User talk:AndrewGNF/Archive2

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Archive This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page.

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Telomerase reverse transcriptase

Hey Andrew! I hate to complain, but I really can't understand the PBB_Summary text you put in Telomerase reverse transcriptase. (on a related note, I can't understand why the body of this article is partly inside a template; that's very unusual). The summary seems to consist entirely of information on telomerase in general, but not on TERT specifically. Also, the summary contains no links, which makes it difficult to understand since it contains so many words that I, and other laypeople, don't know. I was wondering if you might be willing to edit it for clarity. Thanks! --Hyperbole (talk) 23:17, 15 January 2008 (UTC)

Hi Hyperbole... The text in the PBB_Summary template is taken from the Entrez Gene summary for that gene (click the link in the reference). The edits I made to this page are part of a larger effort with the ProteinBoxBot, which systematically adds content from public databases to create/amend gene stubs. The advantage of encasing that text in the PBB_Summary template is that PBB can then update that text whenever it changes at its source without disturbing the rest of the page. Having said that, I'm confident any amount of human contributions will be far superior to our bot auto-added content. If you don't think the text is relevant, feel free to delete it. If you change it substantially, feel free to extract it from the PBB_Summary template. In short, feel free to override anything that PBB does (and that equally applies to the other pages with PBB content). Cheers, AndrewGNF (talk) 23:39, 15 January 2008 (UTC)

ProteinBoxBot's uploads

Per the switch to the new pre-processor (see m:Migration_to_the_new_preprocessor#Expected_differences), the trick of passing template parameters via {{!}} no longer works. This was actually a bug in the old preprocessor, which can be verified by the fact that it only worked if the template argument was inside a parserfunction. On {{self}} for example it would not work for the second argument, only 2 and beyond, which were inside #if.

Furthermore, a bot should probably not be using {{self}}. It would probably be best to replace all instances of:

{{self|GFDL-no-disclaimers|cc-by-sa-3.0{{!}}[[Genomics Institute of the Novartis Research Foundation]]}}

with:

{{GFDL}}
{{cc-by-sa-3.0|[[Genomics Institute of the Novartis Research Foundation]]}}

Would you be willing to fix ProteinBoxBot's uploaded images to no longer break with the new preprocessor (as per the above suggestion)? --MZMcBride (talk) 02:31, 25 January 2008 (UTC)

Thanks for the note. I'm going to move this discussion over to User talk:ProteinBoxBot for a slightly broader audience. Cheers, AndrewGNF (talk) 12:36, 25 January 2008 (UTC)

"I know we're all on the same page looking from slightly different angles"

Hello there...

I am Treesoulja and I am a new wikipedian. I was browsing Tim's talk page and I stumbled apon a quote of yours that I like. I often harvest quotes that I like for some reason or another to use as away messages on AIM or on facebook etc. and I really like your "I know we're all on the same page looking from slightly different angles." How would I go about citing you considering that all I have to go with is Andrew GNF and you probably don't want to give me your full name? This seems silly and you may laugh at my naivite but I thought I would ask.

Newly wiki

Treesoulja (talk) 04:45, 3 February 2008 (UTC)

You made me laugh, but not at your naivete. It's just not a common accusation that I've said something noteworthy, much less something worth quoting. (I've heard another quote that I think applies -- even a blind pig finds an acorn once in a while...) Feel free to cite me as "anonymous", since I'm sure many others have said similar things before. Welcome to wikipedia... Cheers, AndrewGNF (talk) 05:25, 3 February 2008 (UTC)

Re: Image help

I'd be more than happy, but I do have a question or two.

  1. Do you mind if I use bullets instead of a <br> tag?
  2. Will all the sources use the same URL (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=15075390&dopt=Abstract)?
  3. The _tn images use redirects that no longer work. Should these redirects be removed?

--MZMcBride (talk) 22:47, 8 February 2008 (UTC)

Thanks much for your help... Switching to bullets sounds like a good idea. Yes, all images will reference that same link. And, sigh, what to do with those _tn redirects? I really liked the old behavior actually. Well, what do you think of this change for the thumbnails? [1] Think people will care that one image page will include another image in its text region? AndrewGNF (talk) 00:05, 9 February 2008 (UTC)

I can help with the large number of edits that need to be done, but I need to make sure they get done right the first time. There are a couple questions I have:

  • Exactly what information should be decoded from the image title? How is it decoded?
  • What should happen to the images that had redirect tags on them?

