by Chris George
In this episode of figshare new features, I’ll be talking about some new functionality that has just been launched alongside a retooling of an existing feature.
This week I was at the Research Data Alliance’s 4th plenary meeting. The RDA brings together interest and working groups to focus on some of the specific problems faced by funders, researchers and institutions alike as they try to maximise the value of the research outputs they generate. Although academia is often accused of being late to the party when it comes to embracing new technologies and opportunities that the modern web brings, some of this delay can be accounted for by the very nuanced yet significant use cases in different research fields and territories. This is definitely not a field where one size fits all. As figshare developed out of the academic world, we are very aware that in todays research data landscape, for many of the stakeholders, it’s not necessarily about just ‘open’ or ‘closed’ but about ‘control’.
In order to be in control of research outputs at a funder, institutional or even researcher level, there needs to be an element of trust with regards to the technologies adopted. At a session on standards for trusted digital repositories, a lot of the debate was around the word ‘trust’ and what that means to different people.
The public announcement by the Swets & Zeitilinger Group BV regarding their financial situation has led to some questions regarding figshare's relationship with them and possible impact on the company/products.
There is a non-exclusive sales representation (agency) agreement in place between Swets and figshare for some regions in Europe. The financial situation of Swets, while unfortunate, has no impact on figshare as a company or figshare for institutions as a product.
We are delighted to announce a partnership with Arkivum the provider of large scale, long term, safe digital archiving solutions, to provide UK academic institutions with a service covering the full spectrum of funder-mandated research data requirements.
Increasingly funders in the UK are requiring better data management of publicly funded research. On May 1 2015, the Engineering and Physical Sciences Research Council (EPSRC) policy framework on research data comes into effect. The framework’s principles and expectations promote a culture within academia of sharing, preservation, easy discovery and reuse of research data.
New Radicals is a search led by Nesta, the UK’s innovation foundation, and The Observer to find the top people, projects and organisations offering innovative ways to tackle social challenges. The initiative was launched for the first time in 2012 and this year’s applications and nominations were invited across ten different categories: community action; environment; health; employment/jobs; politics; media; architecture and the arts; science and technology; business; education; and food.
Diving into the haystack to make hay is one of the most inefficient activities imaginable (as well as a figurative absurdity). Doing science inevitably entails discovery, but the process has historically been far more difficult without effective tools to support it. With the quickening pace of scholarly communications, the vast volume of information available is overwhelming. The key puzzle piece might be as hard to find as a needle, and moreover, no scholar has the time to dive into the hay-verse to make more hay.
Since its inception, we have been talking to lots and lots of librarians and research offices about how ‘figshare for institutions’ could work for them. As more institutions start using figshare as a layer in their research data management plans, more nuanced workflows and administrative features become available. figshare for institutions allows administrators to control the research data management of all digital content funded at the university. Our focus for users is based on simplicity, allowing them to fulfil changing funder mandates without spending extra time deviating away from their workflows.
figshare acts as the technology layer which empowers the institution to have more control over the digital outputs of their academic’s research, while storing the content on their own storage solutions, or Amazon Web Service’s S3 platform, for which we can offer preferential rates. This allows the administrators to control the curation of the University’s content through customised workflows.
We are proud to announce figshare is providing the technology to power the newly launched Human Genome Variation Database managed by Nature Publishing Group. The Open Access database captures all the relevant information reported within a published Data Report in the Human Genome Variation journal. A Data Report is a standardized format of reporting genomic variation and variability.
To maximize reuse, the data (i.e. the facts themselves) in the HGV database will be published under a "CC0” license. The potential for text mining and large systematic analysis of the database is particularly exciting as figshare have long been advocating open access, open data and better use of technology in academic publishing.
Data output is increasing exponentially: 90% of all data had been produced in the last 2 years. Research data management(RDM) is therefore fast becoming of paramount importance to research managers and administrators within institutions. To help facilitate a solution to some of the problems facing institutions, Team figshare ran a workshop at the ARMA 2014 conference in Blackpool entitled ‘Research Data Management - What are your problems? Come exchange ideas!’
We asked attendees to write down the biggest issue they’re currently facing so we could group them together into themes for focused discussion groups. The issues of the 40+ attendees from predominantly UK institutions were many and varied but could be loosely grouped into the following 4 themes:
On May 1st 2015, EPSRC (the main UK government agency for funding research and training in engineering and the physical sciences) will expect all the organisations of those they fund to be compliant with their guidelines with regards to the ‘exploitation of research results and collaborative research.’ Research organisations will have to ensure that EPSRC-funded research data is securely preserved for a minimum of 10 years and if it appears that proper sharing of research data is being obstructed, EPSRC reserves the right to impose appropriate sanctions. Of course, this standpoint is one which figshare heartily endorses, as it is closely aligned to our goals for the future of academia.
Quoting directly from their guidelines:
figshare is all about openness – providing a platform to share your research outputs with the world, whether it be a single figure, a poster presentation, a raw data set, or a full-fledged article. For many researchers, open repositories like figshare have changed the way they do research and how they view academic publishing. But for too many more, sharing is not yet the norm.
