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LabArchives to Sponsor BioMed Central’s Open Data Award for 2012

For the second consecutive year, LabArchives is pleased  to be the proud sponsor of BioMed Central’s Open Data Award.  This award recognizes researchers who have published in BioMed Central journals and have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data during 2012.  Earl Beutler, the President and CEO of LabArchives, LLC, will be a member of the judging committee, along with  prominent members of the Open BMC_Research_AwardsScience and Open Data community, which includes John Wilbanks, Peter Murray-Rust, Rufus Pollock, and Cameron Neylon.

psandercock2Last year’s winner of the Open Data Award, Peter AG Sandercock, University of Edinburgh, for The International Stroke Trial database Trials 2011, 12:101 (21 April 2011) says, “I was delighted to win the Open Data Award.  It sends a very positive signal to the clinical trials community that making full data sets publicly available is possible and brings benefits to the trialists.  The IST data, which was posted online has already been used for two further projects.  One is related to what happens to people who first become aware of their stroke symptoms when they wake from overnight sleep.  This was analysis undertaken by a group of researchers in the USA.  They presented the findings at a meeting of the American Stroke Association in 2012, and are now writing it up for a full publication.  Two other groups, one in Nottingham and one in Edinburgh, have used the data to try and work out better ways of using blood thinning drugs in people within the first hours of onset of stroke symptoms.  This demonstrates the value of even quite ‘old’ data to the scientific community – the IST study was published 15 years ago in 1997!.”

There’s just under two weeks left to put your nominations in for BioMed Central’s 7th Annual Research Awards, including the Open Data Award. This award recognizes researchers who have published in BioMed Central journals and have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data during 2012. Nominations close on January 31st 2013.

As part of its partnership with BioMed Central, LabArchives provides a special complimentary version of LabArchives to authors of BMC journal articles.  The BMC Edition provides added storage as well as templates for submission of papers to BioMed Central.  In addition, LabArchives subscribers can assign Digital Object Identifiers (DOI’s) to data sets in their Notebooks that can be linked to articles as supplemental data.

We look forward to participating in the 7th Annual awards!

Widgets – A Major Advancement for LabArchives

We are especially excited about the release of our new LabArchives Widgets which represents a major leap forward for our platform.  Our implementation of “Widgets” expands LabArchives into a completely extensible system, enabling our customers and third parties to create simple (or even sophisticated) tools for the laboratory workflow that can be incorporated into your laboratory notebook.

So…what are Widgets, exactly?  A Widget is a tool developed using HTML and/or Javascript to extend the capabilities of your LabArchives account.  A simple example would be a “template” or “form” that needs to be completed on a repeated basis.  More advanced Widgets could be sophisticated applications.  One of the beauties of Widgets is the fact that they can be created and integrated within LabArchives by anyone with some basic understanding of these technologies.

A Widget can be almost anything, limited only by the needs and the imagination of the developer.  Our team has created a few sample Widgets which are immediately available to all of our customers, including a Periodic Table, a molarity calculator, and a scientific calculator.  Widgets can be used as “floating” tools (i.e. small frames that are available to users within the notebook and are used for reference or calculations), or as “Entries”, in cases where you wish to save the results in your Notebook.  They can be simple forms (for following standard procedures and “filling in the blanks”), or more complicated calculators, as shown below in the molarity calculator:

Molarity Calculator Widget in LabArchives

In addition to developing a number of additional widgets in the near future (including a calendar, a database creator, and a molecular structure editor), we plan to develop a LabArchives store that will enable users and third parties to create and offer Widgets for the entire LabArchives community.

We welcome your suggestions for additional Widgets, and our Customer Support team will be glad to assist you with the creation of your tool(s);  LabArchives development team can also create custom widgets for a nominal fee.

Please log into your LabArchives account and try out this powerful new feature.  As always, we appreciate your comments and feedback!

LabArchives Introduces an iPhone / iPad App

Last week, we introduced our first apps for the iPhone and iPad.  Although (with a minor exception), LabArchives  is fully functional in Safari on these devices, the screen size for the iPhone made it somewhat difficult to navigate and use.

