User talk:Diberri/Archive 5

This month's WP:MCB Article Improvement Drive article
– ClockworkSoul 22:50, 4 September 2006 (UTC)

This month's WP:MCB Article Improvement Drive article
– ClockworkSoul 21:03, 2 October 2006 (UTC)

PubMed tool ISBN feature suggestion
ISBN numbers are hyphenated in certain ways, but I have not been able to discover where to place the hyphens. Most internet sources of ISBNs do not list the hyphens. User:SmackBot sometimes goes through articles and corrects the hyphenation of ISBN numbers. It would be nice if putting an ISBN number into your PubMed tool would not only generate a citebook template, but correctly hyphenate the ISBN number, too. Lyrl Talk Contribs 22:50, 8 October 2006 (UTC)
 * Thanks for the suggestion. If someone suggests a way to determine proper hyphenation, then the likelihood of the feature making its way into the ISBN/PubMed tools would skyrocket. :-) --David Iberri (talk) 23:12, 8 October 2006 (UTC)
 * Lyrl posted this question to User_talk:Rich Farmbrough; here is the discussion: . I think it would be valuable if the PubMed tool could also produce correctly-hyphenated ISBNs. On the web, you can use isbn.org/converterpub.asp to do the hyphenation. This program also checks for validity and returns the ISBN-13 of the ISBN-10 that is input, but only the hyphenation and validity-checking are of current interest. If the PubMed tool could do this additional step, then the reference it allows you to create would have no need of the hyphenation-and-checking pass of the SmackBot. EdJohnston 19:05, 16 October 2006 (UTC)
 * I came here to post the PDF with the hyphenation instructions from Mr. Farmbrough, and I see Ed beat me to linking to the ISBN check script that he uses. Lyrl Talk Contribs 21:15, 16 October 2006 (UTC)
 * Excellent. For the time being I'm using the isbn.org converter, which seems to be working nicely (eg, ). Let me know if you experience any problems. --David Iberri (talk) 02:32, 17 October 2006 (UTC)
 * I'm amazed at your quick turnaround on this suggestion! This is a tool I would start using for all my ISBN fixing if it could equal the converterpub.asp functionality.  Some points from a quick trial:


 * Does not distinguish between invalid ISBNs and rare books. For example ISBN 85-7004-262-0 is a valid ISBN but belongs to an obscure book published in Brazil, which you can confirm by Googling the unhyphenated number (See 'Miscelanea' in Adriano da Gama Kury),  while 0932112092 is an invalid ISBN. They both get "Could not find a book matching the given ISBN."  Since invalid ISBNs are horrible, it is nice if they can be explicitly flagged. If it just can't find the info, that's fine, there are other places that a WP editor can try.
 * Sometimes does not fill in the 'date' fields even though isbndb.com has the information. Example:ISBN 0-226-73936-8 (Schneider and Sagan). Sometimes does not fill in the 'location' field even though isbndb.com has the info ISBN 0-226-73936-8 (Bergmann book). In this case it's harmless because it just appends the location to the publisher field.
 * Speaking just about the 'cite book' template (not an issue with your script) I have had problems with coauthors not printing out correctly; when time permits I'd like to try out your script to see if it can surmount that issue. EdJohnston 21:29, 17 October 2006 (UTC)
 * Note my ISBN hyphenation script (for AWB) is published at http://en.wikipedia.org/wiki/Wikipedia:AutoWikiBrowser/Settings/ISBN-hyph, and I will fix up lists of articles or indivdual article if requested. Rich Farmbrough, 22:38 15 January 2007 (GMT).
 * Wow, that's a colossal script you've got there. I suppose I could probably adapt it to my template builder, but I'd just as soon leave it alone as it seems to be working fine for the time being. Thanks though. If time permits, I'll have a go at it. Cheers, David Iberri (talk) 23:00, 15 January 2007 (UTC)

One more vote for the coordinator of the Molecular and Cellular Biology Wikiproject
Since two of the three editors nominated for Coordinator of the MCB Wikiproject declined their nominations, one more vote has been posted: should the remaining nominee, ClockworkSoul, be named as the coordinator, or should nominations be reopened? Every opinion counts, so please vote! – ClockworkSoul 17:46, 17 October 2006 (UTC)