Figures and data from two of IOP’s journals, Environmental Research Letters and Journal of Physics B: Atomic, Molecular and Optical Physics will automatically be added onto the figshare repository. This will enable researchers to link published information with unpublished supporting material in a citable way, thereby creating a holistic view of their research. It also helps researchers to add/view metrics that will help them understand the true influence and reach of their work.
figshare partners with Atypon making it easier for publishers to deal with data and other research filetypes
figshare are happy to announce a partnership with the academic publisher platform Atypon. figshare already provides content visualisation and storage services to publishers such as PLOS and Nature Publishing Group. By partnering with Atypon, these features are now readily available for implementation at their publisher clients.
Publishers on Literatum 14.1, the newest generation of Atypon’s flagship platform for professional and scholarly publishers, can now embed tables, datasets, videos, and other supplemental material from figshare on article pages in Literatum. First implemented for Taylor & Francis, this new service enables users to view supplemental information hosted by figshare alongside the article in Literatum via the figshare widget, which renders the supplemental material on the publisher’s website. Users who visit this article on Taylor & Francis Online, for example, can watch a related video hosted by figshare and embedded on the page.
What would happen if you lost all of your research data? Imagine if you lost all of the scientific data you’d been collecting for four years. Now imagine the knock-on effect; you wouldn’t get the PhD you’d been working towards, and your career would be ever more affected. This nightmare situation actually happened to Billy Hinchen. Hear his story.
Had a data drama similar to Billy’s? Share your stories with us via #datadramas
figshare and IOP Publishing are joining up to help authors share their work. We are currently working on a collaborative pilot to test new ways to help authors share figures and data from IOP’s journals more easily. The aim of the pilot is to assist authors further increase the visibility of their research and to help IOP explore solutions to questions surrounding open data using existing cloud-based technology.
Two of IOP’s journals, Environmental Research Letters and Journal of Physics B: Atomic, Molecular and Optical Physics, will take part in the initial trial. Figures and data from both publications will automatically be added onto the figshare repository during the trial. This will enable researchers to link published information with unpublished supporting material in a citable way, thereby creating a holistic view of their research. It also helps researchers to add/view metrics that will help them understand the true influence and reach of their work.
As announced last week, we have been working with Mozilla Science Lab and GitHub to investigate ways in which academics can receive credit for their code and software.
Next week sees the release of our new functionality to sync GitHub releases to your figshare account to improve academic credit of code, software and scripts.
As academic domains become more data rich, an increasing fraction of research activity is captured in the tools used to analyse and process these data which raises an important question:
We're happy to announce today our new partnership to aid the visualisation of different types of data across Taylor & Francis journals. figshare will host the supplemental data as well as provide a widget that will enable Taylor & Francis users to view data in the articles in the browser alongside the content.
“We’re delighted to be able to bring this innovative service to authors and to anyone with an interest in research, whether they are working within or outside the academic and scientific communities" said David Green, Global Publishing Director for Journals at Taylor & Francis. "Using figshare will enable us to make supplementary material, which is fundamental to the research process, discoverable to all, in as usable a fashion as possible. Simply by keying in a simple term to a search engine users will be able to unearth a wealth of data, aiding future research and increasing the visibility of authors’ work.”
by Mark Hahnel
We are often asked for pro-tips on how to make the best use of figshare, so we decided to share a few which may help you boost the impact of your research outputs, keeping you organised at the same time. In this part we’ll focus on impact; you can read the post with organisational tips here.
by Mark Hahnel
We are often asked for pro-tips on how to make the best use of figshare, so we decided to share a few which may help you boost the impact of your research outputs, keeping you organised at the same time. In this part we’ll focus on organisation, with impact coming soon.
by Mark Hahnel
Research data management can be tough if you’re an individual researcher, but what happens if you’re looking to manage a whole team. Principal Investigators (PIs) must face this problem a lot.
figshare was set up with the aim to provide a free service where all academics should have a place where they can make their research outputs openly available, under the most liberal creative commons licenses. This is still the core ethos of figshare. What we have found in talking to researchers, librarians and other users is that a lot of people are actually using the private space for storing and sharing their research outputs with collaborators. For our community, it’s not just about open and closed, it’s about being in control of the products of their research!
On top of the usual figshare features that help you comply with funder research data management mandates - making all of your research outputs citable (with a DOI) and the ability to track the impact of all of your research - we can now provide you with the tools you need for your research data management. Our recently released collaborative spaces have enabled academics to better manage their files and collaborations privately and securely in the cloud. Due to the demand for more features, we can now offer the following features for users who wish to upgrade their account.
Detailed step-by-step instructions for using the figshare uploader with the latest MAC OS X Mavericks
As of the latest release of MAC OS X, apps that are not downloaded from the Mac App Store or from "identified and trusted developers" cannot be opened and are denied permissions unless specifically bypassing Gatekeeper. As such, to get the figshare uploader to work on this release of Apple’s operating system, we provide a step-by-step tutorial below. If you had installed the figshare uploader before upgrading to Mavericks, you should follow all of the steps below. For a fresh install, please skip to step 2.
1. Uninstall the figshare uploader
The greatest discoveries in science and academia have come about as a result of great collaborations. figshare's main ethos from day one has been to help researchers of all fields by offering a better way to store, discover and share their data, whilst also getting the credit they deserve. By leveraging new technology and doing without the obsolete processes that developed in science and research over the years, we've been able to make that very easy to do as well. We were set up with the idea that all academics should have a place where they can make their research outputs openly available, under the most liberal creative commons licenses, for free. This is still the core ethos of figshare.