As for all of our software developments, it is the feedback of our customers that drives our priorities.  In speaking to a number of our users, it turns out that many of them were already using iPhones to take photos in the laboratory to document their research.  These included pictures of gels, samples, and even animal colonies.  With our unique “Inbox” feature, these customers were already able to e-mail the photos to their LabArchives Notebooks, but felt it would be more convenient to be able to move them directly.  Thus, the idea for Version 1 of our iOS App was born.

Now available on the Apple iTunes Store, our iPhone and iPad Apps can be quickly installed; for those with a local server, they can be configured in the device Settings menu to use your personal URL.  With this release, users can log in with their normal credentials, choose a Notebook, and then browse through the Notebook Navigator and take photos (or choose from the photo library) and move them into the Page of their choice.  One can also view existing photos in any Notebook.

We are extremely enthusiastic about the new mobile platforms for LabArchives users.  Although most labs have a number of computers, they are often not right at the “point of entry”, so having a tablet or other mobile device that one can carry around is a major benefit to our customers.  We plan for a number of important enhancements over the coming months, and welcome the suggestions of our users.  Years of experience have taught us that it is usually best to get a useful version of an application in the hands of our clients;  having a “starting point” makes it much easier to provide useful feedback, which is how we drive all of our development priorities.

Android users:  don’t worry!  We plan an Android version in the near future.  Microsoft “Surface” users?  Well, there aren’t any of you, yet, since it was just announced this week.  Needless to say, we will be evaluating this platform as well in the near future.

 

LabArchives and the BioMed Central Research Awards

I have just returned from London where, among other things, I was proud to represent LabArchives in presenting the BioMed Central “Open Data Award” that was sponsored by our organization. At the well attended 6th Annual event, BioMed Central’s Research Awards celebrated excellence in scientific research made freely available through open access publishing within their portfolio of over 200 journals and are much like the “Academy Awards” for science.

We are very proud to be sponsoring the Open Data Award this year and are also very excited about our recently announced partnership with BioMed Central.  As you may know, LabArchives offers a web-based solution for the problem of storing, organizing, sharing and publishing scientific data.  Investigators who use LabArchives are able to automatically share data sets with individuals or with the public at large and can easily assign a Digital Object Identifier (DOI) to these data.

BioMed Central authors can obtain a complimentary subscription to LabArchives that enables them to store up to 100 MB of data, a portion or all of which can be published in connection with, or separately from, a journal article.

As the scientific community continues to embrace the concept of open data, it is important that the process of sharing information be as simple and seamless as possible. At LabArchives, we are dedicated to creating easy-to-use and affordable products to bring this important goal to fruition.

The Open Data Award seeks to recognize researchers who have published in BioMed Central journals and have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data. This year we genuinely had the strongest shortlist yet, with excellent nominees from fields as diverse as microbiology, health geographics, rheumatology, clinical medicine, genomics and chemistry.

This  year, the winning paper was “The International Stroke Trial database” by Peter AG Sandercock, Maciej Niewada, Anna Członkowska, the International Stroke Trial Collaborative Group, published in the journal: Trials

Peter Sandercock and colleagues published “The International Stroke Trial database” paper and data set in the journal Trials with the primary purpose of making individual patient data from the International Stroke Trial (IST) available for public use. With more than 19,000 patients this was one of the largest randomized trials ever conducted in acute stroke. The results of the International Stroke Trial were first published in the Lancet in 1997 but the data, which are highly valuable for secondary research, were not publicly available until this article was published, in April 2011.

Sharing and publishing clinical trial data is much needed to improve the reliability and efficiency of health research but remains very uncommon, particularly on such a large scale. Included with the paper was a spreadsheet with the anonymized data from the many patients in the trial. As well as being transparent the authors have been responsible and adhered to available best practice guidelines on protecting anonymity. The paper got the judges’ attention right from the start of and the decision was, remarkably and uniquely for this award, unanimous.

The authors should be commended for their efforts to make such a large amount of data available as data sharing on this scale in clinical medicine shows real leadership. The background care patients received in the nineties is representative of stroke trials currently ongoing in developing countries making the data particularly helpful for planning new trials in these areas – which face a future epidemic of non-communicable diseases such as stroke.