Molecular and Cellular Biology Wikiproject Newsletter
The October edition of the Molecular and Cellular Biology Wikiproject Newsletter has been released. You can read it by visiting the newsletter page. – ClockworkSoul 19:30, 21 October 2006 (UTC)

This month's winner is proteasome!
– ClockworkSoul 22:09, 1 November 2006 (UTC)

Hi!
Thanks for replacing that erroneous image on brachioradialis. It's good to see editors respond when I notice something is off, even if I don't know how to fix it myself. I just wanted to say hi, I'm a first year med student who has found wikipedia to be a fantastic studying resource (in large part to the contributions of yourself and Arcadian, especially the work on the images from grey's anatomy). Robotsintrouble 23:59, 6 November 2006 (UTC)

html2wiki
First, thanks for the wonderful tool. I love it. I was wondering though, I got the command line version to work but is it possible to get your html (web based) code and also how you set up your configuration? Here is my email if you can zip it up and some notes: jbs12345@yahoo.com

Thanks Jbs12345 17:59, 7 November 2006 (UTC)

wikEd


Hi, I have seen that you are using the Cacycle editor extension. This program is no longer actively maintained in favor of its much more powerful successor wikEd.

wikEd has all the functionality of the old editor plus:• syntax highlighting • nifty image buttons • morefixing buttons • paste formatted text from Word or web pages• convert the formatted text into wikicode • adjustthe font size • and much, much more.

Switching to wikEd is easy, check the detailed installation description on its project homepage. Usually it is as simple as changing every occurrence of editor.js into wikEd.js on your User:YourUsername/monobook.js page.

Cacycle 21:50, 8 November 2006 (UTC)

Wikipedia template filling.
[pubmed citations] Your tool is great. Two suggestions Thanks Badgettrg 16:27, 10 November 2006 (UTC)
 * 1) Could you include the doi field? I suspect many users may not find their way thru PubMed to the full text of the article without a direct link.
 * 2) The tool did not work on an e ahead of print article . As issue and page are not known, the tool did not create these fields; however, the tool also did not create authors and year.

Down.
[pubmed] The citation tool seems to be down for PMIDs. (It seems to be working for the other citation types.) --Arcadian 03:40, 20 November 2006 (UTC)
 * Never mind -- it's working now -- sorry. --Arcadian 03:41, 20 November 2006 (UTC)
 * It must be down again...seems to be missing an include (WWW/Search/PubMed/PMID.pm). BTW, are you willing to distribute your code? I'd be happy to host another copy since I use the tool all the time. --Dpryan 22:12, 20 November 2006 (UTC)
 * Whoops, seem to have missed these messages. Is the site still down for you two? I'm able to reach it just fine. As for distributing the code, I'd be happy to. I just need a spare moment to tidy it up and upload it to CPAN. I'll let you know when it's ready. Thanks for the offer to host another copy. Cheers, David Iberri (talk) 15:39, 28 November 2006 (UTC)
 * I've have no problem over the last few days using it, and I've been using it a lot. --Arcadian 19:28, 28 November 2006 (UTC)
 * As Arcadian said, it seems to work now. Thanks much for all of your work. --Dpryan 19:53, 28 November 2006 (UTC)

It's down for me now. I use it pretty frequently, also, so this must be recent. Lyrl Talk Contribs 17:21, 24 December 2006 (UTC)
 * Thanks for the heads-up. Should be back up and running now. Apparently the reason it goes down periodically is that the html2wiki tool running on the same server is going into deep recursion from time to time. (That's mostly a note to myself to get that fixed some time during the holidays.) Cheers, David Iberri (talk) 17:40, 24 December 2006 (UTC)

Punctuation.
I love the tool for filling the journal filling citation. I've noticed one subtle irregularity with punctuation at the end of article titles. Most journal titles end with a period. The template places the article name in quotes, and then adds a period after the quote mark. For example:

produces in the reference list Note the .". at the end of the article name. This is present in most of the pages I used the tool for, and I see it is on your Long-term potentiation article too. Perhaps a modification to the tool to strip the trailing period?  The occasional article name may end with a question mark, but it would probably be correct to have a ?". in the citation. Dlodge 23:22, 5 January 2007 (UTC)
 * 1) ^ Simpson H. "I like donuts.". J Nuclear Power.
 * Thanks for mentioning this. I've added a line that strips trailing periods from article titles, along with an option to disable this feature. Should make everyone happy hopefully. --David Iberri (talk) 00:31, 6 January 2007 (UTC)

