cyberlab, which is leveraging the web, mobile phones and other tools and platforms to enable crowd-sourced scientific research. “We give people across the globe an interactive means to either help with the collection of data or the processing of data, pattern recognition and so forth, and all this makes a very genuine contribution towards science.”
Dr Rayna Stamboliyska, a Research Fellow and Digital Content Coordinator at the Centre for Research and Interdisciplinarity in Paris, believes that technology can be used to bring research into primary schools, and that “we can change the world many kids at a time.” In these programs, PhD fellows work with school children to develop research projects, leveraging and incorporating various technologies and social media. “This not only engages them in the STEM curricula at a young age, but it’s a really gender neutral policy, so we’re addressing the problem of having so few women in science.”
But ground-breaking research often comes across the stumbling block that is lack of funding, and this is where Liz Wald from Indiegogo believes that crowdfunding can help scientists. “it’s really about getting rid of gatekeepers, knocking down barriers and taking ideas right to the crowd,” she said as she went through a few of the projects that were crowdfunded through Indiegogo, such as Kite Patch (a patch that lets people avoid mosquito bites) and uBiome (where you sent off swabs of your bacteria to them so that they could let you know more about yourself and also help the wider project to sequence the Microbiome). The message was that people will not only fund cool and useful gadgets, but all forms of science as long as you tell a good story.
If you missed it on the day don’t worry, all the presentations are on the Mendeley YouTube Channel, so you can watch them any time and let us know what you think! There are also some cool pictures of the day available on our Flickr page, we had a great time and thanks again to all our speakers and community!
This Thursday the 26th September, Mendeley’s Co-founder Jan Reichelt will get together with 8 other innovators from the Open Knowledge Foundation, Zooniverse, Elsevier, Indiegogo, Team Cooper, The Lancet, JoVE and the Mobile Collective to discuss the many ways that technology can change, facilitate and improve things for researchers everywhere.
From “The Article of the Future” and the power of crowdfunding to enable research, to videos that enhance reproducibility and games that harness the power of crowds to solve some of the world’s most difficult scientific challenges, there’s certainly going to be a lot of food for thought…
We’re going to be right at the heart of all the activity in Social Media HQ which will also host events by the likes of Facebook, Nokia, Pinterest, Twitter and Google to name but a few. Spaces at the venue are extremely limited and you have to hold a VIP Pass to attend, but you can watch the event for free and live from wherever you are by following the live streaming link.
If you have any questions, comments or thoughts you’d like to put to the panel, do get in touch! You can leave a comment here, email me on alice.bonasio@mendeley.com or Tweet using the hashtag #smwSciTech
Social Media Week London will soon be upon us and Mendeley is really excited to be hosting a Masterclass in the heart of Covent Garden. This year’s SMW theme is “Open and Connected” and that’s literally what Mendeley is all about. So we thought we’d bring together a few like-minded people to talk about how social media and technology are changing the way we research and what this means not only for the academic community, but for everybody.
Research is not about a “walled garden” any more. It’s global, open and collaborative (the fact that Mendeley just reached 2.5 million users proves that) If you’re a student, have a professional interest in science or academia, are one of the millions of people who have contributed in some way to a citizen science project or thought about supporting research through crowdfunding, then you’re part of this story. And if you aren’t yet, then chances are that you soon will be. People want to participate in science, creating communities around interesting projects and helping to advance the pace of discovery in the process, and now they can even do this by playing Facebook games.
The dynamic format of the event will have 9 high-profile international speakers presenting their ideas in 5-minute PechaKucha-style presentations followed by a 45-minute open discussion between the panellists and the audience (both in the venue and online) mediated by Nicolai Humphreys, Web Editor of the Lancet. We have a very impressive cross-section line-up, and they’ll explore, from a variety of angles, how technology and social media are enabling scientific research and making science more open for everyone. We will look at how games can leverage the brainpower of millions of citizen scientists, how crowdfunding initiatives have helped raise funds for finding new cures for cancer, and how global collaborative platforms are helping to bring together researchers to help solve some of the biggest problems facing us today.
