A New #WordPress plugin for #SCIENCE!

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…and other research too.

I have a work­ing first release of a plu­gin to link to research in a ScienceSeeker friendly way in a WordPress blog. It will only work with self-hosted WordPress installs, it will not work on WordPress​.com blogs.

The way it works is you enter the ID(s) of the thing(s) you want to include then, when you save the draft, the web­site pro­duces a format­ted cita­tion that it will auto­mat­ic­ally append to the con­tent of your post. It will also add a META tag to the head of the page. This will give a way to tell sites like alt​met​ric​.com what paper(s) your blog post is about.

Editing in WordPress

Editing Screen. Click to embiggen.

Citation output

The out­put. Click to largify.


It’s primar­ily built to work with DOIs, because that’s what we use most at AoB Blog. You can type in a DOI as 10.1093/aob/mct168 or http://​dx​.doi​.org/​1​0​.​1​0​9​3​/​a​o​b​/​m​c​t​168 and when the site saves it will get bulked out to the longer ver­sion. You can enter more than one entry, so stick­ing 10.1093/aob/mcp121, 10.1093/aob/mcs287, 10.1093/aob/mcq238 should work too.

Once the ref­er­ence is parsed, it appears as a cita­tion. When you have this cita­tion, you can edit it in this box. You might need to do that if the pars­ing breaks. It’s pos­sible some DOIs will give inform­a­tion in a dif­fer­ent way to most. Currently the plu­gin works with stand­ard DOIs and figshare’s DOIs. It’s very pos­sible there are some other sites that have their own stand­ards so, if you find one, let me know.

To clear the ref­er­ences and cita­tions on a post, delete all the ref­er­ences and save. The plu­gin will wipe the cita­tion box.

You can add arXiv ref­er­ences. I’ve set it so you copy and paste a URL from arXiv to the box to give http://​arxiv​.org/​a​b​s​/​1​3​0​6​.​5​148. If there’s demand it should be pos­sible to send any nine char­ac­ter ref­er­ence with a dot in the middle to the arXiv mod­ule. I’ve spot­ted a bug in the arXiv mod­ule put­ting together the screen shotes (look at the author name). I think I’ve fixed this.

It’s not so good for the Social Sciences and Humanities. Here mono­graphs are still import­ant research out­puts, which means ISBNs. These are more of a prob­lem. You enter them as a straight run of ten or thir­teen char­ac­ters. The only place I’ve found giv­ing inform­a­tion from ISBNs in a friendly format is Google Books. But from here I can only get Title, Authors and Publisher. I can­not get Publisher Location from the data.

For DOIs and arXiv papers it’s obvi­ous to link through to the paper. Books tend not to have a recog­nis­able home page. I’ve linked through to Google Books because that’s where the data comes from. But it’s pos­sible that LibraryThing or the Amazons would be bet­ter places to link to.

This sys­tem doesn’t handle book chapters yet, unless they have a DOI. Lying in bed I thought it could be handled as Chapter Authors::Chapter Title::Page Start::Page End::ISBN and any­thing with a double colon gets passed to a book chapter mod­ule for format­ting. I’m not sure if this is use­ful, or if it’s get­ting to stage where typ­ing the ref­er­ence in is more effort than it’s worth.

At the moment the link is on the iden­ti­fier, because that’s the way Research Blogging and ScienceSeeker work. Alan Cann has sug­ges­ted mak­ing the whole ref­er­ence click­able. I’m not sure if this is a good idea or not. It’s a big­ger click­able tar­get, and CSS styl­ing makes the present­a­tion a mat­ter for whoever’s site it is.

The plu­gin doesn’t work for Research Blogging yet. Research Blogging needs ref­er­ences asso­ci­ated with a sub­ject. The first way I’d writ­ten this meant that sub­jects would have to be hard­wired in. Now I think it should be pos­sible to tweak the plu­gin to add Research Blogging top­ics on a post-by-post basis, but not (yet) on a citation-by-citation basis. This would work for most people cit­ing just one paper in Research Blogging posts, but some people cite mul­tiple papers in one post. The way I’m think­ing would label all cita­tions in one post as being the same topic.

