Features

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To lookup an article using a document object identifier, there’s a cheap and cheerful way to do it based upon the work we did earlier to add access to pubget.

Without it, you can always resolve a DOI. Here’s a simplest example: Let’s say the DOI is 10.1021/ac7018574. This is an article by Cameron Neyland. If you want to redirect t the document, you can use an open DOI like this:

http://dx.doi.org/10.1021/ac7018574

You can therefore represent a DOI  in OpenWetWare like this:

[http://dx.doi.org/10.1021/ac7018574 doi:10.1021/ac7018574]

That would display the string, doi:10.1021/ac7018574. Clicking on the link would bring you to the paper. This won’t provide any information about the document. Clicking on it will redirect your browser to the paper.

In addition to PubMed lookup, Pubget also includes a DOI resolver. You can access it via an RSS feed within OpenWetWare.

I’ve added a page including a set of examples and instructions to OpenWetWare to illustrate how this can be done as well as how the previous examples. You can look at the list of examples (and, please, add more!) here:

http://openwetware.org/wiki/OpenWetWare:Information_management/Pubget#DOI_Lookup

The result is that the title of the doc and a link to allow you to read the document are displayed. There’s currently no way to format these string directly but it’s coming. Look at the page to see an example. I’ll simplify this to allow an even shorter syntax to display it.

Just as pubget uses information about a university to determine what periodicals you have access to, the DOI system uses a ‘resolver’ to map a DOI into a reference to the periodical and the document described.

Biblio, the reference/citation extension in OpenWetWare currently does not support DOI’s. There is limited support for importing the metadata such as periodical, edition, authors, and even title, to do this withougt a bit of hacking. Let me know if anyone is interested in seeing this support added.

If anyone has questions about the use of a feature like this, please let me know. As I mentioned, don’t hold back on adding examples to the page in OWW.

Thanks.

My life at OWW has been an endless stream of messages articulating Austin’s far-too-old feature and technology suggestions that I slowly get around to adding. The “flash” (of insight) to “bang” (of getting the idea online) is not great; I would hope the time will diminish eventually. But for now, this is what it is!

The latest is a big one. That would make it a “big bang”. So maybe a better way of saying it would be a “marginal thud” to a “moderate drop”. I’ve started the process of adding support to OWW for Javascript Gadgets. This is a centrally managed method of deploying ‘sanctioned’ Javascript that then can be enabled or disabled by every user. This extension is already in use on various WikiMedia servers; we are long overdue.

What it means is that there are scores of ways people more javascript-savvy than me have created small extensions to MediaWiki that do all sorts of useful things. The ‘quick-nav’ item on the sidebar, written by Austin, as an example, could be included in this general category. I created an extension to enable it for everyone since it is so useful to anyone who has ever forgotten the last 15 pages he/she visited.

I’ll provide a full list of these extensions when I’ve completed the import of them.

Once we have access to all of them, I would imagine that a set of much more research- and life science-specific entries would be useful. Since the Venn diagram representing “biologists”, “OWW users and viewers”, and “Javascript hackers” may be initially limited to Austin, it may be a while before we have many OWW-specific extensions available.

Personally, I think we should all do our best to start keeping him company.

If there’s something you have to do over- and over- again in OWW to do your work, consider using the discussion area I’ll add in order to get the ideas flowing.

Expect the first set of Gadgets, with instructions, to be available this week.

If anyone wants to volunteer to help out with testing Gadgets prior to our including them in the central library, please let me know. We’re not limiting inclusion of Gadgets because we want to suppress open science, by the way. It’s just that in programming, anything that can fail, will. I just don’t want an infinite number of new lab notebook pages to be created just because someone wanted to automate his or her own task and didn’t test!

Here’s a link for more information on MediaWiki Gadgets:

wikimedia.org: Gadgets

By the way. Don’t confuse Gadgets with Widgets. We may add Widgets as well. Unlike Gadgets, once enabled, Widgets can be added by anyone to any of their pages. Where Gadgets are more related to creating content and using OWW, Widgets will be useful for extending OWW to interact with external data.

Thanks.
Bill

PS: Thanks again, AC.