The way scientists and researchers communicate their work is evolving. Predictions indicate that scientific publishing will change more in the next 10 years than it has in the past 200. There has been an explosion in the number of open access journals, data sharing platforms and open source projects in recent years and there has never been more ways to share and publish your work.
by Andy Farke
It’s almost cliché now to say that paleontology is undergoing a digital revolution. The first medical CT (computed tomography) scans of fossils were published nearly 30 years ago, and the first publicly distributed digital dataset for a fossil was pressed onto CD-ROM over 20 years ago. CT scans are almost routine for many vertebrate fossils, laser scanning allows rapid digitization of surface anatomy, photogrammetry helps turn photographs of fossils into accurate digital models, and 3D printing can turn digital fossils back into hard copy. Literally terabytes worth of fossil specimens are sitting on hard drives around the world.
by Mark Hahnel
This week, nature published several articles on impact - link articles on impact to the paper here, one of which I contributed. There is also a great piece from David Shotton looking at Open Citations. I focussed on investigating what the dissemination and tracking of a plethora of new research outputs meant for academic credit, the impact factor and citations. I have expanded on parts of this piece here to highlight some of the issues originally raised by Jason Priem in a Nature commentary last year and give a bigger picture of the background behind my reasoning.
By Graham Steel
In the UK, earlier this year, the parliamentary House of Lords Select Committee on Science and Technology conducted an enquiry into the implementation of the Government’s policy on Open Access (OA). This sparked many conversations and submissions such as here, here, here, here and here.
by Mark Hahnel
figshare today announces the launch of ‘figshare for Institutions’ - a simple and cost-effective software solution for academic and higher education establishments to both securely host and make publicly available its academic research outputs. figshare, allows academic institutions to publish, share and get credit for their research data, hosting videos, datasets, posters, figures and theses in a cost-effective way.
His eyes brighten and his voice rises as he tells me about his latest results. He is excited. He should be. His lab is unravelling the details of how new memories are formed in the brain. Then I ask him where he will be publishing the work. He deflates. And begins to recite a formula I have heard before: “Well, we submitted the paper to Nature Neuroscience, but it was rejected. Then, we sent it to Neuron – rejected again. Next, we are thinking of sending it to PNAS. If that doesn’t work, we’ll probably send it to the Journal of Neuroscience.” Down the glamour publication ladder we go.
We’ve previously blogged about the amazing new research management tool, and our Digital Science stablemate, Projects. When it comes to organising research outputs, we’re big believers that this should not have to take up any of the time you could be spending researching. We believe it should be happening automagically, as part of your daily routine. The starting point for a lot of academics is saving your research files on your computer.
One area that figshare is really focussing on is incentives for making your data openly available. As the funding bodies push to mandate making all research outputs they fund available under open licenses, we want to make life as easy as possible for the researcher to comply. At the same time we want people to want to share their research outputs. One way of doing this is using metrics, so academics can track the impact of their non-traditional outputs. There is another avenue that we are exploring and that is by providing immediate ‘added value’ to the research. We are exploring several different techniques in this space and the first we would like to talk about is a small collaboration with Tim Brock of Data to Display.
by Mark Hahnel
This post relates to the ideas of and subsequent conversations I have had with Sean Thomas and Sands Fish of MIT. This post is based on their original concepts (more of which can be read about here) that I have developed a bit with relation to figshare. The question they posed was; how much information can be inferred from the logs of the academic repository at MIT with regards to helping deliver academic content to those who need it the most? In this specific example they were referring to those searching for information on endemic diseases in sub-Saharan Africa.
by Mark Hahnel
Last week I attended the Linked Open Data for Libraries and Museums (LODLAM) summit in Montreal. There audience was mainly academic and members from the ‘Galleries, Libraries, Archives, Museums’ (GLAM) community. What is interesting about the GLAM community is that there is often a big overlap with academic librarians and many of the problems they are trying to solve involve managing large amounts of digitized content. This is a problem that academic librarians now face as they try to deal with the growing volume of research data being produced. Fortunately, this means that a lot of the interesting techniques that can be applied to research data in order to link it up have already been implemented in the GLAM space.
Publishing: Evolution, Disruption & the Future was a one day Conference held in the main Auditorium at the Edinburgh Business School on 12th June 2013. Details about the event are here, speakers here and programme here. The event was streamed live on Google+ and also live tweeted, please see the Storify at the end of this post.
All advances to the figshare site have been led by user suggestions. One of the big ones that we’ve been trying to get out for a while goes live today - embeddable figshare content.
This allows users to take content that they have uploaded to figshare and embed it in their personal webpages, lab websites or blogs. We want users to effectively disseminate and make their research available to as many people as possible. By allowing users to embed content, we are hoping that the research on figshare can reach an even greater audience, giving it even more impact
A key component of figshare’s offering is working with publishers to provide visualisation tools and better management of large datasets. You can read more about our publisher offerings here. Continuing our development of the offering for publishers, today we’re launching 2 publisher portals on figshare, PLOS and F1000 Research.
