Talk:Main Page/main-04

From Ganfyd

Jump to: navigation, search
Archived  by me today from Main page Discussion to about end of August 06 Mlj 21:08, 3 October 2006 (BST)


Articles to direct attention toward: stubs

There are 341 stubs[1]. I think we should focus a little attention on these, out of the 1500 articles at present, and the many more that we shall write, and bring some of them up to a standard where they may be incomplete, but are much better than stubby. We might perhaps have a template for incomplete rather than stub, to reflect a status we want to remark on? Midgley 16:24, 5 April 2006 (CEST)

I agree a clean up would be an idea, but of course all articles are incomplete ,...thats why I like Wikis. Isn't Template:draft enough ?. Any suggestions as to when we remove stub. I leave it when important stuff exists that I think a doctor should know on subject but have not time myself to get it right.
On WP (which doesn't mean we have to follow it) a stub is not more than a paragraph or two. I think we need a careful phrase, and a template to enact it - "this article as yet lacks significant portions" as a first effort. Alternatively, we could take to marking articles we regard as "finished" and warning about all not so marked. Revising a finished article doesn't worry me, it is someone who thinks they are consulting a complete reference where there is a section simply not yet done that I think might need an explicit warning (and invitation to add something). Midgley 04:12, 6 April 2006 (CEST)

There are now 462 stubs[2] labelled now. Partly this is because there are lots more articles, which is good. Midgley 23:07, 29 September 2006 (BST)

DNUK Forum

Now open: Mark ong

You see. That's my powers of persuasion for you! Rupert (Talk) 13:30, 19 April 2006 (BST)

Yes, whatever would we do without you? ;) Mark ong

Good show. I wonder if that means DNUK's look at a Windows-based wiki has been shelved? Midgley 15:50, 22 April 2006 (BST)

Meanwhile, Statistics:: there are 1,653 pages that are probably legitimate content pages. Midgley 15:50, 22 April 2006 (BST)


Who wants it? Rupert (Talk) 12:08, 23 April 2006 (BST)

Yes please! --A.l.brown 13:56, 23 April 2006 (BST)
I think it will be good in long term as an option as I had to go commercial to get a good package, but mind you this was for 3D modelling. I will look further because the script language is challenging and will only save a few bytes.Mlj 14:43, 23 April 2006 (BST)
Ok. The XyMTex server is down, but the answers I needed were at Development and Application of XyM2Mol System for ConvertingStructural Data by XyM Notation into Connection Tables Kei ITO, Nobuya TANAKA and Shinsaku FUJITA J Com Chem 2005 . Essentially XyMTex uses a different number convention to IUPAC which is a real pain - you have to have the manual to do the mark up (and its not available as I write from the definite source.) The article is interesting as it tells us the best free alternatives to ChemSketch 9.0 and Chem3D 9.0 which I have been using. It does not suggest any easy way to go backwards from a MOL file or KCF file or pubchem files to generate the markup.Mlj 16:04, 23 April 2006 (BST)
Well I had a go anyway, but I couldn't install it. Don't know why not. It's just a collection of macros but latex wouldn't find it, even though I updated the search paths to include it. I hate computers. Rupert (Talk) 18:49, 23 April 2006 (BST)
If the file formats are both specified then writing a converter should be fairly mechanical ... it would take me a lot of getting to understand it before I could start though and I usually find someone has done it before. Midgley 05:25, 30 April 2006 (BST)

saving edit call fails

on new page with

Fatal error: Call to undefined function: memsess_key() in /homepages/1/d143003564/htdocs/wiki/includes/User.php on line 1695

Midgley 18:32, 25 April 2006 (BST)

I'd left it open for over a day... When I recreated the page as a new blank and pasted teh material into it it saved nicely. Midgley 18:34, 25 April 2006 (BST)

Downstream trouble - Hubmed down

Domain name expired on 04/24/06! Do we know who to remind about that? Midgley 16:58, 29 April 2006 (BST)

that is a pain. I may change pharmcybox and chembox etc to pubmed searches Mlj 17:32, 29 April 2006 (BST)
I can change the link from hubmed to pubmed in the hubmed thingy and change it back when hubmed is up again. --A.l.brown 17:57, 29 April 2006 (BST)
Actually it looks like Alf has spotted it - it is registered til 24/04/2007, and is back up and running. Your DNS records may be a little behind if it still looks down to you. --A.l.brown 18:00, 29 April 2006 (BST)
When I revert the templates I will offer both Hubmed and Pubmed formats so we don't get stuck again