In addition to the well-deserved recognition for their contribution, the authors receive a cash award which we hope will serve as a small token of the appreciation from the publishing and scientific communities, as well as an additional incentive for other scientists to publish important data that may more quickly advance the progress of science in ending disease and improving our understanding of the world around us.

LabArchives is very proud to be participating in these awards, and looks forward to continuing our involvement for many years to come.  I would like to personally thank the members of the BioMed Central team who organized and attended the Awards and created a truly enjoyable evening for me personally as well as everyone in attendance.

LabArchives and BioMed Central: a new platform for publishing scientific data

Note from the Editor:  This guest blog is written by Iain Hrynaszkiewicz, Journal Publisher at BioMed Central

Introduction

One reason that the worldwide web worked was because people reused each other’s content in ways never imagined or achieved by those who created it. The same will be true of open data.
– Tim Berners-Lee and Nigel Shadbolt, The Times, New Year’s Eve 2011

As part of our commitment to reproducible research and transparency, BioMed Central has partnered with LabArchives to work together for the shared goal of making datasets supporting peer-reviewed publications available and permanently linked to online publications – and available under terms which permit reuse freely, as Open Data.

A growing number of repositories for scientific datasets – which with persistent identification can be cited in and linked from published articles – are available but many fields still lack an obvious repository. There has been debate about whether institutional or subject-specific repositories (and journals) are the best solution for data archiving and publishing. But what is absolutely clear is that, for data, one size does not fit all – literally and metaphorically.

When available, data repositories are usually the best place for larger datasets which cannot be included as additional files, and we have been working to increase awareness of repositories of interest to our authors. But some scientists who are willing to share data may, understandably, be reluctant to deposit data in a repository with which they are not familiar, or which cannot guarantee permanence, or perhaps has suboptimal or ambiguous licensing terms.

LabArchives, an Electronic Laboratory Notebook, enables individual scientists to manage, share and publish data files, providing an accessible platform for sharing and publication which is controlled by authors themselves. LabArchives is web-based, or may also be installed on a local server, enabling a user to access their laboratory documents, protocols, notes and data from any location (you can read more about the features of LabAchives on their website).

As part of this partnership, all BioMed Central authors are entitled to an enhanced free version of LabArchives. This ‘BioMed Central Edition’ of the software offers additional storage capacity compared to the standard free edition, integrated manuscript submission to BioMed Central journals, along with important open data publishing features.

Key data publishing features of LabArchives – BioMed Central Edition

Permanence, citation and linking of datasets
In 2011 LabArchives introduced the ability to assign digital object identifiers (DOIs) to datasets stored and shared with the software. DOIs facilitate data citation, discovery and earning of academic credit for data publication, and datasets assigned DOIs through LabArchives will remain available in perpetuity. The DOI system is used by journal and data publishers, such as DataCite members, to ensure online permanence of published articles. DOIs are indexed permanently by the International DOI Foundation and are much more favorable than URLs for permanently linking content online.

DOIs are assigned in LabArchives through the ‘DOI Management’ tab in the software’s share settings (pictured). DOIs should only be assigned in instances in which data are to be permanently shared with the public.

Image

A LabArchives user can choose to share a data set as it exists at the time of publication, or they may enable users to continue to view changes as they are made, while, importantly, maintaining the version which supports a peer-reviewed publication.  So, a DOI can be assigned to data as of the time the article was published and authors or re-users of the data may then continue with their research.

Data which are available for integration and reuse
Datasets published via the LabArchives platform and assigned DOIs are available under a Creative Commons CC0 waiver. CC0 helps dispel legal uncertainties about what a person or machine can do with data – or any other content – they discover on the web. CC0 enables cultural (scholarly) norms of citation to take precedence over legal conditions, such as requirements for attribution, for ensuring scientists receive appropriate credit for their contributions. CC0 furthermore complies with the Panton Principles for Open Data in Science, which hold that for society to gain the full benefits of scientific endeavors, data must be free to reuse, integrate and build upon without legal or other barriers. In short, data published through the LabArchives – BioMed Central Edition are open data.