Finally, like me, it doesn’t fail grace­fully. I’ve spent quite a while get­ting the damn thing to work. Deliberately break­ing it, so I can make it fail nicely, hasn’t enthused me yet.

You can down­load it from my Dropbox at https://​www​.drop​box​.com/​s​/​k​b​0​w​0​2​j​r​3​4​a​g​r​2​v​/​r​e​s​e​a​r​c​h​l​i​n​k​s​.​zip. You install it by going to your plu­gin menu and upload­ing the zip file. You make sure you upload it to your test site, because this is still beta soft­ware. I think this will be com­pat­ible with the final ver­sion, but I’m not will­ing to guar­an­tee. If you have installed the pre­vi­ous ver­sion, this ver­sion is utterly incom­pat­ible and using the two at the same time will break access to your blog in a very emphatic way. This is why I test on a desktop server.

I’ll be test­ing this shortly, in par­tic­u­lar the way it handles COinS. There may be a simple and eleg­ant way of adding COinS to ref­er­ences, but I don’t know what it is.

Teaching with Social Media

Road building in Nepal
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Road building in Nepal

Road build­ing on the Annapurna cir­cuit, Nepal, surely a path to enlight­en­ment? Photo by rpb1001.

I think I took my PhD at Leicester at almost exactly the right time — if you ignore the cata­strophic down­turn in edu­ca­tion fund­ing. The reason is I’ve had the oppor­tun­ity to work with a few people who have been inspir­ingly innov­at­ive in their teach­ing. Derek Raine intro­duced me to Problem-Based Learning, when he built a new degree in Interdisciplinary Science around it. +A.J. Cann also help by let­ting me help out on some of his numer­acy / study skills courses for Biological Sciences and that’s what he’s blog­ging about today at Of Schemes and Memes and on his own blog at Science of the Invisible.

I’m sure I’ve had plenty of study skills train­ing but I don’t remem­ber much of it. At its worst it was a part of the first year course teach­ing how to use vari­ous sys­tems I might want to use in the third year. By which time the sys­tem might well have changed or else I would have for­got­ten it through lack of use. I don’t do well if I have do some­thing in order to learn how to use a sys­tem. I work bet­ter if I learn how to use a sys­tem in order to do some­thing else.

Alan Cann has a focus on how and why stu­dents want to learn some­thing. To explain the dif­fer­ence, when I was taught I might be shown how to use PubMed. Fill in all the boxes and that’s a pass. In con­trast Alan sets tasks that have a pur­pose and explains PubMed or Web of Knowledge are the easi­est ways to get the inform­a­tion stu­dents need. The cleverest part is that this is wrapped up with social media icing.

Getting cohorts onto Google+ gets them think­ing about pri­vacy, but also makes com­mu­nic­a­tion online a more nat­ural act. Students can build their own sup­port struc­tures. These become more import­ant as the stu­dents move toward inde­pend­ent study later in their degree. Another clever thing work­ing through social media does is it helps dis­solve bar­ri­ers between modules.

In my first degree what I learned in mod­ule A applied to mod­ule A. What I learned in Module B applied to Module B. I wasn’t mak­ing con­nec­tions between the two. On Google+ the work their is for Alan’s mod­ule, but stu­dents dis­cuss more than that. They’ll talk about other mod­ules and make con­nec­tions about why some­thing puzz­ling is hap­pen­ing because we know from this mod­ule that this occurs so when you apply it to that lab exper­i­ment you should expect that and so on.

Another fea­ture is that Alan doesn’t give the same course twice. He’ll drop what thinks doesn’t work and come up with some­thing bet­ter. This shouldn’t be rad­ical. I’ve been on count­less courses as a post-grad that talk about the import­ance of reflec­tion in teach­ing. Usually this reflec­tion in the sense of “how can you bet­ter guide stu­dents along the path to enlight­en­ment?” Alan and Derek have both taken the approach that ques­tions if the path is right in the first place. Even if it’s basic­ally sound, do we need all these wig­gly detours to des­tin­a­tions no one vis­its anymore?

This post is a good entry point to some of what Alan is doing with teach­ing. Science of the Invisible is the place to go if you want to read more.