Interesting extension to mimic

Adds one Wikipedia article to your Google search. Are you thinking what I'm thinking yet? Midgley 19:33, 13 June 2006 (BST)

It is a bit slow, but somewhat interesting. I may have to elarn how to write Firefox extensions. Midgley 12:02, 27 June 2006 (BST)

Induction course

I think when we get a wave of new people joining, we shall need a few pages to use as an induction course, rather than expecting them to pick up the current mood and practice straight off. Midgley 13:21, 19 June 2006 (BST)

WP:Writing medical articles

Useful list of tools relating to references. We might wish to import some of them? Midgley 11:23, 25 June 2006 (BST)

The wikimedia tools don't do it in standard Vancouver style format as well as the one our heros have whipped up. Mind you an interesting improvement would be for a pubmed reference number to automatically inject the reference. So [[pubmed:16773614|]] produces Frigerio R, Sanft KR, Grossardt BR, Peterson BJ, Elbaz A, Bower JH, Ahlskog JE, De Andrade M, Maraganore DM, Rocca WA. Chemical exposures and Parkinson's disease: A population-based case-control study. Mov Disord. 2006 Jun 13; [Epub ahead of print]
Just an idea everyone that would only work if page injection of HTML is allowed which I understand is being depreciated in extensions and you understood how Hubmed was done Mlj 18:46, 25 June 2006 (BST)
Good find, Adrian. Michael, after doing all those references in hypertension it occurred to me how useful something that does this be. It's easily possible. I'll see what I can do tomorrow afternoon. Btw, "injection of HTML" is not being deprecated. It's something that MediaWiki has never wanted in it because it permits insertion of malicious HTML by anybody who can edit a wiki (so not a problem here, but a big one on WP.) The sort of thing they're worried about is code which exploits the latest browser bug for example. Now, extensions will always be able to output whatever HTML they want because they are installed by someone who has write access to the files of the mediawiki installation and are written by someone whose responsibility it is to make sure they never output harmful HTML. Rupert (Talk) 19:42, 25 June 2006 (BST)
So far, I have an extension which takes <pubmed>3169953</pubmed> and renders Timio M, Verdecchia P, Venanzi S, Gentili S, Ronconi M, Francucci B, et al. Age and blood pressure changes. A 20-year follow-up study in nuns in a secluded order. Hypertension. 1988;12:457-61. A link would be trivial to add. So that would be better than nothing, especially if combined with some sort of caching thing. I would prefer it if the content was substituted in at the time of saving though, like ~~~~. I'll look into that tomorrow afternoon. Also, does anyone have ideas about syntax? I think [[Pubmed:3169953|]] might be do-able. If so, would this be good? Rupert (Talk) 23:46, 26 June 2006 (BST)
agree the best way to do it would be substitution at time of saving . Would syntax like [[Pubmed:3169953|????]] meet with approvial if the syntax is only parsed for this in a pubmed call? Mlj 00:12, 27 June 2006 (BST)
My reasoning behind [[Pubmed:3169953|]] is that it is currently invalid syntax and is in keeping with the rather poorly implemented pipe trick. If you prefer ???? though that would be equally easily arranged, once I work out how to do any of this! I quite fancy **** because it looks more like magic rather than an unknown! One thing that would be great is automatic retrieval of online links to from the PMID. I don't know how I'd fit this into any sort of [[Pubmed.....]] syntax though. I can't think of any examples, but I'm worried that if it inserts too much stuff, it will be a deterrent to its use, although I guess I can only envisage it being used in references, which will be in the table at the bottom, where one would normally want it. And if one didn't you could delete it after saving, I suppose. Still. It seems naughty to take that and turn it into two links rather than just one. Rupert (Talk) 15:16, 27 June 2006 (BST)
Also, you had apparently suggested [[Pubmed:3169953|]] above! Rupert (Talk) 15:24, 27 June 2006 (BST)
See Ganfyd:Fetch Reference Caption Extension Rupert (Talk) 17:40, 27 June 2006 (BST)
If it can cope with the illegal syntax cleanly I'm all for it. Really my ???? suggestion was a tired brain storm. The advantage of pubmed is that it is totally free, and the database won't change. BMJ is not totally free access any have to wait 6 months or be a member. I might have personal web access to the Lancet, NeJM and BMJ and a few other journals in my areas of interest but thats far from typical in my experience. Its not exactly cheap but sure saves time when you want to find a high quality review on a topic so I can keep up with the specialists.Mlj 21:29, 27 June 2006 (BST)
Done. See Ganfyd:Pubmed Caption Fetcher. Rupert (Talk) 21:42, 28 June 2006 (BST)
There is a significant problem though, as implemented at present, which is that the page now depends on a distant website/database. If that goes down then our page is unusable, even by someone with a library to hand. I think we had better have the title etc of th ereference in teh page as text, regardless of otehr clevernesses. Can it be automatically substituted in perhaps? Midgley 23:55, 2 July 2006 (BST)
Bugger. That was the whole point. And the thing hasn't worked. Aaaargh! Rupert (Talk) 00:07, 3 July 2006 (BST)
Mended. (I introduced a bug when I removed substitution within nowiki sections.) Rupert (Talk) 00:27, 3 July 2006 (BST)

