I read a good quote the other day:

“Bollocks to waiting 10 years for progress. I want people to know about it now, and then do something about it” – Dr Paul Fisher

So why do we wait? Why isn’t there immediate publication, analysis and dissemination of data? Publication of Scientific data as it stands is a broken business model…for the most part. The advent of journals like PLoS and their subsequent success shows that the scientific community is taking note of what steps need to be taken. In my short life as a scientist, there has always been one thing that really annoys me. The inefficiency of scientific publishing and subsequent global sharing of knowledge. In terms of making significant advances available to wide audiences as peer reviewed publications, PLoS has it covered. But what about the rest of your research?

What percentage of the figures that went into your undergrad, masters or doctorate thesis were ever published? The ones that you didnt publish were probably good basic science, or figures that didnt tell a complete story. As a PhD student, I became very aware of the fact that a large amount of my data, although good, would never be published as it did not show significant differences. I then began wondering how many times experiments had been repeated globally unnecessarily. And so FigShare started life as an idea for researchers to publish all of their data that would otherwise never leave their lab books. By categorising and tagging the research, it becomes very searchable and other scientists should not reproduce experiments and waste money when they have been conducted several times by other labs. Following the alpha release, FigShare received a lot of attention and a lot of feedback. This caused the site to develop and it now allows the upload of Figures, Datasets and most recently media (eg. videos).

This is not a new idea, and big data and data sharing projects have won several big JISC grants, but your average researcher needs this to be simple in order to adopt. The CKAN repository is a fantastic project which allows you to upload data from any field, such as government finances, weather forecasts and traffic reports. Where I feel this becomes inaccessible for scientists is the ease of uploads. A choice from 50 licenses for your data is intimidating enough to make most postdocs turn and run. For a project like FigShare, the more research that is uploaded, the more useful the site becomes. In order for this to happen, uploading research needs to be simple. This is what FigShare gives you. Give your bit of research, be it a figure, dataset or some other media format a name, hit upload, add details like your name, some tags and you have a nicely presented, citable, published figure.

FigShare now also serves as a repository for preprints figures. ie. Figures that will one day be published but feedback is requested on the prelimonary data. FigShare can be used as a platform to collaborate where users can contact one another and request to use figures in their publications etc. This means that previous unused figures, maybe from unfinished postdocs or PhD projects can be published, gaining the author more publications.

There is also the ability to easily share your figures, datasets and videos via a host of social media platforms through ‘share buttons’ on every page. This is a new way of bringing scientific research online and to a new audience. An example of how this can benefit science is already producing examples such as this one – A lot of scientists hear how social media can benefit research and yet there has been little evidence of how these tools can be exploited to make science more efficient. Imagine real time discussions about science you did yesterday, not last year when you first submitted your paper.

FigShare is a permanent database of your research. To further ensure this, FigShare is supported by Systems Institute. Systems Institute is a not for profit which is providing ongoing support for the hosting of FigShare as it expands. This also allows FigShare to make backups of all of your data each and every day.

So please, upload your data now and do your bit to help science progress in an efficient manner. It’ll probably do wonders for your academic career too!

I just found this presentation, and thought it’s worth bringing it to the attention of ap.com readers:

Anita de Waard is the director of Disruptive Technologies at Elsevier. A company that has a position with such a name has my sympathy. Looks like publishers are slowly realizing that they can have a huge impact on how science is done, and how fast it moves, if they simply paid more attention to modern trends.

Only habit prevents us researchers from realizing that the media we use the most, a paper article with a review cycle of years, is woefully wrong in this day and age.

A somewhat related idea are the 5 stars of open linked data:

★ make your stuff available on the web (whatever format)

★★ make it available as structured data (e.g. excel instead of image scan of a table)

★★★ non-proprietary format (e.g. csv instead of excel)

★★★★ use URLs to identify things, so that people can point at your stuff

★★★★★ link your data to other people’s data to provide context

If scientists and publishers have opendata in mind (and the trend is there!) doing research becomes more fun immediately (no more mails to the authors asking for data that get no response). Seeing that the academic publishing industry has at least one person (Anita) that gets it makes me feel good. Looks like Elsevier has a head-start.

The first public beta of Paperpile–the latest entry in the crowded arena of free reference management software–has been recently announced. As I write, a test version is available for Linux, but Mac and Windows versions should be released soon. From the screenshots gallery, it looks like Paperpile will feature a streamlined (although quite typical) 3-column interface, support for tags/labels as well as the standard Web import functionality from online bibliographic databases.

It will be interesting to see how this software compares with cross-platform biggies such as Mendeley or established tools for specific environments such as BibDesk or JabRef.

Citation copy-editing is one of those deceptively small burdens that have a way of taking over the working day. If left untended, the task of tidying up casually scribbled references can snowball to crisis proportions as a submission deadline approaches. Similarly, when a submission to one publisher is unsuccessful, significant effort may be required to recast its citations in the format required by another. Collaboration outside of one’s own field can bring with it an unwelcome tangle of fresh style-guide quandaries to ponder and fight through. These are things that the machines, if they want to make themselves useful, should be doing for us.