I am somewhat busy, or I would be able to do this tomorrow. But I can definitely get the code ready in the first half of this week. — Carl (CBM · talk) 06:05, 9 February 2008 (UTC)

Thanks Carl for your offer of help too... I don't know if MZMcBride was particularly excited to help out with this, and if he's started I'd hate for someone else to start making a similar set of changes and have two people stepping on each other's toes. So, at the point that one of you actually starts coding, can you leave a note here so the other knows? Sound reasonable?
Regardless, your questions are good ones, regardless of who does the work...
  • Image titles look like this: PBB_GE_XXXXX_gnf1hYYYYY_at_ZZ.png. the "XXXXX" is a variable length string (nums and chars) that is the gene symbol. "YYYYYY" is var length string that can be ignored here. and "ZZ" is always two chars -- "fs" or "tn". (fs = full size, tn = thumbnail). The gene symbol should go into the description line in the Summary section (e.g., replacing "NIP1A" in "Gene expression pattern of the NIPA1 gene." in Image:PBB_GE_NIPA1_gnf1h07157_at_tn.png)
  • All of the "tn" used to redirect to the "fs" images. So, I propose to replace the redirect by displaying the FS image itself. For example, [2].
Hope that's clear, but let me know if anything isn't. Appreciate both of your offers for help... Cheers, AndrewGNF (talk) 06:44, 9 February 2008 (UTC)
I was the one who asked Carl for help, because the changes that need to be made are more complicated than a simple find / replace. Either Carl or I will take care of this shortly, depending on who has the time / ability. --MZMcBride (talk) 07:01, 9 February 2008 (UTC)
Some of the images have titles with an extra letter t hat you didn't mention, like PBB_GE_ACTB_200801_x_at_fs.png and PBB_GE_ACSL4_202422_s_at_fs.png. Should I ignore that? It looks like I will be able to start this today, although it will take a while to complete. — Carl (CBM · talk) 13:30, 9 February 2008 (UTC)
Also, we should say who holds the copyright on the images. Is that you? — Carl (CBM · talk) 13:48, 9 February 2008 (UTC)
Super, thanks much to both of you. Yes, that extra character should be treated as part of the YYYY here. As for copyright, is it sufficient to use {{GFDL}} and {{cc-by-sa-3.0|[[Genomics Institute of the Novartis Research Foundation]]}} as in Image:PBB GE NIPA1 gnf1h07157 at tn.png? (Actually, all images should be properly tagged with those templates -- MZMcBride helped make those changes previously...) AndrewGNF (talk) 16:30, 9 February 2008 (UTC)
I just wanted to find out who created the diagrams - did you create them? Also, what do you think of the full reference at Image:PBB GE A2BP1 221217 s at fs.png? — Carl (CBM · talk) 20:37, 9 February 2008 (UTC)
As long as we're editing anyway, may be worthwhile to switch Template:GFDL to Template:GFDL. --MZMcBride (talk) 20:41, 9 February 2008 (UTC)
I made one change to the formatting of the reference at Image:PBB GE A2BP1 221217 s at fs.png -- figured we might as well use a standard reference template. And yes, I created them. Agreed on the update to {{GFDL}}. Thanks! AndrewGNF (talk) 00:29, 10 February 2008 (UTC)
Not to throw another wrench in the machinery, but perhaps a template for the source information could be used instead of inserting "Description:..." 20,000 times. A template could simply be {{Protein_cite|A2BP1}} or whatever. It would make any future changes a lot easier (wording, grammar, adding links, etc.). --MZMcBride (talk) 01:02, 10 February 2008 (UTC)
Yes, that would made sense. — Carl (CBM · talk) 01:07, 10 February 2008 (UTC)
Andrew: If you made the images, even if the numerical data come from somewhere else, the copyright is probably yours; I want to make sure everything is perfect before making all the changes. Is this right - you got numerical data from somewhere, and made the images from that? — Carl (CBM · talk) 01:07, 10 February 2008 (UTC)
The copyright for both the images and the data should go to the Genomics Institute of the Novartis Research Foundation. Although I made the images, I did it with resources provided by them and (loosely) under the guise of an academic project funded by them. Hope that makes sense... AndrewGNF (talk) 01:15, 10 February 2008 (UTC)
Oh, also want to point out that the gene symbol was parsed out incorrectly. I made the change on our example Image:PBB GE A2BP1 221217 s at fs.png. AndrewGNF (talk) 01:18, 10 February 2008 (UTC)
Took a crack at the citation template (e.g.,{{PBB Image citation|TEST}}):