Photo: Road build­ing on the Annapurna cir­cuit, Nepal by rpb1001. Licenced under a Creative Commons BY-NC licence.

This post also appears on Google+.

Snapseed review

The same Greenhouse at Kew after Snapseed
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I’ve had a quick play with Snapseed for Mac. Below is a neut­ral photo of a green­house at Kew expor­ted from Aperture, and one after a couple of minutes of editing.

Greenhouse at Kew, neutral version

Greenhouse at Kew, neut­ral version.

Snapseed works with a mod­i­fied form of Nik’s UPoint inter­face. You can make global changes, but on some fea­tures you can make masked adjust­ments. Here I put a point on the left of the sky in a blue part. I pulled the size to make it a big area, but when I did the clouds were auto­mat­ic­ally masked off, so it was only going to be the blue parts of the area that were affected. There’s handy red high­light­ing as you do this to show where your effect will apply. I reduced bright­ness and increased sat­ur­a­tion, then duplic­ated the point and moved the duplic­ate to the other side if the blue sky so that all the area was covered.

Snapseed at work

Snapseed at work.

There are other ways of doing the same thing in other photo apps, but this is usu­ally a pain­less way of select­ing an area. It works well for com­plex shapes, like if you want to select flower­heads in a shot. My ver­sion of PhotoShop Elements is out-of-date so I don’t know how good the smart select­ors are in that now, but the ver­sions I have used have been much harder to do the same thing with.

It’d be great if you could do that with all the effects, but you can’t. The range of point options is lim­ited to bright­ness, con­trast and sat­ur­a­tion. If you want a lot of con­trol then it’s $99 for Viveza or Color Efex. The rest of Snapseed’s effects are global. I applied the Structure+ effect to bring out details in the stones and clouds. That’s a scal­able effect, so if you think I’ve gone over the top you could pull a slider down to ease off.

That’s all I did because then it looks like a bug kicked in and I couldn’t apply any more effects like Vignette or Drama. In this case it might be a bless­ing but it’ll annoy me if that’s per­sist­ent. Looking at the res­ult I think I’d want to push it back in to Aperture to blur the sky a little. I could do some­thing sim­ilar to remove struc­ture in Snapseed by adding a point and turn­ing down the con­trast a little. If there hadn’t been the bug.

The same Greenhouse at Kew after Snapseed

The same Greenhouse at Kew after Snapseed.

I keep think­ing about buy­ing Viveza, HDR Efex or Color Efex, or the bulk suite, but I keep get­ting put off because whenever I look the price in Europe is much higher than from the US store, even after allow­ing for VAT. The only excep­tion was a recent sale where things were up to 50% off. A $10 instruc­tion video was indeed 50% off, but the sav­ings on the soft­ware were bring­ing down the prices to US levels, which doesn’t feel like a sav­ing. This adds an extra span­ner to Nik mar­ket­ing machine, because this does a lot of what I want from Viveza or Color Efex. Ok, I don’t get the Sunrise Glow fil­ter, but how often would I use it? I like to sleep in. The last thing I want to do is make people think I’m will­ing to get up at the crack of dawn to pho­to­graph some­thing. I’d get even less use out of the “Cross-processed on a rainy Tuesday” fil­ter and so on. Have Nik lost a sale, or have they worked out that tools, excel­lent as they are, are aimed at the pro mar­ket and they need some­thing dif­fer­ent to prise money out of the hobby market?

It is expens­ive to com­pared to a lot of the photo fil­ter apps in the MacStore, but if you don’t have any app and you don’t need fine con­trol like Color Efex or Viveza then it’s a good buy. If you’re happy shuff­ling pho­tos between an iPad and a Mac and you already have Snapseed, then it’s not worth the pur­chase. Altering your pho­tos by touch feels nicer.

A post that ori­gin­ally appeared on Google+.