The PLOS portal can be found here:plos.figshare.com
The F1000 Research portal can be found here:f1000.figshare.com
figshare was one of the ORCID launch partners and since said launch back in October, we have been looking for ways to take advantage of the new functionality to streamline the figshare user experience. Our first step in this is the release today of figshare-ORCID bi-directional syncing. For those who don’t know what ORCID is, here are some details:
Ever since the launch of the figshare desktop uploader, we have had users enquiring about when the cross-platform versions would be available. The first release of the desktop uploader was the Windows version. Today we’re happy to announce the beta release of the Mac and Linux versions.
By Graham Steel
On April 22nd , F1000 Research hosted an evening of ‘provocative’ talks in celebration of Open Science Publishing. As we covered in this earlier post, by partnering with figshare, F1000 Research can host large volumes of content and display them in the web based journal in a manner that has not previously been explored.
By Graham Steel
Last month, after the UKSG Conference in Bournemouth, see this recent figshare post, the UK witnessed another interesting Conference entitled Rigour & Openness in 21st Century Science. The two day event took place in and around the Lindemann Lecture Theatre in Oxford. It also featured a Debate entitled Evolution or Revolution in Science Communication? which took place in the Oxford Union at the end of day one. The Conference was a follow on from one in 2012, the video of which can be found here which we touched upon in this post last year.
Open Access is one of the most important shakes ups in academia for the last 50 years. At figshare, we are strong believers in the power of open access to do good. Allowing researchers to build on top of the findings of their peers makes the whole system more efficient. Included in this is the ability to reuse, remix and mine the content, looking for hidden patterns in large amounts of research. This is why all research uploaded to figshare is released under CC licence
Scientific Data is a new open-access, online-only publication for descriptions of scientifically valuable datasets from Nature Publishing Group. The ethos of the initiative is tightly aligned with that of figshare, focussing on making the data open under Creative Commons license, encouraging re-use and giving academics credit for all of their research. These are just some of the reasons why we are excited to be working with Nature on this journal. A few more details of their aims with Scientific Data can be seen below, taken from their website.
By Graham Steel
Back in May 2010, a proposal was put forward for a workshop “to crowd-open source the electronic printing press of the 21st century with the goal of improving how science is disseminated and comprehended”. This resulted in a Workshop held on January 19-21, 2011 at University of California San Diego entitled “Beyond The PDF”.
writeLaTeX is a free service that lets you create, edit & share your scientific ideas easily online using LaTeX, a comprehensive & powerful tool for scientific writing. The site offers you an easy to use two-panel interface. The left pane is used for editing text; the preview of your text is updated in the right pane. Over the weekend, the team at Write LaTeX went live with a ‘push to figshare option.
The US office of science and technology policy last week responded to the call from a petition to make all research outputs available. The request asked the US government to ‘Require free access over the Internet to scientific journal articles arising from taxpayer-funded research’.
The petition that has thus far had over 65,000 signatures (as of time of going to press) can be found here and the response can be found here. If you cannot be bothered to dig through this, we’ve tried to pull some of the most important bits out.
By Graham Steel
“After a close family friend died from pancreatic cancer, I turned to the Internet to help me understand more about this disease that had killed him so quickly. I was 14 and didn’t even know I had a pancreas but I soon educated myself about what it was and started learning about how it was diagnosed. I was shocked to discover that the current way of detecting pancreatic cancer was older than my dad and wasn’t very sensitive or accurate. I figured there had to be a better way!”
Welcome to the opening part of the narration of Jack Thomas Andraka.
The figshare team had a hackbreak this weekend. This is a Digital Science inspired event where the development team works on all those cool features that you’d like to implement someday, but cant justify prioritizing on a normal day.
The projects we battled our way through included:
Academics are constantly battling against their peers to climb the academic ladder. In a similar manner, institutions have to prove to Government and funding bodies that the research they fund is being put to good use at said institution.
Traditionally academic papers have been the currency by which the volume and impact of research is being measured. However, as the complexity and size of academic output increases, funders are now wanting to track different, equally important outputs. The most notable example of this comes from the National Science Foundation (NSF) who recently announced that they would not be measuring an academic’s research performance based on ‘papers’ but instead on ‘products’. This has not gone unnoticed by academic institutions who wish to be able to report on these metrics to the funders.
By Graham Steel
Today see’s the start of another important chapter in scientific publishing and open science, as PeerJ publishes its first articles.
“PeerJ is an Open Access publisher of scholarly articles. PeerJ aims to drive the costs of publishing down, while improving the overall publishing experience, and providing authors with a publication venue suitable for the 21st Century. Our tag line is: "Your Peers, Your Science. Academic Publishing Is Evolving" and we are committed to improving the process of scholarly publishing”.
PLOS has always been an organisation that we admire here at figshare, which is why we are delighted to announce today our new partnership to aid the visualisation of different types of data across the PLOS journals. figshare will host the supplemental data for all seven PLOS journals, as well as provide a widget that will enable PLOS users to view data in the articles in the browser alongside the content.
“PLOS believes in making data as visible and useful as possible,” said Kristen Ratan, Chief Publishing and Product Officer at PLOS. “Partnering with figshare is an important step in increasing the accessibility of the data associated with our research articles.”
The figshare community has been growing amongst academics who are telling their friends and colleagues that they can get credit for all of their research outputs, as well as managing their research data from anywhere, for free.