How does that look? (good idea MZMcBride, hopefully that will make this be the very last mass edit we need to make...) AndrewGNF (talk) 01:23, 10 February 2008 (UTC)

Thanks for pointing out the parsing error and for making the template. I understand the copyright better now. I'm going to set things up and make a few test edits. — Carl (CBM · talk) 01:27, 10 February 2008 (UTC)

I made two test edits, at Image:PBB_GE_A4GALT_219488_at_fs.png and Image:PBB_GE_A2BP1_221217_s_at_tn.png. Let me know if those look right. — Carl (CBM · talk) 01:48, 10 February 2008 (UTC)

Looks great to me! AndrewGNF (talk) 02:54, 10 February 2008 (UTC)
Carl, just wanted to say that the image corrections look great! I'll be in and out for the next couple of days (mostly out), but just wanted to note my appreciation... Many thanks! AndrewGNF (talk) 15:24, 10 February 2008 (UTC)
No problem, you're welcome. I'm also very busy this week, and I forgot to leave a note here a couple days ago when the corrections finished. I think the images are all changed, but I'll double check in the coming week. — Carl (CBM · talk) 12:57, 14 February 2008 (UTC)

Speedy deletion of Template:GNF SymAtlas

A tag has been placed on Template:GNF SymAtlas requesting that it be speedily deleted from Wikipedia. This has been done under section T3 of the criteria for speedy deletion, because it is a deprecated or orphaned template. After seven days, if it is still unused and the speedy deletion tag has not been removed, the template will be deleted.

If the template is intended to be substituted, please feel free to remove the speedy deletion tag and please consider putting a note on the template's page indicating that it is substituted so as to avoid any future mistakes (<noinclude>{{transclusionless}}</noinclude>).

Thanks. --MZMcBride (talk) 21:31, 14 February 2008 (UTC)

Thanks for the note. I think that must have been an obsolete template we played with while we were developing. No objection from me for this deletion... AndrewGNF (talk) 21:49, 14 February 2008 (UTC)

My what a lovely bot!

Hi Andrew, I constantly stumble onto the many pages created by your wonderful ProteinBoxBot, which I think is great for getting the basic gene/protein info to all us sciency folks who need it. However, as I run into these pages, I always find I need to tag 'em with the MCB wikiproject tag, to alert the project a new stub is out there that needs some work. Is there any way you could get the bot (or a "follow up" bot?) to automate this process too, when a new page is created? Otherwise, I don't think we'll be able to keep up ;o)

All the bot would need to do is add:

{{Wikiproject MCB|class=stub}}


to the top of each talk page that exists for a ProteinBoxBot generated page. Is it possible, or too difficult to do - I am not a programming genius, so have no clue what is involved!!! ~ Ciar ~ (Talk to me!) 23:43, 15 February 2008 (UTC)

Thanks for the note Ciar. And yes, I've noticed you're been among the faithful few who have been adding the wikiproject templates, so thanks for that. Unfortunately, right now we're trying hard to wrap up the version 1.0 run of the bot without making too many changes to the code itself. (Incidentally, I think we're pretty close. I count 8427 PBB-enabled gene pages in existence.) Adding the MCB template is definitely on our list of Version 2.0 specs, but no promises on when that may get done. A separate "follow up" bot may also be a possibility... Sorry to be noncommittal, but you're welcome to try to drum up support at the MCB proposals page or the bot requests page. Cheers, AndrewGNF (talk) 01:19, 16 February 2008 (UTC)

Re: have we met?

