Moderator Ed Hovy picked out 6 quotes to summarize Beyond the PDF’s sessions on Annotation.
Papers are stories that persuade with data.
But as authors we are lazy and undisciplined.
Communicating between humans and humans and humans and machines.
I should be interested in ontologies, but I just can’t work up the enthusiasm.
Christmas tree of hyperlinks.
You will get sued.
Tags: Beyond the PDF, beyondthePDF, quotes
Posted in future of publishing, information ecosystem | Comments (1)
Nicole Henning suggests that academic libraries and scholarly presses work together to create the ultimate mobile app for scholarly ereading. I think about the requirements a bit differently, in terms of the functional requirements.
The main functions are obtaining materials, reading them, organizing them, keeping them, and sharing them.
For obtaining materials, the key new requirement is to simplify authentication: handle campus authentication systems and personal subscriptions. Multiple credentialed identities should be supported. A secondary consideration is that RSS feeds (e.g. for journal tables of contents) should be supported.
For reading materials, the key requirement is to support multiple formats in the same application. I don’t know of a web app or mobile app that supports PDF, EPUB, and HTML. Reading interfaces matter: look to Stanza and Ibis Reader for best-in-class examples.
For organizing materials, the key is synergy between the user’s data and existing data. Allow tags, folders, and multiple collections. But also leverage existing publisher and library metadata. Keep it flexible, allowing the user to modify metadata for personal use (e.g. for consistency or personal terminology) and to optionally submit corrections.
For keeping materials, import, export, and sync content from the user’s chosen cloud-based storage and WebDAV servers. No other device (e.g. laptop or desktop) should be needed.
For sharing materials, support lightweight micropublishing on social networks and email; networks should be extensible and user-customizable. Sync to or integrate with citation managers and social cataloging/reading list management systems.
Regardless of the ultimate system, I’d stress that device independence is important, meaning that an HTML5 website would probably the place to start: look to Ibis Reader as a model.
Tags: beyondthePDF, mobile, scholarly publishing
Posted in books and reading, future of publishing, information ecosystem, library and information science, scholarly communication | Comments (5)
Springer’s LaTeX search service (example results) allow searching for LaTeX strings or finding the LaTeX equations in an article. Since LaTeX is used to markup equations in many scientific publications this could be an interesting way to find related work or view an equation-centric summary of a paper.
You can provide a LaTeX string, and Springer says that besides exact matches they can return similar LaTeX strings:
Or, you can search by DOI or title to get all the equations in a given publication:
Under each equation in the search results you can click “show LaTeX code”:
Right now it just searches Springer’s publications; Springer would like to add open access databases and preprint servers. Coverage even in Springer journals seems spotty: I couldn’t find two particular discrete math articles papers, so I’ve written Springer for clarification. As far as I can tell, there’s no way to get from SpringerLink to this LaTeX search yet: it’s a shame, because “show all equations in this article” would be useful, even with the proviso that only LaTeX equations were shown.
A nice touch is their sandbox where you can test LaTeX code, with a LaTeX dictionary conveniently below.
via Eric Hellman
Tags: beyondthePDF, LaTeX, markup search, Springer, structured search
Posted in future of publishing, information ecosystem, library and information science, math, scholarly communication | Comments (1)
What if you could rerun computational experiments from within a scientific paper?
The GenePattern add-on for Word for Windows integrates reusable genomic experiment pipelines into Microsoft Word. Readers can rerun the original or modified experiments from within the document by connecting to a GenePattern server.
Rerunning a pipeline inside Word
I don’t run Windows, so I took this screenshot from a video produced at the Broad Institute of MIT and Harvard, where GenePattern is developed.
Readers without Word for Windows can also access the experimental pipelines by exporting them from the document: just run a GenePatternDocumentExtractor command from a GenePattern server. The GenePattern public server was very easy to access and start using. Here’s what the GenePatternDocumentExtractor command looks like:
Running GenePatternDocumentExtractor at the GenePattern public server
Unfortunately the jobs I ran didn’t extract any pipelines from the Institute’s sample DOC. I’ve sent in an inquiry (either I’m doing something wrong or there’s a bug, either way it’s useful). I was very impressed that I could make my jobs public, then refer to them by URL in my email, to make clear what exactly I did.
The GenePattern add-on for Word is another find from the beyondthepdf list. Its development was funded by Microsoft. See also Accessible Reproducible Research by Jill P. Mesirov (Science, 327:415, 2010). doi:10.1126/science.1179653, which describes the underlying philosophy: have a Reproducible Research System (RRS) made up of an environment for doing computational work (the Reproducible Research Environment or RRE) and an authoring environment (the Reproducible Research Publisher or RRP) which links back to the research system.
Tags: beyondthePDF, GenePattern, Microsoft Word, Reproducible Research Environment, Reproducible Research Publisher, Reproducible Research System, Word for Windows
Posted in books and reading, future of publishing, information ecosystem, scholarly communication, Uncategorized | Comments (1)