Phantoms, spaces, isbn field.
The location at has an extra "[", and the author at  has an extra "," — problem with the source? Also, can you remove the spaces before and after the =s and after the |s; and add the new "|isbn= |oclc= |doi=" fields? E.g.:

Ta. -- Jeandré, 2007-01-14t20:24z


 * The "[" in the first citation is indeed due to a problem with the isbndb.com's data. See (you'll need an isbndb.com developer's key to see the page).
 * I've added the other fields you requested (removing the 'id' field because it seems redundant if we're using the 'isbn' field now) and fixed the space issue you mentioned. Cheers, David Iberri (talk) 02:27, 15 January 2007 (UTC)


 * [[Image:WikiThanks.png]] -- Jeandré, 2007-01-15t19:04z
 * It is not yet clear that the SmackBot can check ISBNs for validity if they are provided with the new 'isbn=' keyword of the cite book template. SmackBot works fine with the old method of using 'id=ISBN xxxxxxxxx' in 'cite book'. This is a current discussion, so I hope Rich Farmbrough will have something to say. EdJohnston 22:18, 15 January 2007 (UTC)
 * Thanks for letting me know. I wasn't aware of SmackBot, but it seems that the isbn\s*=\s*... solution should do the trick. I'll keep on eye on the discussion. --David Iberri (talk) 22:56, 15 January 2007 (UTC)

This thing ROCKS!!
This tool is officially the COOLEST thing I have discovered online in a while. A robot that will bother to type up a formatted reference citation if I merely feed it an ISBN. And I thought I was already lazy when I was holding a book in my lap but searched it up on Amazon so that I could copy-&-paste the pub info rather than rekey it from the book's frontmatter. This thing brings me one step closer to the ideal goal of never rekeying any information that has already been keyed anywhere on Earth before. THANK YOU! Lumbercutter 03:38, 23 February 2007 (UTC)

In search of free license histology images
I'd appreciate your thoughts over at http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Clinical_medicine#Getting_Image_Permissions_from_a_Med_School Robotsintrouble 19:51, 1 December 2006 (UTC)

This month's winner is RNA interference!
– ClockworkSoul 14:31, 2 December 2006 (UTC)

Thank You So Much for Your Expert Opinion on the Nervous System Diagram!
I truly appreciate you pointing out the errors on the Nervous system diagram.png. I tried to correct the problems but I'm still not sure if I got the length of the spinal cord right. Could you please refer back to Image talk:Nervous system diagram.png again? Thank you.¤~Persian Poet Gal (talk) 21:20, 5 January 2007 (UTC)

Here's a pic that I found that might be more accurate: http://instruct.westvalley.edu/granieri/nerve%20plexuses.jpg. Should it correspond to something that? With a long stem of nerves emerging from underneath the end of the spinal cord? Sorry if I ask so simplistically for I am a graphics artist :P and not so keen a scientist...I have already made such an edit to the diagram but before I upload I would like to check with you first if that is a good reference. Oh and by the way your comment about ending it along the level of the iliohypogastric nerve helped give me a way better idea, thanks again.¤~Persian Poet Gal (talk) 01:53, 6 January 2007 (UTC)

Sorry if I am spamming your talk page but one more thing, I've sent an email. If it is not too much trouble could you read that as well? Thanks again.¤~Persian Poet Gal (talk) 02:26, 6 January 2007 (UTC)

Thanks for the response, I have sent the new version to you.¤~Persian Poet Gal (talk) 21:43, 6 January 2007 (UTC)
 * Have you already sent it? I haven't found it in my inbox yet. --David Iberri (talk) 22:01, 6 January 2007 (UTC)


 * Hey there, sent a couple more to you ;)...check when you have the time, thanks again.¤~Persian Poet Gal <sup style="color:purple;">(talk) 05:18, 9 January 2007 (UTC)