Some have said that an image is worth a thousand words, or at least a dozen or two data points. Taking measurements is a given in any lab, working in any field of science.

Therefore, we have set up an extension on OWW that allows one to easily generate some simple line, bar or pie charts by simply introducing some wiki code and comma separated values.

The charts are generated automatically via the Google Charts API and therefore any changes made to the values within the wiki code values, will generate a new chart, on-the-fly.

We have set up a page with some very simple examples on how to produce such charts. There is more info at the official extension’s page at Google Code.

If you happen to be looking for something more complex that can handle not only data points but also equations, then you are looking for another feature we also support via gnuplot. You can find more info on this feature/extension here.

wikisym2008Coming up next week is WikiSym 2008, the 4th International Symposium on Wikis, taking place in Porto, Portugal.

OpenWetWare will be presenting a poster and also a demo of how we use MediaWiki software to produce an environment that enables collaboration and sharing of scientific information among life science researchers.

So, what exactly is WikiSym?

WikiSym is the foremost conference devoted to using, developing and researching wikis. In our fourth year, only WikiSym brings together organisations that use wikis to meet face to face with leading and emerging vendors, active researchers and leading wiki consultants.

WikiSym 2008 explores and extends our thriving wiki community, building on the past 4 years to again bring together researchers, practitioners, and technical writers to gather, discuss, share best practices and develop knowledge .

For more details on the OWW poster/demo please visit “our” page on the wiksym2008 wiki.

As many of you may have noticed, we’ve been adding a few new features to OWW’s side bar over the last few days. Among them you’ll find the quick nav, the feedback box and invite box.

Let me go over some of these new features so that you can take full advantage of them. Keep in mind that some of these features are only available for OWW community members. If you are not yet an OWW member, feel free to join us.

Quick NavThe Quick Nav
The quick nav is a cool dropdown select menu that displays your last 15 or so moves around OWW. This comes in handy when you are bouncing between pages. Just click and you’re there.

Bookmarking linksBookmarking tools
We’ve added a few little icons that link to bookmarking tools like Connotea, CiteULike and del.icio.us. This will allow you to quickly save the revision of the page you’re currently looking at with all the relevant content required by these bookmarking services.

Feedback is goodThe Feedback box
As a way to further interact with our visitors and community, we’ve set up a quick feedback box that allows anyone to let us know their opinion regarding a specific question we happen to display within that box. It’s just a matter of typing in your short comment and click! It’s that simple.

 

Invite a researcherInvite a friend
We are always interested in having new and interesting people join OpenWetWare. Therefore, we’ve set up a quick invite box that allows current OWW community members to invite their friends/colleagues to join.

We are cooking up the next batch of cool features… Do you have any ideas or suggestions for features you’d like to see developed/implemented on OWW? Let us know!

LaTeX logoIn the May/June issue of the Mathematics Association of America‘s news magazine MAA Focus, you’ll find an article titled “Student Collaboration using a LaTeX wiki” [pdf].

The article demonstrates the usefulness of the LaTeX extension for MediaWiki by enabling this great syntax to be used online in a collaborative environment such as a wiki.

It just happens that the LaTeX extension referenced in the article was written by Austin Che, a member of OpenWetWare’s steering committee. Which means that we’ve had a LaTeX enabled wiki for quite a while now :)

If you don’t know what LaTeX is, I’d first suggest a read at Wikipedia’s LaTeX page.

If you’ve got a grasp of what LaTeX is, I’d recommend you head over to OWW’s LaTeX page where you’ll find information on the advantages and disadvantages, software for writing LaTeX, PhD thesis LaTeX templates and more…

Jonathan over at Working the bench has just recently posted about how impressed he is by OpenWetWare and the available protocols:

It takes a little digging, but the website is really sweet simply because it gives you the feel that, for any given protocol, you are looking at something that works. It’s been tested, validated, and in many cases even commented on and modified by any number of additional people.

Jonathan makes a good point here where he mentions that you are looking at something that has been tested, validated and in many times worked on collaboratively by a group of OWW members.

What Jonathan doesn’t mention is that although OWW is a great resource for protocols, there are other great features like the materials section, indexed reference sources and above all, a large community of researchers from all over the world.