We think that these users should be rewarded for their enthusiasm. Today we are beginning that reward process with the figshare Advisor scheme. In exchange for presenting figshare to your colleagues at a lab meeting or journal club, you can become a figshare Advisor.
By Graham Steel
Late last month saw an important publication entitled “The Human Brain Online: An Open Resource for Advancing Brain Research” in PLOS Biology by Ball et al.
From the introduction, “With an estimated 86 billion neurons and about a trillion synapses per cubic centimeter of cortex, the human brain is arguably the most complex system in the human body, and it is the seat of diseases and disorders that affect an estimated one billion people worldwide. Yet the human brain remains poorly understood. Model systems are essential to progress in neuroscience, but a true understanding of the human brain and the diseases and disorders that affect it ultimately requires analyses of the human brain itself. Human brain tissue is a rare commodity and therefore inadequately explored. Published studies point to the scarcity of high-quality postmortem human brain tissue, particularly disease-free control brains; the largest brain bank in the United States reported last year that only 40–50 control brains become available each year.
By Graham Steel
The Future of Academic Impacts, was a free, all day conference hosted by the LSE’s Impact of Social Sciences project team, which was held on Tuesday, 4th December 2012 at Beveridge Hall, Senate House, London. (Details of last year’s Impact Conference are here).
“The event is to mark the end of the three-year Impact of Social Sciences project based at the London School of Economics that has been funded by HEFCE. Working with colleagues at Imperial College London and the University of Leeds, we have looked at the nature and measurement of impact of academic research in the social sciences on government and policymaking, business and industry, and civil society.
It has been quite a year since the figshare site went live last January. Perhaps the most rewarding statistic is that hundreds of thousands of research output files that would have otherwise gone unpublished are openly available to all on figshare. We were also very proud to be included in the Royal Society’s report on Science as an Open Enterprise.
Today sees the launch of the first figshare desktop uploader. The first release of the desktop uploader is a beta version and is only Windows supported, but versions for other operating systems will be coming soon.
It’s a very simple app that allows resumable uploads to your private ‘My Data’ section of figshare, where you can add some metadata and make your research outputs sharable, citable and discoverable, or keep it private. You can read more about the types of research outputs you can upload to figshare here.
“The digital environment of today’s research enables the collection and analysis of many more data sources and types than ever before, which trace the dissemination and reach of the article itself. Article-level metrics (ALMs) measure these activities at the level of the article and provide a valuable service lacking in traditional metrics: a real-time indicator of impact for research. In addition to the conventional measure of citations, ALMs incorporate altmetrics, newer measures of scholarly interaction based on the social web. Overall, they can provide much-needed new checks and balances, greater speed of feedback, and superior relationship mapping and influence tracking, none of which can be replicated by the traditional impact factor. They can form the basis of recommendation and collaborative filtering systems able to power navigation and discovery of articles synchronized to the needs of the researcher, publisher, institutional decision-maker, or funder”.
By Graham Steel
Princeton’s Ethan O. Perlstein describes himself as an ”Evolutionary Pharmacologist, Open Scientist, Self Publisher.” As of this weekend, he can now describe himself as the most successful crowdfunding researcher to date. His project Crowdsourcing Discovery, looking at how amphetamines really work was succesfully funded on Rockethub, to the tune of $25,000.
Today marks the culmination of a good few months listening to what users were saying and acting upon it. We have just rolled out our new ‘My Data’ section. This is the part of figshare that allows you to manage your research outputs. As well as being more more intuitive and simple to manage your research data both publicly and privately in the cloud. There are also a few new features to help make the free service as useful as possible.
What is SpotOn London?
SpotOn London (formally Science Online London) is the annual, flagship SpotOn conference. This year, it took place on Sunday 11th and Monday 12th November at the Wellcome Collection Conference Centre. The programme is available here and more details about the event can be found here.
Today see’s figshare metrics become available on the altmetrics (alternative metrics) gathering platform Impact Story. Through our API, figshare exposes the metrics on the publicly available research outputs. This includes, downloads, shares and views of each object. Altmetrics are becoming increasingly important as researchers, academic institutions and funders look for new ways to track the impact of research outputs in a real-time manner. Previous attempts which have pinned all hope on the (questionable) impact factor gives a lag time thought to be over 2 years. There has already been some evidence that altmetrics can be a leading indicator of citation counts.
By Graham Steel
November 1st 2012 sees the launch of yet another significant milestone for Open Access in the form of Europe PubMed Central (PMC). Please see this announcement on the Europe PMC blog. Details of Europe PMC were announced on July 13th 2012 by the European Research Council. This is a continuation of the transition of PubMed morphing from an Abstract only database of life sciences and biomedical research literature into a full text database. PubMed itself launched in January 1996.
“The Open Science Summit unites researchers, life science industry professionals, students, patients and other stakeholders to discuss the future of collaborative science and innovation.
Today see’s the release and subsequent integration with figshare, of ORCID (Open Researcher and Contributor ID), where researchers can distinguish themselves by creating a unique personal identifier.
Accurate identification of researchers and their work is growing in importance as researchers look to get credit for all of their research and track their ever-growing volume and diversity of academic outputs.
Victor Henning is a co-founder and Chief Executive of Mendeley. Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.