Heading for 2000 articles

Statistics for the wiki suggest that 1933 pages are probably articles... so 2k aproaches. Looking at a shelf near here I see that Bailey & Love is about 1300 pages, Price is 1400 and there are a load more books on the shelf, but nevertheless 2000 pages even with some of them being short ones is a significant quantity. Midgley 10:51, 30 June 2006 (BST)

Administrative stuff

1. Do we have a way of generating a user account for someone? In a plain MW it works well but I think that is closed off here. It may be a useful thing.

You can send them an invitation by completing register.php with their email address, but as Adam wrote it to require authentication of the email address, there is no way to set it up completely for them, no. Rupert (Talk) 14:50, 28 July 2006 (BST)
There is a way of generating a user account for someone, at - it is password protected. If you are an admin you can get the password from me. It is a bespoke bit of code which worked before the change to the new server, fell over with PHP5 and I think works again now. I promise that once job applications and end of training assessments and the like are out of the way I will rewrite the admin tools. --A.l.brown 13:08, 29 July 2006 (BST)

2. There is a typo in the page that produces a null result on search and the suggestion that one may wish to create the page _youself_. Where is that page? Midgley 09:58, 28 July 2006 (BST)

MediaWiki:Nogomatch I'd change it myself but I'm due back at work in 10 mins & give a man a fish/teach a man to fish etc. Rupert (Talk) 14:50, 28 July 2006 (BST)
Being back, I've done it now. Rupert (Talk) 22:32, 28 July 2006 (BST)

Between stub and draft I place a planet

It bodes well that we have so many articles which are bigger than stubs, but perhaps not what one would yet submit to a publisher as a draft. I think we need a classification intermediate - unfinished article of some size but acknowledged and even warned about as being unfinished and incomplete. The list/category of those would offer a target for anyone who wanted to write but didn't feel like picking a subject and starting one. What might we call it? Midgley 14:05, 9 August 2006 (BST)

Mutli-lingual support

Wikipedia approach:

The take home message is type away in Unicode to your hearts content. Let's not replicate all that templatey stuff. Rupert (Talk) 00:01, 22 August 2006 (BST)
I agree. Having now tested the site on at least 6 browsers & OS I think we just wait until everything is unicode and forget about certain issues with old M$ software. Mlj 19:38, 26 August 2006 (BST)

Where Next? Interactions with DNUK etc

Interestingly, DNUK have tweaked the previously decrepit interface of their medipaedia and have put a link into the recent bulletin. There have been a handful of contributions, but no serious efforts. The licence issue has been quietly swept under the carpet.

I also note the proliferation of web-sites that continue to emerge. Some are good for what they are, e.g. gpdesktop [3]. Others haven't quite taken off the way they were intended [4]. There are a few other sites that I've come across on DNUK.

Not to denigrate the work and effort put in by other people, but our platform and philosophy have a lot to recommend. It might be a good idea to make ourselves more visible so that people don't feel the need to set-up yet another project. However, it seems we have a few things to think about in terms of future direction:

  1. Polishing up a few technical issues, esp. the registration part.
  2. What to do with funding?
  3. How best to raise awareness? e.g. BMJ Careers?