I feel its pretty safe to upload now, I added just a couple more strands at the bottom per your advice but I think as you said at this point it gives enough of a general idea without the need for more major editing. I'll allow your inbox some forgiveness now and upload the final version on Wikipedia :). Thanks for all your help.<b style="font-family:comic sans ms; color:purple;">¤~Persian Poet Gal</b> <sup style="color:purple;">(talk)  16:27, 9 January 2007 (UTC)

This month's MCB Collaboration of the Month article is Peripheral membrane protein!
– ClockworkSoul 18:51, 14 January 2007 (UTC)

Further comment on my Reference Desk question
Thanks for taking the time to answer my question. I was really hoping I could ask the question in a different way, but I was afraid it would be misinterpreted as a request for medical advice. You see, my aunt came down with a cold about a week ago and started complaining from pain in her throat. Naturally she visited a doctor, but I was very surprised when the doctor gave her Amoxcillin. I've always been outspoken about the haphazard use of antibiotics in my country, but this was too much. I tried to find a justification for what he did, so I hypothesized that he must have thought she had developed bacterial tensolitis (even still, Amoxcillin wouldn't really be your first choice for treating an uncertain bacterial infection). Hence my question about the relationship between tonsilitis and the common cold. If as you say, the tonsils can get inflammed as a result of the immune response itself, then I guess prescribing an antibiotic wasn't really justified. Any thoughts on the matter? &mdash;  Lestat deLioncour t  19:05, 18 January 2007 (UTC)


 * Of course I realize that this is not medical advice. But thanks anyway; I just wanted to share my indignation :). I would probably agree that had the doctor identified her as having an increased risk for strep infection, this wouldn't be such an unusual prescription. But the doctor has absolutely not medical history on her, and all he did was take a look at her mouth. Is this how people are diagonsed for high susciptiblity to strep infections? I think not. By the way, I have just discovered that my aunt had her tonsils removed when she was a small kid, which makes the situtation even stranger. Do you think it would be polite if I asked him about the reason behind his prescription? &mdash;  Lestat deLioncour t  20:29, 18 January 2007 (UTC)


 * All right. Thanks for all your help :) &mdash;  Lestat deLioncour t  13:59, 21 January 2007 (UTC)

Template filler
I've just discovered your template filling tool. It's a great time saver. Thanks for creating it. --Joelmills 03:27, 28 January 2007 (UTC)
 * Thanks for the thanks. It's my pleasure. Cheers, David Iberri (talk) 03:38, 28 January 2007 (UTC)

none needed
Howdy! Well, I certainly hope that hasn't troubled you since 2004! No apology necessary (though it's always gratifying when soneome agrees with me that I'm right)! As disputes go, that one wouldn't have made it past the speed trials into an actual race, which is just as well, as I'm sure you've noticed there are some really world-class annoying arguers on Wikipedia that you'd be competing with. :) - Nunh-huh 06:05, 29 January 2007 (UTC)

LTP
I'd be happy to help on the LTP page. I just scanned over it quickly, and I think I could add a section on silent synapses that might be useful. thanks, Cecig 23:06, 6 February 2007
 * I agree. It's sorely missing. Have you read silent synapse already? User:Nrets and User:Synaptidude may have something to say on the subject. --David Iberri (talk) 01:03, 13 February 2007 (UTC)

Thanks for the template builder!
bless you greatly for writeing the template builder; nice tool. Please do add "pages=" to the cite book template, though. -- 71.128.189.190 (really User:JesseW/not logged in) 00:01, 9 February 2007 (UTC)
 * Done. Thanks for the suggestion. --David Iberri (talk) 23:56, 10 February 2007 (UTC)

Reference Desk
Thank you for your attempt to answer my question Reference_desk/Science. --Parker007 06:21, 9 February 2007 (UTC)
 * My pleasure. --David Iberri (talk) 01:01, 13 February 2007 (UTC)