HDR and Reality

The Lovell Telescope at Jodrell Bank
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A com­ment on this link HDR: Love it or or Leave it? pos­ted by +Matt Shalvatis.
The Lovell Telescope at Jodrell Bank

The Lovell Telescope at Jodrell Bank

This has been on my ‘to-blog-about’ list for years. On the one side there’s the artistic effect, which you can debate. I get the impres­sion HDR is a per­sonal taste, so telling people it’s the right or wrong way seems point­less to me. In my view my early HDR stuff was poor. In par­tic­u­lar it was often over-saturated so I could see what was hap­pen­ing (I have odd col­our vis­ion). These days if I can can do some­thing I want without HDR I will, and I find adjust­ing the white and black points is often enough for what I want, but when it isn’t a light touch in Photomatix can make a big and subtle difference

The other side is that it can have prac­tical uses in some­thing like archae­ology. I have seen too many pho­tos of pitch-black church interi­ors. HDR can provide a much bet­ter impres­sion of what the human eye sees than the lim­ited dynamic range of a cam­era because you can expose the shot for a wider range of light and shadow. The altern­at­ive is to bring a massive light­ing rig along with you, and that’s not practical.

I know some people think this is bad because it’s manip­u­lat­ing the pho­to­graph and there­fore not a ‘true record’. They’re right it isn’t ‘true’. But the auto func­tion on a cam­era isn’t neut­ral. It makes its own judge­ments on what the set­tings should be. The dif­fer­ence is that these set­tings are often hid­den from the user when they’re made, so it’s harder to see what assump­tions are being built in. Just because you can’t see the manip­u­la­tion of set­tings hap­pen­ing doesn’t mean it isn’t happening.

I don’t ever see the same angst about real­ity in archae­olo­gical illus­tra­tion though. I think a lot of archae­olo­gists will laugh if you say the cam­era never lies, but I think there’s a bias to believ­ing that cam­eras can be neut­ral. Maybe with pho­tos look­ing so much closer to real­ity we sub­con­sciously insist devi­ations from real­ity are flaws not art.

A post that ori­gin­ally appeared on Google+.

Teaching Apples and Oranges

Introduction to Monstering
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Introduction to Monstering

There’s an inter­est­ing story on the BBC News web­site: Teaching ‘bet­ter at school than uni­ver­sity’ — survey

When asked to com­pare teach­ing at school and uni­ver­sity, less than one-in-five privately edu­cated pupils favoured their uni­ver­sity tutor­ing. Almost two-thirds declared that the teach­ing they had at school had been better.

The res­ults are not a sur­prise. I took A-levels (pre-university exams) twice. The first time I was taught maths, chem­istry and phys­ics and I learned about chem­istry and physics.

The second time was a few years later for Economics and Law even­ing classes. Here I was taught what I needed to know to pass the exams. In the case of Law, there were always four ques­tions in Paper II, Homicide, Tort, Contract and Constitutional law. You needed to answer two of four, so the even­ing class only covered Homicide and Tort. I do not have a roun­ded legal edu­ca­tion, but the col­lege was not graded on my edu­ca­tion it was graded on the res­ults I got. Behind trained for the exam was a huge suc­cess and I scored more UCAS points on my one year even­ing class courses than in my two year stand­ard courses.

Every year for over twenty years the num­ber and qual­ity of A-level passes has gone up. The argu­ments are usu­ally over whether or not the exams are get­ting easier, or the pupils bet­ter. What is less often noted is that schools are graded and com­pared against their neigh­bours on their pass rate. Unsurprisingly they’ve become more and more ruth­less about train pupils to pass an exam because that’s what mat­ters, not whether or not they under­stand why they’re doing what they’re doing.
Continue read­ing

Plugins for an academic group blog: Referencing & Footnotes

A plug. Photo by Pulpolux!!! CC BY-NC
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For reas­ons that will hope­fully become obvi­ous this sum­mer I’ve been think­ing what plu­gins would be use­ful for an aca­demic group blog on WordPress.

Referencing & Footnotes

In terms of integ­rat­ing ref­er­ences the three big pro­grams are EndNote, Mendeley and Zotero. It would be easy to get lost in an argu­ment about which of these is the best sys­tem. I don’t think that mat­ters. What is best for me is not neces­sar­ily best for you. Also two of these sys­tems are on the web, so they could be very dif­fer­ent in six months. What is best now might not be best soon. So the best solu­tion for integ­rat­ing with WordPress is to be able to handle as many sys­tems as possible.