There is plenty of collective experience in this line, and as fate would have it, there are also plenty of collective solutions. In the TeX/LaTeX world, authors and their editors can today choose between BibTeX and BibLaTeX — both of them excellent utilities — with the several variants of the former supported by no fewer than four separate versions of the BibTeX program. [1] Users of WYSIWYG word processors can look to the bibliographic support built into Word or Open Office, or they can turn to an external solution such as EndNote ™, ProCite ™, Reference Manager ™, or more recently Zotero or Mendeley. Migrating data between these environments is a process fraught with uncertainty, but it is sometimes unavoidable when you need this kind of output, and it can only be produced on that kind of system …

… with so many solutions to choose from, it’s hard to go right. [2]

The citeproc-js citation processor is a Javascript implementation of the Citation Style Language (CSL), an XML schema for describing citation styles that aspires to strike this problem at its root. CSL is a general, open standard that enables fully modular control over bibliographic formatting. This means that CSL is capable of accurately describing styles used in many disciplines, from the sciences, through the humanities to law. It also means that a CSL style description can be used with any other application that understands the CSL language. And it means that the style description is separated to the extent possible from the target document; you can switch styles at any time, even after the writing process is complete. Generality, a comprehensive pooling of community resources, user-centric ease of use: all areas where, collectively, our current menagerie of productivity tools could do better.

CSL first saw wide application in the Zotero project. [3] Citeproc-js has been developed in the first instance for use in Zotero, [4] but it runs as a separate module via a (relatively) simple API, and with appropriate wrappers, it can be deployed pretty much anywhere. Potentially, any application that generates dynamic content — text processors, word processors, weblog environments, and dynamic websites — can use CSL and citeproc-js to provide publisher-correct citation and bibliography facilities without exceptional programming effort. [5]

Development of the CSL language has been spearheaded by Bruce D’Arcus. The citeproc-js processor adheres to version 1.0 of the CSL specification, [6] which has been engineered and documented during the past year primarily by Bruce and Rintze Zelle, with incidental contributions by myself and others. It will debut, together with the new processor, in Zotero 2.1, which should begin to emerge, if all goes well, during this calendar year.

Meanwhile, the processor itself is complete, documented, and more or less ready to go. [7] Here is a short run-down of some of the highlights:

Disambiguation

In author-date citation styles, works by the same author must be distinguished from one another in some way. The current Zotero processor performs name and cite disambiguation as required by the Chicago Manual of Style. There are in fact at least six other disambiguation methods in general use. CSL 1.0 and the new processor will support all of them.

Sorting

The AGU journals, in particular, impose extremely demanding sorting rules in the bibliography. [8] CSL 1.0 and the new processor support multiple sort keys with arbitrary sort order for each key. A wide variety of sorting schemes can be implemented, including the AGU sort.

Parallel citation support

Many legal styles, including the Bluebook style common in American law journals, require that law cases appearing in multiple reporters be cited to each reporter, with the case name in front, and the court and year of decision at the end. [9] The new processor supports this behavior.

On-the-fly document updates

The API of the new processor supports targeted context-sensitive updates of citations in a document that are affected by an insertion, deletion or edit, for efficient transactions with a word-processor or weblog plugin.

Localization of dates

CSL version 0.8 currently supports the use of localized terms for style-supplied labels and the like. CSL 1.0 will add sophisticated localization of dates; both the language of month names and the ordering and formatting of elements will adjust appropriately when the language of a citation style is changed.

Sophisticated names handling

A great deal of work has gone into enhancing the handling of names in CSL 1.0. European conventions on the handling of particles such as “von”, “van”, “di” and the like can be accounted for appropriately both in the sorting and in the rendering of individual names.

In-field formatting

For scientific publishing, the new processor recognizes a limited subset of HTML as markup within titles, enabling superscript, subscript, small capitals, italics, boldface. The processor also implements the flip-flopping of italic and boldface, and of quotation marks, to avoid ambiguity in rendered citations. The HTML used in markup is transformed by the processor into the selected output format (HTML, RTF, LaTeX, or whatever) during rendering.

Multi-lingual citation support

The new processor implements experimental support for multi-lingual citations, providing a flexible mechanism for the transliteration of names and titles, for the supplementary translation of titles, and for the use of alternative sort strings needed for Asian languages.

As it leaves my laptop, citeproc-js is just a bare Javascript module with some test suite wrappers to check that it actually performs as advertised. But with the widening availability and increasing efficiency of Javascript runtime tools, I do hope that it has some prospect of escaping from its cage and wreaking order on the world of bibliography management. If you’re an integrator or site administrator, the fine citeproc-js manual is your first point of reference. If you’re an end user, keep an eye out for the CSL mark, coming soon (maybe) to an application near you!

It was a matter of time before someone wrote a robot that grabbed latex  and returned an image after latex processing. LaTeXy does exactly that and has just increased tenfold the usefulness of wave for academics.