Anyone publishing data through LabArchives should ensure that CC0 is appropriate for their data and that they are in the position to apply this waiver to the data.

Complimentary additional storage
The enhanced free version of LabArchives has an increased allotment of 100MB of storage (the standard free edition includes 25MB), enabling publication of larger datasets which cannot be published as additional files with journal articles. BioMed Central authors can continue to submit virtually unlimited numbers of additional files to our journals, up to 20Mb per file –  twice as much as some publishers, but in the age of ‘big data’ this can still sometimes be limiting . Users who choose to upgrade to the full version of LabArchives can store up to 100GB of data (see footnotes).

Integrated file viewers
LabArchives includes viewing software for a variety of file types.  This feature enables those who discover your information to be able to see the data, even when stored in certain proprietary formats.  Viewers are currently included for Microsoft Office files, PDFs, and all standard image formats.  The list of viewers is regularly expanded by LabArchives.

View data in context
Readers (and reusers) of data published and shared through LabArchives can view files in context.  LabArchives’ hierarchical file structure enables meaning to be conveyed to the reader through logical organization of data files.

Integrated manuscript submission to BioMed Central journals
Publishing data permanently online – especially when well-labelled, conforming to community standards, and in open file formats – increases potential for data reuse and collaboration. But peer-reviewed journals undoubtedly add value to data, such as detailed methods, context and discussion. For publishers to continue adding value to science communication, to speed publication and reduce barriers to data sharing it’s important to better integrate with scientists’ workflows and tools, upstream of journal submission and publication. The LabArchives – BioMed Central Edition includes integrated manuscript submission to BioMed Central journals. Authors submitting research manuscripts can, directly from LabArchives, choose the most appropriate of any BioMed Central journal, and authors preparing data notes can link directly to BMC Research Notes’ submission system. Our manuscript templates for research and data notes are also incorporated to help speed the process of manuscript preparation.

With transparency comes responsibility
We encourage authors to comply with available field-specific standards for the preparation and recording of data. We recommend authors review the BioSharing website, and a special article series published in BMC Research Notes, for information on best practice in their field for sharing of data, with particular attention to maintaining patient confidentiality.

All journals in the BMC Series including BMC Research Notes now include information about LabArchives’ BioMed Central Edition in their instructions for authors, and the feature will be added to other journals as, when and if the Editors feel it is service that will be valued by their authors. The first articles which describe and link to data hosted in LabArchives are currently undergoing peer review.

As John Wilbanks, Senior Fellow at the Kauffman Foundation and Open Network Biology Editorial Board member said on the BMC Blog in November 2011: “[M]aking data available will serve as a strong attractor for the smartest people in the world to come and begin building things that utterly surprise and shock us.”

We are looking forward to working with our authors and LabArchives to make more data openly available for integration and reuse in 2012 – and beyond.

Footnotes

Use of LabArchives’ software will have no influence on the editorial decision to accept or reject a manuscript, and use of LabArchives or similar data publishing services does not replace preexisting community data deposition requirements set out in individual journals’ instructions for authors.

The full version of LabArchives including 100GB of storage requires payment. BioMed Central does not receive any commission from LabArchives.

BioMed Central remains committed to work with all data repositories which enable linking of data to publications particularly where specific journals and communities endorse them – such as for example the Dryad repository, with which we are working towards submission system integration with BMC Ecology and BMC Evolutionary Biology. More information on data deposition requirements relevant to BioMed Central’s journals can be found on our supporting data resources page.

LabArchives now includes 100 GB of storage for each user

If you’re reading this blog, you are probably familiar with LabArchives and our leading Electronic Laboratory Notebook (ELN).  But we view LabArchives as more than just an ELN.  Our mission is to make it the “hub” of your scientific research through strategic partnerships and integration with leading scientific software and information providers.   Our mission is to allow you to “live” within LabArchives while in the lab, placing all the tools and information that you need at your fingertips (no pun intended).