Hello, Andrew. :) Yes, we briefly before I left for my extended wikibreak about a year ago. We worked on the WP:MCB a little together. – ClockworkSoul 20:09, 25 February 2008 (UTC)

Thanks

Thank you so much for all your help. I was struggling to get the references right! You're a life saver. My genetics professor had us expand a wiki stub for a quiz. Thanks again. ~Daisher


Wanted to let you know I told my professor that you helped edit my references and actually she had a good laugh when I told her the story how I kept editing and you broke in saying, "If you stop editing for a min I will help you". She said the purpose was to find more info on the topic and expand the article, not the actual posting as much. Thanks once again! —Preceding unsigned comment added by Daishermj (talk • contribs) 05:32, 1 March 2008 (UTC)

Gene expression data on Insulin Receptor Protein Box

The gene expression section of the protein box makes no sense (even to an Affymetrix user) as the images are unlabelled when you link through to them. Thus rendering it simply a pretty picture devoid of information. I can update the at_xxxx tag info when I get time. But at present you can't work out why there are two graphs or why the expression data is so different. Just a comment in case this isn't just a problem with this single protein... Ianmc (talk) 21:22, 3 March 2008 (UTC)

Hi Ianmc... I'm not sure what you mean by "unlabelled when you link through to them". Can you clarify? Also, yes, undoubtedly some of the gene expression graphs do not report meaningful data. Thankfully, in the case of INSR, it was easy to see which was the "dead" probe set so I went ahead and deleted it from the page. Cheers, AndrewGNF (talk) 01:45, 4 March 2008 (UTC)
For instance the source article is human and mouse, but the graph is actually human data. Also you might want to point out that the title shown on the graph is a microarray code and can be ignored or what the bars actually represent. I don't mean to teach you to suck eggs but also a general rule in scientific publishing is that a figure (+legend) should be interpretable without reference to the text. I assume you would be able to add a couple of sentences of boilerplate to you bot to cover all of the preceding suggestions. Hopefully this is constructive criticism I think it is a very useful piece of information to include in the protein box (I spend all day making this sort of data :-). Ianmc (talk) 23:12, 4 March 2008 (UTC)

RE: Too biting?

I understand what you mean, but I don't think the warning was too severe. It points out what he did wrong instead of saying "don't do this or else". WEBURIEDOURSECRETSINTHEGARDEN aka john lennon 20:00, 4 March 2008 (UTC)

Ok, will keep that in mind, thanks mate WEBURIEDOURSECRETSINTHEGARDEN aka john lennon 20:12, 4 March 2008 (UTC)

Move, sure

No probs. Tim Vickers (talk) 22:51, 4 March 2008 (UTC)

Protein/gene stubs

You may wish to comment on this proposal to split up the present Cat:protein stubs, as it would affect the large number of gene articles your bot's been creating. (Not deleteriously, I trust.) Alai (talk) 04:53, 16 March 2008 (UTC)

Reply

Thank you very much for offer, but I consider my activities in WP mostly as entertainment. You can tell thanks to WP community in general if you wish.Biophys (talk) 21:12, 19 March 2008 (UTC)

I have definitely done that, with particular emphasis on the MCB project. Anyway, thanks again for past and future feedback... Cheers, AndrewGNF (talk) 00:16, 20 March 2008 (UTC)

'Protein Box Bot' and 'GNF Protein box'?

Hi! Great bot! Really staggeringly cool!

I am here because I started to try to unify the various {{PDB}} templates... I would like to turn all calls to all the different templates [3] into simple {{PDB link|1xyz}} calls.

If I do this, can you change your bot to use {{PDB link}} in future? Or do you prefer {{PDB}}?

Anyway... I was wondering also if you could add all pages that use the 'GNF Protein box' into a "GNF Protein" Category (or similar)? I was going to do this myself, but I am not sure if a suitable category already exists.

Finally, what other "protein box"es does Protein Box Bot (or you) maintain? Can you make a category for the boxes that protein box bot is in charge of? Sorry - but I didn't see an easy way to navigate to that data if it exists.

BTW, I didn't read all your work in detail yet, how do you handle user edits of database derived data? Do you have any protocol / plan to sync data back to the source databases?

If you are interested, you may like to look at the site I set up with some friends of mine here PDBWiki - if you have any interesting ideas for bots on that site we would be very interested to collaborate :-D

In the mean time I will read up more about your work!