The space in the venue is limited to only few guests and VIP pass holders, but we’ll be streaming everything live, so wherever you are in the world you can watch the sessions and send in your comments.
So if you have a question (whether it’s for on of the panelists or a general issue about technology and research you’d like to explore) get in touch via Twitter using the hashtag #smwSciTech or send an email to alice.bonasio@mendeley.com and we’ll try our best to include it!
Jan Reichelt, President and Co-Founder at Mendeley, dubbed the “Facebook for Scientists” – a collaboration platform with 2.5 million users worldwide that also offers researchers workflow and content management tools to accelerate the pace of scientific discovery. In April 2013 Mendeley was acquired by Elsevier, one of the world’s largest scientific publishers
Nicolai Humphreys Web Editor, The Lancet, one the world’s best known, oldest and most respected medical journals, founded in 1823 and published by Elsevier since 1991
Rachel Greene– Director of Marketing at JoVE (Journal of Visualized Experiments) the first peer-reviewed and internationally recognised Scientific Journal that uses video content
IJsbrand Jan Aalbersberg Senior Vice President Journal and Content Technology at Elsevier . He heads the Article of the Future project, which is an initiative that looks at how the traditional paper/pdf based article will evolve to accommodate the wealth of multimedia content that researchers will increasingly rely upon to build scholarly conversation
Margaret Gold Director and Co-Founder of the Mobile Collective,which includes projects such as Citizen Cyberlab, looking to build tools and platforms for citizen science as well as collaborative environments and software tools that stimulate creative learning.
Emma Cooper, Business Development Director at Team Cooper, the developers of Facebook game Fraxinus which harnesses the power of citizen science to find a cure for ash dieback disease
Liz Wald, Head of International at Indiegogo, the largest crowdfunding platform on the web which has successfully enabled scientific research via projects such as uBiome and iCancer which raised funds as well as awareness through their highly successful campaigns.
Back in 2006, Moshe Pritsker thought to use video technology to capture and transmit the intricacies of life science research, facilitating both the understanding and reproduction of experiments and techniques. This idea of “letting scientists look over each other’s shoulders” led to the launch of JoVE, the Journal of Visualized Experiments, which is peer reviewed and PubMed-indexed. As a scientific journal, it has an editorial board and hierarchical structure, and ensures consistent quality of its video content by maintaining a network of professional videographers spread across major science centres. Scientists from leading institutions participate by submitting video articles that visualize their experiments.
As science advances, processes and tools also become more complex. Procedures and techniques such as growing stem cells are tremendously complicated and difficult to accurately follow with just a set of written instructions, and visiting labs in person can be a very expensive alternative beyond the resources of many researchers. This challenge of poor experiment reproducibility is what JoVE tries to address, claiming that traditional written and static picture-based print journals are no longer sufficient to accurately convey the intricacies of modern research. Translating findings from the bench to clinical therapies rely on the rapid transfer of knowledge within the research community.
This month’s issue features an article by Connors et al of Massachusetts Eye & Ear and Harvard Medical School, who have developed an audio-based virtual environment simulator that uses audio cues and a video game context to build cognitive maps of three-dimensional spaces and help blind people improve their navigation skills. Other videos include a new non-invasive method being developed at the Massachusetts General Hospital and Harvard Medical School for measuring brain metabolism in new-born babies, and a demonstration of how a biopolymer gel derived from polysaccharides found in brown algae can help patients with heart failure.
There are also other companies operating in the scientific video space, but what they offer is a looser user-generated environment. One of the most successful of those is SciVee, which is backed by the Public Library of Science and features videos that sit alongside traditional journal papers.
So is this the new frontier? Are we actually looking at a situation where most researchers will feel comfortable communicating with their peers using video? Has the scientific community truly given its blessing to such new approaches to science communication? We’d love to hear your thoughts.
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