A data management plan is a formal document that outlines how you will handle your data both during your research, and after the project is completed. The goal of a data management plan is to consider the many aspects of data management, metadata generation, data preservation, and analysis before the project begins; this ensures that data are well-managed in the present, and prepared for preservation in the future.
Many funding agencies, including the National Science Foundation (NSF), the National Institutes of Health (NIH), and the National Endowment for the Humanities (NEH), require a data management plan (DMP) as a component of grant applications. This requirement encourages researchers to consider in greater detail how their data will be preserved and shared.
A most interesting announcement came out today from our good friends over at ReadCube. For a quick overview of ReadCube, check out this page and video on their website. A Press Release about today’s announcement can be found here.
Also worth a look at is this short video which takes you through in basic terms what today’s announcement means in practical terms.
figshare has been in attendance at a plethora of conferences recently and so we'd like to give you a round-up of all things that seem to be going on in the world of open science, open access, open data and open research. In the last month, we have been represented at the following:
VIVO 2012: Revaluing Science in the Digital Age - Was attended by Scholars, scientists, researchers, developers, publishers, funding agencies, research officers, students, institutional officials and those supporting the development of team science.
After some very successful private beta testing, figshare is happy to announce the public beta release of our API. A big part of figshare’s goal is to allow the simple distribution of research outputs and the ability to build on top of the research in an efficient manner.
This is what the API is for. You can push data to figshare, or pull data out. This first version is a basic implementation that allows you to manage your figshare account or build applications on top of the figshare platform and public research. We will continue to develop the API and add new cool stuff like resumable uploads and more advanced search filters.
So, just what is the Patients Participate! project, how did it come about, and where is it going?
The project was commissioned by JISC in 2011 and “...carried out by the Association of Medical Research Charities, the British Library and UKOLN, Patients Participate! asked patients, the public, medical research charities and the research community, ‘How can we work together in making sense of scientific literature, to truly open up research findings for everyone who is interested?’ The answer came from patients who explained that they want easy-to-understand, evidence-based information relating to biomedical and health research.
Every day people are bombarded by health news, advice columns, medical websites and health products and making sense of this information can be difficult. Tracey Brown, Director of Sense about Science says, ’We have been working with scientists and the public for some years to challenge misinformation, whether about the age of the earth, the causes of cancer, wifi radiation or homeopathy for malaria’ ". SOURCE
Jan Velterop is a science publisher. Since the mid 1970’s, Jan has worked for Elsevier, Academic Press, Nature Publishing Group, BioMed Central and Springer. He left Springer in 2008 to work on applying semantics in science literature and since January 2009 he is also involved in the Concept Web Alliance as one of the initiators.
figshare is happy to announce our involvement with the Reproducibility Initiative in collaboration with Science Exchange and PLOS. The Reproducibility Initiative is a new program to help scientists, institutions and funding agencies validate their critical research findings.
“In the last year, problems in reproducing academic research have drawn a lot of public attention, particularly in the context of translating research into medical advances. Recent studies indicate that up to 70% of research from academic labs cannot be reproduced, representing an enormous waste of money and effort," said Dr. Elizabeth Iorns, Science Exchange’s co-founder and CEO. “In my experience as a researcher, I found that the problem lay primarily in the lack of incentives and opportunities for validation - the Reproducibility Initiative directly tackles these missing pieces."
Here at figshare, we appreciate that the name can sometime be misleading. It literally means the sharing of figures, nothing to do with the fruit. Last weekend at scifoo, this topic of conversation came up with Michael Nielsen, who wondered if people may just think that we host static images.
We believe the future of academic publishing involves the raw outputs of the research, whether that is a video, dataset, pdf or any other file type you can think of. In this sense the ‘figure’ represents a unit of research, which bring us to the next question we get asked a lot:
An interesting paper was picked up this week by major news outlets such as the New York Times. The article focussed on a paper in cell called "A Whole-Cell Computational Model Predicts Phenotype from Genotype". This paper describes how Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism.
"The scientists and other experts said the work was a giant step toward developing computerized laboratories that could carry out many thousands of experiments much faster than is possible now, helping scientists penetrate the mysteries of diseases like cancer and Alzheimer’s."
This week saw the government unveil plans to make publicly funded scientific research immediately available for anyone to read for free by 2014, “in the most radical shakeup of academic publishing since the invention of the internet.” Open Access has been the driving force behind some big changes in the academic publishing world.
Last week we announced that figshare would be partnering with F1000 research to bring integrated research articles with the appropriate associated data files. The first articles have gone live on the F1000 Research site today and illustrate how the future of scholarly publishing is changing and how figshare is offering the tools to help publishers move forward to accommodate these changes.
One of the articles published today contains over 10GB of raw data files within the article, freely available to anybody to peruse in the browser and download should they wish. One of the widgets contains 1474 files. This is what science looks like now, it is not 6 static images in a pdf. As research outputs grow in size and number, academic publishers need to adapt in order to transform the research outputs so that they can be disseminated in this traditional manner.
We are happy to announce our latest partnership with F1000’s innovative new journal F1000 Research. figshare will host the results in whatever format the author decides is most appropriate. This is translated back into the academic article on the F1000 Research site through an embeddable widget. The widgets will display the research object as the author intended, be it video, sets of images, spreadsheet data or any other file type.