As Adam has previously alluded, the 1 year anniversary might be a good impetus/opportunity to address all of the above. Mark ong 23:53, 23 August 2006 (BST)

Concur. Clearly there is at least one paper in here, and BMJ Careers may not be the hottest target for it, if we work out what to measure, and for at least one article. I think we had best have registration ideal before publicising, and we need a convenient way documented for admins to induct new people who they know and can vouch for, rather than by sending them through the faxing route to registration. If we wanted to run a meeting who would we like to attract? NeLH et al perhaps.Midgley 09:18, 24 August 2006 (BST)
Mike Harris was interested in an article from me for the ACP News, about IT and medicine, which could incorporate a significant amount about ganfyd. I've been so snowed under with exams/audit/research/job interviews/RITA (in that order), that everything else has fallen by the wayside (until mid-September hopefully). I'd be keen to resurrect this article though. --A.l.brown 15:06, 26 August 2006 (BST)
The DUNK effort is still useless and actually has no hope due to software constraints. I do not think we need to worry about our skin that much as its better than many wikis. Content, indexing. ease of visual content addition and easy to follow links are our most important strength Concur with other points. I have just chased Adrian on Bank account as I want to put some in before my pay packet goes down as NHS financial system failure hits me. Remain very wary of commercial sponsorship having just seen my medical director taken in by patient advocacy group that was more subtle than some in hiding its conflict of interest. Mlj 21:08, 26 August 2006 (BST)
DNUK announcement about closing Medipaedia forum. Agree that that DNUK interface is sorely disappointing. No easy way to do several obvious and very essential wiki functions, e.g. wikify, roll back changes, cite references, upload images, create categories, etc. I wonder what DNUK mean by this: will enthusiastically explore ways to work together with for your benefit. Please be reassured that has contacted representatives and the commencement of this dialogue is eagerly anticipated.
As fas I can see, there has been no movement on the licence issue (or any of the other issues raised in the forum discussions). Fundamentally, I think we have to accept that for a whole host of reasons, the DNUK medipaedia may/will never meet what we envisaged when was set-up.Mark ong 15:29, 29 August 2006 (BST)
I never thought it was a good idea that so much ganfyd internal discussion was done on DNUK. It was and is a good place to promote it, but I imagine we will lose all the ideas that were on the medipaedia forum and that is a shame. Do we want to resurrect the mothballed forum? Rupert (Talk) 17:16, 29 August 2006 (BST)
I tend to like email discussion lists, rather than such fora. Midgley 17:21, 29 August 2006 (BST)
Some of the DNUK MP contributions are actually good essays. They strike me as essentially Web 1.0 efforts, whereas we are tending toward Web 2.0 - they are assertions and may even have a byline, even if there is provision for editing by others. Interestingly there is nothing in the Ganfyd licence to stop someone copying chunks of a ganfyd page into a DNUK MP page, but the licence is viral, and such a page would then be very difficult to justify publishing under a different licence, and after a while very difficult to unpick... :Some of them as I say are distinctly good, and the authors clearly have every right to place them in here as well if they choose, but nobody else does.
We have far better furniture, better wiki functionality, a more accurately defined mission, more diversity, a wider constituency but a less convenient entry system - the front step to start writing. That is something we must work on. Midgley 17:21, 29 August 2006 (BST)
Agree, presently our greatest weakness is in our potential for attracting contributers when there are so many other distractions and ways to communicate knowledge, some of which pay money (declaration of conflict of interest: I have been paid money for writing I have done but no-one would ever think I'd earn enough to go free lance!). I think our present entry system isn't a complete disaster.Mlj 21:16, 29 August 2006 (BST)
In the time frame of the one year anniversary I think DNUKs invitation today to meet at least 4 of us (Adam, Adrian, Mark & me) is interesting with no obvious down side from the GANFYD project point of view and have suggested that other's such as Rupert for one should be included. Contact one of us for more details Mlj 21:41, 1 September 2006 (BST)
I have e-mailed back expressing interest, but have said that I am based in Ediburgh, so may have difficulty travelling down to Abingdon. I am still curious to know what we can offer each other given the inherent commercial interests of DNUK.
So we should be. I think it is healthy to have a degree of paranoia which is not quite paranoia. But I talk all the time with pharmaceutical companies and NHS managers which have distinctly different interests to mine and have benefitted patients as a result without I think total compromising my principles. I've walked away from both in my time too.Mlj 23:14, 4 September 2006 (BST)
On a different point, I am not sure where we stand with the DNUK forum following DNUK's decision not to close the Medipedia forum. In what appears a generous move, they have renamed it Medical Wikis. I find the DNUK forum more convenient, but I do understand Rupert's unease (see above) about using DNUK's fora. Mark ong 22:27, 4 September 2006 (BST)
DNUK fora are useful as they are on the regular check list of most of us, I already can't keep up with all the fora I might be interested in or have been interested in but have drifted away from.Mlj 23:14, 4 September 2006 (BST)

