Posts Tagged 'lab notebook'

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.

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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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