Each day we move closer to achieving this goal.  We have integrated with leading software providers such as GraphPad Software and FlowJo, and continue to add powerful, yet easy-to-use features that expand the role of LabArchives in the lab.  At the same time, we must overcome objections and concerns of the scientific community that might prevent them from adopting our solution as an electronic lab notebook.  One such objection has been the potential long term cost of storage.  Since LabArchives serves as a permanent repository of all of your research, the amount of data is continuously growing.  And while the cost of storage continues to fall, it will never reach zero.

We recognize that the decision to move to LabArchives is not taken lightly:  It is meant to be a long term partnership with a strong commitment by both parties.  Thus, we reached an important decision to expand the amount of storage provided in a LabArchives subscription by more than an order of magnitude.

As you may know, the original launch of LabArchives in 2010 offered 5 GB of storage per user, which could be shared by all members of the lab.  Thus, a 5 person lab could share 25 GB of storage.  For many this was more than adequate, even for the long term.   For example, one of our customers has been actively using LabArchives for nearly 18 months, and still have only 50 MB of data.  Others, however, have been pushing these limits, and we know there are many who have chosen to remain with paper notebooks due to this concern.

So…we are pleased to announce that effective immediately, all users of the Professional Edition of LabArchives receive 100 GB of storage per user!  So a 10 person lab will actually receive 1 TB included in their subscription.  If you look under Subscription –> Account Information, you will see these new limits have been implemented.

As good partners, LabArchives is prepared to sacrifice immediate profits in order to provide a better, more acceptable service to our customers.  We believe this new policy will make LabArchives far more accessible to the vast majority of scientists throughout the world as it continues to emerge as the worlds leading electronic lab notebook.  Please spread the word to your colleagues!

iOS 5: LabArchives on the iPad

Yesterday, Apple released its long awaited iOS 5 operating system for iPads and iPhones.  This latest edition includes a number of improvements, most significantly (at least for our rapidly growing list of LabArchives  customers), compatibility within Safari for “Rich Text” editing.    This means that effective immediately, you can now enter and edit rich text within your LabArchives Notebooks.

To take advantage of this capability, you will need to upgrade your iPad and/or iPhone systems via iTunes.  Once completed, this feature will automatically be enabled.  As you probably know, LabArchives automatically recognizes when you log in from an iPad or other tablet device.

Here at LabArchives, we are extremely excited about the rapid evolution of tablet devices, which are a nearly ideal device for use in the laboratory.  Unlike a desktop or laptop computer, they can be carried around with you, and are always “at the ready” when you want to record a finding or other bit of information.

Our future plans call for an “app” for both iPad and Android devices, which will provide an even better experience for our users.   However, there is no need to wait…just visit http://mynotebook.labarchives.com and log in.  LabArchives “knows” you are on a tablet and provides an optimized interface for that session.

LabArchives, Electronic Lab Notebooks, and Education

As those of you who follow scientific education are painfully aware, the U.S. has slipped dramatically in the production of capable scientists.  According to Mariette DiChristina, Editor-in-Chief of Scientific American, “American students are now ranked 22nd and 31st among their international peers in science and math, respectively.”   In order to help improve the situation, last May, Scientific American, along with its parent company, Nature Publishing Group, launched a program entitled “1000 Scientists in 1000 Days” which is designed to connect volunteer scientists with K-12 students to advise on curricula, answer a classroom’s questions, or visit a school.

LabArchives, maker of one of the leading and most innovative Electronic Laboratory Notebook (ELN) software, applauds this effort and has also launched a parallel program to help bring improved information technology into laboratory courses taught in both K-12 and undergraduate institutions.  Now called the “LabArchives Student Edition”, our new product includes virtually all the power and features of our Professional Edition at a per student cost that is less than that of a paper notebook.  LabArchives Student Edition has been in Pilot for the fall semester at a number of leading colleges and high schools throughout the US, and we have been enormously gratified by the reception from both the students and instructors.

Not only is LabArchives Student Edition “green”, it improves the experience of the students by being simple to use and accessible from anywhere.  In addition, like our Professional Edition ELN, LabArchives stores every version of every entry that is made into each Notebook.  Not only does this teach the proper application of the scientific method, but it is more fun to use, saves trees, and reduces our carbon footprint.  Perhaps most importantly, the built-in collaborative features of LabArchives enables instructors to more easily review and grade the work performed by the students.  Instead of having to collect 20-100 paper notebooks at various points throughout the term, bring them home, grade and comment, and return to the students, the instructor can, at any time, view the work that is done and make appropriate comments from any computer that is connected to the Internet.  This often enables instructors to provided needed guidance along the way…well before a student has gone astray.