More DNUK Developments

As posted by Adrian on the DNUK medical wikis forum: This 'announcement' is irritating on several levels. Mark ong 15:43, 21 September 2006 (BST)

What utter bollocks. I know we'd be more gracious than that if the successes of the two efforts were reversed. (Not that we wouldn't all have abandoned the floundering one long ago and be working on theirs in that case.) Adrian, thank you for flying the flag for ganfyd and doing it so diplomatically too. Rupert (Talk) 21:26, 21 September 2006 (BST)


OK, this is a big suggestion, but one I have been thinking about long and hard for some time. Ganfyd is a knowledge base, and as such helps to promote education and learning. I think that this can naturally evolve to allow collaborative projects and groups to form along the lines of social networking. This would not in any way muddy the wiki or detract from it. I would like to propose adding Elgg to ganfyd. This would allow contributors to collaborate on projects in ways that a straight wiki cannot, and would allow a culture of personal learning to sit along side the didactic approach of a wiki.

  • Firstly, this proposal would in no way alter the wiki at all, and users could choose to ignore the elgg part altogether if they so wished.
  • Secondly, this proposal would add little in the way of server/database load, as elgg is quite efficient (far more so than MW!).
  • Thirdly, this proposal would require the use of a MW-independent authorisation/registration system (which is what we ought to be looking at anyway), and methods to do this are being developed (such as the OpenAcademic project).
  • Fourthly, this proposal would provide medics and students with a fantastic resource for personal education.
  • Fifthly, we'd need to get together to work out how to implement, though it won't be as much hard work as it initially sounds. A small alteration to the registration system (registering through elgg rather than mw) would be required, plus some additions to elgg. All of these would be transparent to the user.
  • Sixthly (I should have just used numbers!), it would be a good opportunity for a reskin. I know Adrian favours the WP look, but personally I feel we have made enough of a name for ourselves to have our own look, and I think the WP look is messy.

Any views? If everybody hates the idea I could set it up in the background for you to have a look at. You really need to have a very long look at elgg - at first it doesn't look like it would add anything, but on prolonged inspection it has much to offer.

--A.l.brown 13:22, 5 September 2006 (BST)

Sorry I missed this when you first posted it, Adam. I can see there's more to Elgg than meets the eye so yeah, let's have it! We can either have synchronised usernames and passwords between MediaWiki and Elgg, but better than that is single sign-on, which has already been done and released: We need to have them both on the same domain. That's no problem. So far there are two sorts of URL on ganfyd: "" and "" the latter all being pages to actual content. I think what we should have are "", "" and "" with the first being either a redirect to the wiki or a welcome page with icons for the wiki and Elgg. (Probably redirect to the wiki to start with.) Preserving links to the old page names can be done using mod_rewriteRupert (Talk) 17:33, 14 September 2006 (BST)
I've just been reading a bit more about the integration system above. I don't like the thought of being redirected to the Elgg log-in for MediaWiki at all. It will upset me! I don't like the way it won't test the log-in until you try to edit something either. As soon as you click from Elgg to MediaWiki you should get the personalised MediaWiki pages that logged in users get. Rupert (Talk) 17:41, 14 September 2006 (BST)
Don't worry about the log-in - thats changeable I think --A.l.brown 18:38, 14 September 2006 (BST)
I feel quite relaxed about all this. The Eagle and Child pub by the way is where Tolkien used to meet Caroll et al and among other things drink and proof read. Moodle is well-regarded and Elgg seems to connect to that. I like the movement toward establishing larger collaborations and information spaces. Midgley 21:54, 14 September 2006 (BST)
I am easy, but it looks like a lot of work to maintain and seems likely to function best as a closed community (ie sort of DNUK like but libre and no doubt more solid software in due course if not now). I presume if implimented you would want to hide it on two new partitions, a test one and the real one Mlj 22:38, 14 September 2006 (BST)