By partnering with figshare, F1000 Research can host large volumes of content and display them in the web based journal in a manner that has not previously been explored. The author centric set-up of figshare which focuses on smaller publishing units also allows researchers to cite individual research objects within a article.
Lab webpages are often relatively dry affairs, which is why it is so refreshing to see a researcher at Princeton being innovative with the way they translate their research. Rather than being a static list of publications, Ethan Perlstein has built a dynamic and interactive lab web page built on top of the APIs of some of the best research tools for academics.
By Graham Steel
As far as I am aware, until a few weeks ago, there had only been one public debate about Open Access (OA) in the UK, which took place in late February this year. There's a great blog post about over at F1000 Research. The event was live tweeted and shortly afterwards, a video of the event appeared here at University of Oxford.
"identify the principles, opportunities, and problems of sharing and disclosing scientific information and asks how scientific information should be managed to support innovative and productive research that reflects public values."
You can add your profile badges to blogs, e-mails and websites as a quick and easy way to let people know who you are and what you do. There are several different designs and you can share your automatically updating real-time metrics on your research objects on figshare as you go.
As of today, all figshare content will have it's own DOI. Research objects need to be citable in order to be usable. DOI stands for 'Digital Object Identifier'. DOI links work wherever they appear on the world-wide web. As defined by the International DOI Foundation:
'A DOI provides a means of persistently identifying a piece of intellectual property on a digital network and associating it with related current data in a structured extensible way'
Today is officially Open Access Monday or #OAMonday. This is because a petition set up by John Wilbanks, Heather Joseph, Mike Carroll, and Mike Rossner requiring 'free access over the internet to scientific journal articles arising from taxpayer-funded research' has passed the required number of signatures in order to ascertain a US governmental response.
Peter Murray-Rust has been quoting Churchill in reference to the fact that we appear to be at a tipping point with open access: "this is not the end. This is not even the beginning of the end. But it is perhaps, the end of the beginning." At the RSP event last week 'New Developments in Open Access', Alma Swan quoted Ghandi in a similar manner, "First they ignore you, then they laugh at you, then they fight you, then you win." It appears the inevitability of open access is unstoppable now, a point emphasised further by David Willetts recent announcement that the UK would be making all publicly funded research openly available to all.
Here at figshare, we want to help you raise your profile. Researchers are generally transient beings, moving labs, countries and in and out of industry and other spaces. This can be problematic, especially in terms of maintaining an up to date profile and web presence. I experienced this first hand upon completing my PhD. My university profile page, which for years was what you would find when you googled me, disappeared.
When choosing a lab to work in, what do you look for? Personally I looked for an interesting project, at a well respected institution with a well respected PI.
Here at figshare, we are constantly trying to get across a point about the reusability of research data. Researchers are often under the impression that some of the research that they generate will not be useful for others if it isn't immediately relevant to them.
Last week, another great example of how this isn't the case was presented in the popular magazine io9. io9 is a daily publication that covers science, science fiction, and the future. The story we are referencing has a controversial title, "Everything you need to know about the scientific controversy that could change Triceratops forever", but it is based upon real research, some of which is openly available on figshare.
Following the news that the UK government will be requiring all research to be made available through open access, US researchers are hoping for a similar response from their government via a petition. The Whitehouse makes a formal response to these "We the People" petitions if they reach 25k signatures within 30 days.
This petition, organized by new PLoS advocacy director, Cameron Neylon is detailed below:
TL;DR - Message to David Willetts and the UK government is this. Well done on such a positive move, please don't mess this up. You don't need to reinvent the wheel and you do need to mandate licensing at least as un-restrictive as CC-BY.
It is a proud day to be British, for good intentions at least! UK minister of state for universities and science David Willetts announced on Tuesday in a piece in the Guardian that the UK would be making all publicly funded research openly available to all: "Giving people the right to roam freely over publicly funded research will usher in a new era of academic discovery and collaboration, and will put the U.K. at the forefront of open research".
At figshare, one of the things we are looking to create, is a place where as much research data as possible can be visualised in the browser, regardless of the file format. It is often the case with traditional publishers, that you can only upload your research in a strict number of formats.
This is something that figshare aims to fix. To this end, this week we updated the platform with a range of updates focussed around visualising data. Increasingly research is being produced in new formats which traditional publishers do not support.
figshare and the CLOCKSS Archive have partnered to preserve figshare's publically available content in CLOCKSS's geographically and geopolitically distributed network of redundant archive nodes, located at 12 major research libraries around the world. This action provides for content to be freely available to everyone after a "trigger event" and ensures an author's work will be maximally accessible and useful over time.
For those who don't know about them, a preprint is a draft of a scientific paper that has not yet been published in a peer-reviewed scientific journal. Nature Precedings was an open access electronic preprint repository of scholarly work in the fields of biomedical sciences, chemistry, and earth sciences that released the following statement on their homepage this week:
"As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all."
Until recently, we were unaware of iEvoBio, a forum bringing together biologists working in evolution, systematics, and biodiversity, with software developers, and mathematicians.
However an innovative competition called Synthesizing Phylogenies drew our gaze. The competition is being run in collaboration with it's sister meeting Evolution 2012. The principles behind the contest are explained here:
figshare was recently featured in a nature materials paper that all researchers should see. The paper provides a list of useful tools for researchers to use in order to make the best use of their time and get credit for all of their hard work.