Chembox
I wanted to bring Wikipedia talk:Chemical infobox to your attention. At some point someone will probably (ever so politely) ask you to add a feature to your template population tool, filling in molecular formula and weight from a PubChem ID, so I wanted to involve you earlier in the process, if possible. --Arcadian 01:01, 11 February 2007 (UTC)
 * Thanks for the heads-up. I've started a PubChem module and will be incorporating it into the template builder shortly. Cheers, David Iberri (talk) 14:57, 12 February 2007 (UTC)
 * The Chemical infobox seems to be gaining in usage, so I guess the person to make the request will be me -- when you get a chance, could you put in a PubChem module? Your builder has been so helpful for other templates, and I'm sure it would be a great help for this as well, even though it could probably only populate four fields. --Arcadian 23:13, 28 March 2007 (UTC)
 * Thanks for the gentle nudge -- admittedly I forgot about this. :-) I made quite a bit of progress on it last night and will try to finish it up over the weekend. If not, it'll have to wait until after exams (a week from tomorrow). Cheers, David Iberri (talk) 18:16, 29 March 2007 (UTC)
 * I spent a few more minutes on it just now and then I realized that Template:Chembox is used in a very different way than most other infoboxes. The main problem is that it insists you subst the template into the article, then re-edit the article to specify the details about the chemical. My wiki template builder isn't ready to deal with that just yet, so I'll have to take a look at this later after exams. --David Iberri (talk) 20:13, 31 March 2007 (UTC)
 * Sorry, I should have been more clear. The old chembox was like that, but Template:Chembox new is just like DrugBox and the others. It just requires the fields as they exist at Template:Chembox_new. --Arcadian 23:03, 31 March 2007 (UTC)
 * Thanks for putting it in! --Arcadian 22:35, 8 April 2007 (UTC)
 * I see you've noticed it. :-) I wasn't quite finished yet, but I had a spare moment this morning to tidy things up. It should be relatively ready for prime-time, so I announced it at Wikipedia talk:Chemical infobox. --David Iberri (talk) 16:52, 9 April 2007 (UTC)

Wikipedia template filling
--Hoffmeier 00:39, 13 February 2007 (UTC)
 * 1) Great tool!
 * 2) The tool did not create authors with . http://diberri.dyndns.org/wikipedia/templates/?type=pmid&id=17176062
 * Should be fixed now. Thanks for letting me know. --David Iberri (talk) 01:00, 13 February 2007 (UTC)
 * Thanks for the fast fix. Greetings, --Hoffmeier 08:27, 13 February 2007 (UTC)
 * David, is there a way to share your code? I ask you, because your prog is also very useful for the german community, with some minor configs for our citations. Cheers, --Hoffmeier 21:00, 13 February 2007 (UTC)
 * Absolutely. School is keeping me occupied, but I'll put the code online when I get a spare moment. Thanks, David Iberri (talk) 20:20, 14 February 2007 (UTC)

I've updated cite book and cite journal to have explicit isbn=, oclc=, issn=, and pmid= fields. — Omegatron 00:29, 15 February 2007 (UTC)
 * Cool. The template builder now uses "pmid=xxxx" instead of "id=PMID xxxx" for journal article citations. I'm not familiar with issns, so I'm not too sure what to do with that field (does PubMed provide an article's issn?). Book citations should already be using isbn and oclc. Cheers, David Iberri (talk) 02:58, 15 February 2007 (UTC)

I wrote a bookmarklet for using the template builder with a "PMID" without copy & paste (see here: PMID bookmarklet). Maybe you can leave this bookmarklet on the template builder page for everyone who is interested. Greetings, --Hoffmeier 17:17, 16 February 2007 (UTC)

Orphaned fair use image (Image:Cajal.jpg)
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The Template Builder is down!
Your brilliant masterpiece isn't working! I can't get pubmed citations!!!  I tried it from two different IPs with different DNS servers... something's screwy. Jolb 04:57, 23 February 2007 (UTC)
 * Somehow I missed this. Are you still experiencing the problem? --David Iberri (talk) 16:15, 17 April 2007 (UTC)

Adrenaline/Epinephrine
User:The Right Honourable has moved/renamed Epinephrine to the combined Adrenaline/Epinephrine (also Noradrenaline/Norepinephrine). This goes against WP:NC and sets a bad precedent. As an Admin, can you move these articles back please. Thanks, Colin°Talk 09:36, 6 March 2007 (UTC)
 * I've replied at Talk:Epinephrine. --David Iberri (talk) 23:28, 6 March 2007 (UTC)