That’s why I like Martin Fenner’s plu­gins BibTeX Importer and Link to Link. Everything out­puts Bibtex, so any selec­tion could be uploaded as Links in WordPress’s sys­tem with the importer. Then Link to Link makes it easy to pull out the links as you write. Mix in a good foot­note sys­tem and you and make good bib­li­o­graph­ies. The only draw­back is that WordPress’s sys­tem requires these links link to some­thing, like a DOI or URL. That’s not cer­tain for archae­olo­gical ref­er­ences so it’s not a per­fect solution.

Two other ways involve link­ing the bib­li­o­graphic sys­tem to WordPress. That requires that the sys­tem is online, so no EndNote. Zotpress integ­rates with Zotero and with upgrades over time it does is bet­ter and bet­ter. The latest ver­sion sits as a wid­get by the side of the edit area for insert­ing short­codes. In fact simply tag­ging the rel­ev­ant entries in Zotero with a hashtag like #blogentry20110517 gives you a single tag to look for and then you can type in one Zotpress short­code to com­pile the whole bibliography.

A sim­ilar trick can be done with the Mendeley plu­gin, though the inter­face is a little less friendly, while the short­codes are much friend­lier. It is tempt­ing to thing the choice of which plu­gin in to use is one or the other. You can’t have two identical bib­li­o­graph­ies in a post so you only use one? The blog­ger will only type one short­code in the post, but can choose which on if both plu­gins are installed. I think the plu­gins only use the pro­cessor if they’re invoked by the short­code so there’s no trouble using them both. I think with Zotero becom­ing unhooked from Firefox, the choice between Mendeley and Zotero will mInly be social. You’ll use what your per­sonal net­work uses.

An addi­tional Mendeley fea­ture is that you can also add a related research plu­gin. This works, even if the blog­ger uses Zotero for the bib­li­o­graphy in the post, if you remem­ber to add tags, so it seems like another use­ful add-on.

This leaves just a mat­ter of how to insert foot­notes. I like WP-Footnotes because it degrades grace­fully. You insert a foot­note with double brack­ets some­thing sim­ilar to but not exactly {{like this}}. When you use plain brack­ets it becomes a foot­note. ((Like this. Actually test­ing this shows that Apture will be a prob­lem if Footnotes are used. The reason is the anchor for the foot­note will be hid­den by the Apture bar with search etc. So too will the back link. It’s prob­ably a choice between foot­notes and Apture. If an aca­demic blog uses foot­notes reg­u­larly I can see Apture being a miss.)) Apart from being simple, if you deac­tiv­ate it, then all your older posts don’t auto­mat­ic­ally look unread­able. It’s lim­ited in what it does, but what it does it does extremely well. But I won­der if my reluct­ance to use short­codes in the past means I might be over­look­ing Footnotes for WordPress. One ques­tion is why do you need foot­notes on a blog?

Footnotes make sense in print by mov­ing dis­cre­tion­ary text out of the way. They make sense for ref­er­ences, though for plain text using foot­notes is often a sign you’ve writ­ten some­thing badly. Endnotes make sense on paper in that they’re easier to type­set than foot­notes. But blogs are not on paper. References could be dir­ectly hyper­linked. I think one reason this has never taken off in human­it­ies aca­demic blogs is partly the expect­a­tion of what text should look like and partly because if a source isn’t online it’s not obvi­ous what the link should link to. Even so, do we really need to scroll down for notes in elec­tronic texts? Footnotes for WordPress takes advant­age of blog­ging by includ­ing an option for hov­er­ing foot­notes. I used to think float­ing notes or tool­tips were gim­micks. If mak­ing them becomes as simple as typ­ing [ref]footnote here.[/ref] then maybe it’s time to rethink what it is you want foot­notes to do. I think there’s still a need for col­lated ref­er­ences at the end of an elec­tronic text, as it still serves a use­ful Further Reading func­tion after fin­ish­ing read­ing a text. Adding float­ing notes won’t remove that list, but it will make those same notes and ref­er­ences more accessible.