The LabArchives Student Edition Pilot will continue through the 2011-2012 academic year, and we welcome new participants at all levels.  For more information, or to enroll in the program, please contact us at support@labarchives.com

LabArchives is proud to be participating in a nationwide effort to improve the performance of students in science and math, and are devoting significant resources to enhance our leading electronic laboratory software to provide even better functionality for this market.

LabArchives and “doi’s”

LabArchives is especially excited to announce the addition of  doi’s to our flagship product.

But “what is a ‘doi’”, you might ask? And what does that have to do with my laboratory data?

DOI is an acronym for “Digital Object Identifier”.  Most people are familiar with doi’s from reading journal articles, most of which include a Digital Object Identifier.  For journal articles, this is a permanent (or “persistent”) identifier that enables readers to locate the online version of an original article.   You can do so by going to sites such as http://dx.doi.org or http://crossref.org.

The doi system was created and is managed by The International doi Foundation (IDF).  It was born out of the need to establish persistent identifiers for a wide variety of digital information, including publications and data.  Unlike URL’s, which may change, or vanish, a doi is “forever”.  Only select organizations, now including LabArchives, may assign doi’s, which are managed by the IDF.

So…back to LabArchives.  One of the most powerful features of LabArchives is the ability to easily share selected data:  Within the lab, with collaborators, or with the entire world.  This function has always been available through the assignment of a URL;  now, users can assign a “DOI” to any collection of data and make it available in much the same way.

In addition, with our new doi system, a user can choose to share a data set as it exists now, or they may enable users to continue to view changes as they are made.  For example, if you publish a paper and want to make all data related to that paper available, you can assign a doi configured to make it available as of the time the paper was written.  You may then continue with your research, but viewers will not be able to see any new results (until you choose to make them available).

Why is this new feature so important?  Among other reasons, the National Science Foundation (NSF) recently mandated that all NSF funded research must include a plan to share all data after a suitable embargo period.  This can be an odious task:  Scientists must attempt to gather all files, observations, notes, etc. and find a “repository” to which they must then upload all their data.

Not so for LabArchives users;  all (or select) data in any Notebook is ready for sharing.  Simply assign a doi to those data of interest and you are done.

LabArchives Features new Viewer for Office, PDF, and Text

LabArchives is excited to announce the release of a major new capability that greatly enhances the utility of the leading Electronic Lab Notebook (ELN).  While LabArchives has always provided for the ability to store any type of files within Notebooks, the new viewer feature, released over the weekend, now provides the ability to view Office, PDF, and text documents in their entirety without the need to launch any additional software.  Both existing and new documents are automatically compatible with the viewer, so even Notebooks that have been in use for years will immediately benefit from this new feature.

Here is an example of a typical file in the context of a Notebook:

Sample PDF

PDF file shown in the LabArchives viewer

Using the left and right arrows, one can now navigate through the entire document without leaving the Notebook page on which the file appears.

The current version of our viewer works with PDF’s, Microsoft (both 2003 and 2007) Word, Excel, and Powerpoint documents and Text files.  Our plan is to continually add support for additional scientific file types, with the ultimate goal of providing the ability to view a wide range of scientific data without ever leaving the LabArchives Notebook.  As always, we welcome the suggestions of our users for file types that they would like to see supported by our Viewer.

As you may know, last month we released our new LA Docs features, that also enables users to create and edit Office docs directly within their Notebooks.  Combined, these features move us closer to our goal of providing a central “hub” in the laboratory, so that our users may conduct all of their research…including planning, experiments, collaboration, and publishing…all from within the LabArchives platform.  Through features like these, as well as collaboration with other leading vendors of scientific software, including GraphPad Prism and Treestar software’s FlowJo, we are rapidly moving toward achieving our vision.

As always, we welcome your comments and suggestions.  Please comment here, or visit our Support Forum at www.labarchives.com.


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