"Strong competition and funding squeezes require scientists to look for ways to increase their profile and impact within and beyond the scientific community. Online tools and services can help them communicate and publicize their research more effectively."
As with so much of scholarly communication these days, an interesting conversation has played out on twitter this week. It all started with a fantastic idea for authors to retain copyright from Prof. Lorena A. Barba, a professor in Mechanical Engineering at Boston University.
Idea: upload figures to @figshare under CC-BY and add citation to my own figures in my own paper before submitting so journal can't own them— Lorena Barba (@LorenaABarba) March 14, 2012
Guest post by figshare user Ross Mounce. Ross is a PhD student at the University of Bath, and Systematics Association council member. His research is on the importance of fossils in phylogeny. In the course of this work he often encounters unnecessary barriers to research: lack of data sharing, lack of online data availability, and lack of data in usable digital formats. Thus he regularly campaigns for scholarly reform, particularly with regard to the provision of Open Data for science.
As we have previously noted, traditional journals often have limits on the number of files that you can put into the paper, even as supplemental information.The use of figshare to break open the restraints of current traditional publishing models has been demonstrated this week in a publication in PLoS ONE:
Roberts SB, Hauser L, Seeb LW, Seeb JE (2012) Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing. PLoS ONE 7(2): e30908. doi:10.1371/journal.pone.0030908
Researchers are finding more and more innovative ways to share their research on figshare. It's always fascinating to see users come up with ideas that hadn't yet crossed our minds. An example of one occasion when this happened was at Science Online in January, where Antony Williams of ChemSpider, fed up of not having access to his own publications stated that in future, he would upload a copy to figshare so he'd always have access.
I was reminded of this when I saw some uploads by Jan Halborg Jenson. He has uploaded his funded grant applications, and has described his reasoning for doing so in a blog post on the 'Proteins and Wave Functions' blog.
figshare is in San Francisco this week for the Strata conference. If you are going to be at the conference, or if you are San Francisco based and would like us to come and present thoughts on figshare and open science at your lab meeting or journal club, let us know at email@example.com or via twitter, facebook or google+.
By creating an environment where users can make all of their research objects available in a citable, sharable and discoverable manner, figshare is offering a form of publication and dissemination of your research. Openness on data has another important aspect: the fight against scientific fraud. For this reason we have become a member of 'The Committee of Publication Ethics' - COPE, in order to adhere to the best guidelines for research publication and dissemination.
Have you ever found yourself limited by the constraints of a journal? Traditional journals often have limits on the number of files that you can put into the paper, even as supplemental information. We now have the technology to easily make all of the supporting information available, and yet are limited by journal restrictions. The examples below show limits both in terms of number and physical size:
A recent report from the Committee of Economic Development called "The Future of Taxpayer-Funded Research: Who Will Control Access to the Results?" details the importance of getting research out to the masses quickly:
"For researchers, developments that increase the speed and breadth of dissemination of cutting-edge research accelerate their own research production."
Following on from Science Online 2012, I made my way to New York to join Science Online NYC, or #sonyc. The monthly meet-up is set at Rockefeller University and organised by Lou Woodley (Nature) Jeanne Garbarino (Science 3.0) and John Timmer (ARS Technica). John summed up the discussion in the following way:
"Scientific papers are still the primary way of getting information on research out to the rest of the scientific community. But they also tend to generate lots of data-negative or confusing results-that will never make it into a paper. And there are many other ways that researchers can contribute to their field that don't fit neatly into papers, like making a new tool or building a database."
The launch of the new figshare site recently was immediately swamped by the chaos that is the Science Online conference in North Carolina. The conference, which also goes by the name #scio12 is one of the most interesting and best organised of all conferences I have been to.
"Artwork at Open Notebook Science session, by Kwinkunks"
Sorry, we couldn't resist the title, but we also realise the irony given the general failure of the attempts to build a "facebook for Scientists". But scientists dont necessarily need a facebook, they have facebook. So why would scientists need a YouTube?
Today see's the launch of new figshare site, built completely from scratch with the needs of researchers always coming first. This is a new clean site to be developed with new features and improved functionality in the coming months.
The support from Digital Science has enabled figshare to grow from a proof of concept idea into a real solution for researchers looking to get credit for all of their work. As the UK government commits to transparency and open access to publicly funded data, figshare will continue to allign itself to the best interests of the researchers whilst also nudging users towards the benefits for both themselves and the scientific community of publishing all of their research outputs.
This is cross-posted on the DCC blog here, by Kirsty Pitkin.
FigShare will be at the IDCC Conference in Bristol, December 5th-7thth 2011. Please come and say hi.
In the third of our preview posts, Mark Hahnel from FigShare, Digital Science, gives us his perspectives on the issues we hope to address during the rapidly approaching 7th International Digital Curation Conference...
It is with great pleasure that I can announce that the FigShare is collaborating with Digital Science. Digital Science provides software and information to support researchers and research administrators in their everyday work, with the ultimate aim of making science more productive through the use of technology.
As part of this agreement, FigShare remains an open independent organisation and is in no part owned by Digital Science. The support from Digital Science will help FigShare develop and expand on it's current range of features in order to help scientist manage their data in an easily searchable, sharable and citable manner.