All the best, --Dan|(talk) 13:20, 3 April 2008 (UTC)

Hi Dan, I replied to your post over at the MCB help page. In short, we use {{PDB2}} because it is the most visually concise method, and that helps keep the overall infobox a manageable size. As far as categorization, all pages maintained by PBB are tagged with Category:Human proteins. The goal was not to create a PBB-specific category, since categories should really reflect the scientific concept and not the technical aspect of how content is created/maintained. In terms of edits to database-derived data, we certainly encourage people to correct missing/incorrect content, and they can turn off automatic-updates using the {{PBB_Controls}} template found at the top of every PBB-maintained page. No mechanism to propagate that data back to the source databases since NCBI hasn't given me the keys to their database yet... ;) Phil Bourne did point out PDBWiki to me recently. Looks cool! I offered to change our PDB links to go there instead, but never heard back from him whether that would be desirable. Hey, maybe an interesting bot task would be to add a link to the PDBWiki from all the PDB images that PBB uploads? That would be a very useful link to have somewhere (although it would be one link deep...) Cheers, AndrewGNF (talk) 16:17, 3 April 2008 (UTC)
Hey Andrew, I am really glad that you like PDBWiki - its an ongoing experiment in user contributed feedback and collaborative annotation... Its going to be fun to see how it turns out. Links to PDBWiki from Wikipedia would be really great, as I think it (partly) solves the debate about which derived database we should link to. PDBWiki links each 'PDB entry' page to a growing (and user contribute-able) list of external databases. In this way people could click through to their favorite derived resource, instead of having one specific external link as it is at the moment. Thanks for the comments on the {{PDB}} - it all makes sense. BTW, do you have examples of user edits to database derived data? Do you check for (and annotate) conflicts as part of the update process? I am still in awe of what you have achieved with PBB. I am really looking forward to watching this all pan out! All the best, --Dan|(talk) 17:09, 5 April 2008 (UTC)
If Dan tells which PDBWiki entries have been annotated and contain information of interest, we could make some links to them. Right now, this can better work the opposite way: Dan should make the links from PDBwiki to Wikipedia. Of course Dan could ask Phil about a possibility of making links from original PDB entries (rather than from PDBWiki entries) to WP. In the long run, all PDB entries should have at least one link to WP articles, but that would be a tall order.Biophys (talk) 17:47, 5 April 2008 (UTC)

Hmmm, what do you guys think about combining this task with the mass upload of PDB images we discussed earlier? (I know Willow is tentatively signed up to take this on, but it looks like she's got her hands full with the action potential FAR. Dan, if you wanted to take this on, I don't think she would object...) Then, on the image pages themselves, we can put links to all the various databases (including PDBwiki) in a "See also" section so that readers can individually pick what pros and cons matter to them. Thoughts? AndrewGNF (talk) 19:55, 5 April 2008 (UTC)

Right. I left my suggestions there. If Dan or someone else can implement this, it would be really great.Biophys (talk) 16:13, 6 April 2008 (UTC)

DCC Page

Hi Andrew, thanks for the positive comments! (Hopefully this is a good place to reply to them.) The wiki page was a project completed for a course on the genetics of cancer. This was the first year the course has been run, so I'm not sure if they'll continue the idea for next year, but it was well received by the students. Approximately 30 students created similar pages on cancer related genes for the course, but I believe that only some of them received approval (and bonus marks) by the course director for wiki posting. Thanks for the edits - we were given instruction on wiki functions, but not much in the way of style or formatting details. I'll forward what you've posted on to the course director and hopefully he can include some of that in the syllabus for the next round. If you'd like to take a look at the course page, here's the link - http://burgundy.cmmt.ubc.ca/medg421/wiki/index.php/Category:Genes. Kkott (talk) 00:33, 23 April 2008 (UTC)

Hi there! I just stumbled on your page by accident and saw this bit regarding the educational assignment, well I just happened to have been involved (as a wikipedian, not student or professor) in the last three months in what was the most ambitious and highest achieving WP educational project to date. In the end, 3 featured articles and 8 Good articles were created and alot of lessons learned. The professor involved user:jbmurray wrote an essay about the experience and is in the process of writing a guide of sorts, which I belive would be very usefull to anybody wanting to use WP as an educational tool. The project's page is WP:MMM. It might be worth taking a look. Cheers! Acer (talk) 00:50, 27 April 2008 (UTC)