RE: Illustration request
Great to hear from you again Diberri! This week is slightly busy for me but I think I might be able to do something within the month of April or May. Since you are quite an expert with correcting the accuracy of these medical illustrations, I need to know what exactly may be some key things that need correction in a new image. One more thing I would suggest is to present an image change on the talk page and contact some of the editors of that article you know. That way if I do get around to constructing a new image, most people would agree with changing the one already posted on the article. Pleasure chatting with you!<b style="font-family:comic sans ms; color:purple;">¤~Persian Poet Gal</b> <sup style="color:purple;">(talk) 17:51, 28 March 2007 (UTC)

Wiki markup rather than cite template
Would you consider an option for your tool to generate Wiki markup for the citation rather than templates? If you are too busy, I'd be happy to help if the code was available. You may be interested in the PMID discussion at Wikipedia talk:WikiProject Medicine. Colin°Talk 07:38, 6 April 2007 (UTC)
 * Thanks, Colin. I've replied at Wikipedia talk:WikiProject Medicine. --David Iberri (talk) 17:30, 6 April 2007 (UTC)

Template filler down
The template filler appears to be down. --Arcadian 11:42, 13 April 2007 (UTC)
 * Thanks for the notice. Hunk-o'-junk server ran out of memory, but it's back up now. --David Iberri (talk) 14:32, 13 April 2007 (UTC)

Problem with - causes template filler to error David Ruben Talk 00:13, 17 April 2007 (UTC)
 * Got it. Problem was that one of the authors had no forename listed on PubMed, and until two minutes ago the script assumed a forename would always be present. Fixed now. --David Iberri (talk) 16:14, 17 April 2007 (UTC)

Problem with - its an internet publication ahead of print. The filler tool gives "author=Dorsch, Dorsch, Dorsch, Dorsch, Dorsch, Dorsch, Dorsch, Dorsch, Dorsch" when it should have been "author=Dorsch MP, Lee JS, Lynch DR, Dunn SP, Rodgers JE, Schwartz T, Colby E, Montague D, Smyth SS". Thanks David Ruben Talk 23:27, 29 April 2007 (UTC)
 * Yup, that's weird. I'll take a look at it over the next few days. --David Iberri (talk) 23:49, 29 April 2007 (UTC)
 * Interestingly, the problem went away as soon as I started using the  part of the XML output. There's obviously something I'm not understanding about the way I'm accessing the XML, but I suppose I'll just have to live with that for now. :-) The problem should be (at least symptomatically) resolved now. Cheers, David Iberri (talk) 20:34, 1 May 2007 (UTC)

An excellent response
I just thought I'd drop you a note to applaud your detailed and well-referenced response to a question on the Science Reference Desk: Reference desk/Science.

Keep up the good work! TenOfAllTrades(talk) 02:11, 19 April 2007 (UTC)
 * Thanks! Will do. --David Iberri (talk) 00:55, 23 April 2007 (UTC)

New feature for the template builder
I was thinking, It would be convenient if you could add a "access date" feature to your template builder. So that it automatically adds access dates when you format the studies from pubmed. Is that possible? Wikidudeman  (talk) 10:15, 26 April 2007 (UTC)
 * Good idea. I've added an option to add it when filling out the cite book and cite journal  templates. Cheers, David Iberri (talk) 02:50, 28 April 2007 (UTC)
 * Thanks. This will surely save me a lot of time. Wikidudeman  (talk) 21:33, 28 April 2007 (UTC)

Cite journal language
The template builder correctly shows a paper's title enclosed in square brackets if this is an English translation. PubMed also though shows which language the original was in - could the template filler define the language parameter when this is defined (i.e. if not in English) - it might simplify calls for a seemingly redundant location parameter for the template (see my posting at Template talk:Cite journal). As always, many thanks David Ruben Talk 12:02, 30 April 2007 (UTC)
 * The template builder now fills in the "language" parameter. Thanks for the suggestion. --David Iberri (talk) 18:42, 30 April 2007 (UTC)