Wikipedia talk:WikiProject Molecular and Cell Biology

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A thorough review of the gene article[edit]

Transcluded from Talk:Gene/Review

To WP:MCB, WP:GEN, WP:BIOL and WP:EB

The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo)talk 09:49, 31 March 2015 (UTC)

It appears the main reason gene was delisted as a GA was sourcing (see Talk:Gene/GA1). The following free textbook is probably sufficient to document most basic facts about genes:
a second one is even more relevant, but unfortunately not freely accessed:
I will start working on this as I find time. Boghog (talk) 17:58, 31 March 2015 (UTC)
Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to give it some attention. Opabinia regalis (talk) 19:19, 31 March 2015 (UTC)
I'll probably go through and make all the necessary MOS tweaks for FA status to the article within the next week. Too preoccupied with other articles at the moment to make any substantive content/reference changes though. Seppi333 (Insert  | Maintained) 03:24, 1 April 2015 (UTC)

Glossary[edit]

Snooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. --Squidonius (talk) 21:47, 1 April 2015 (UTC)

Including a glossary could be useful, but I think it should be concise and tailored specifically for this article. Currently {{Genetics glossary}} contains 22 entries and some of the definitions are quite lengthy. A shorter glossary, closer to the size of {{Transcription factor glossary}} or {{Restriction enzyme glossary}}, IMHO would be more effective. Another option is to transclude the {{Genetics sidebar}} which in turn links to {{Genetics glossary}}. Boghog (talk) 06:38, 2 April 2015 (UTC)
...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence. Seppi333 (Insert  | Maintained) 07:25, 2 April 2015 (UTC)
Collapsed or not collapsed, {{Genetics glossary}} is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article. IMHO, a long glossary defeats its purpose. Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse. Boghog (talk) 08:30, 2 April 2015 (UTC)
Fair enough. Might as well make a new one since it's not referenced anyway; imo, glossaries should cite sources, preferably another glossary, because it's article content. Seppi333 (Insert  | Maintained) 08:39, 2 April 2015 (UTC)
Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article genetics glossary. (I'm not really sure we need both.) I agree that the template is way too long, and as constructed is hard to ctrl-F for a term.
I suggest just linking to the MBC glossary as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers. Opabinia regalis (talk) 21:47, 2 April 2015 (UTC)

References[edit]

I'm planning on adding some more Molecular Biology of the Cell references to the article using {{rp}} to specify chapter sections. I went to the MBOC 4th ed. online page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for Biochemistry 5th ed. online? Alternatively, maybe there's a more easily refernced online textbook for general citations. T.Shafee(Evo﹠Evo)talk 11:30, 20 April 2015 (UTC)

I had the same train of thought here on the regular talk page. How about something like this? Uses {{sfn}} to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'. Opabinia regalis (talk) 06:09, 21 April 2015 (UTC)
You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful. T.Shafee(Evo﹠Evo)talk 08:06, 21 April 2015 (UTC)
I am not a big fan of {{sfn}} templates. They are more complicated and harder to maintain. Plus they don't directly address the problem of searching Molecular Biology of the Cell. What seems to work is to search for the chapter or subchapter titles in quotes. For example search for "DNA and Chromosomes" provides a link to the introduction of chapter 4. Then one can reference the chapter or subchapter number with {{rp}}. I am busy this week but should have more time this weekend to work on this. Boghog (talk) 12:21, 21 April 2015 (UTC)
I mis-described my own suggestion; it's actually {{efn}} (not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use {{rp}} like this, but I think the links police won't like that. Opabinia regalis (talk) 18:03, 21 April 2015 (UTC)
OK, I now see what you mean. The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
or have separate citations for each chapter where only the |chapter= and |chapterurl= parameters differ:
Boghog (talk) 18:47, 21 April 2015 (UTC)
My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a bit silly. I think I like that idea in combination with {{rp}} chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting. Opabinia regalis (talk) 20:49, 21 April 2015 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat. T.Shafee(Evo﹠Evo)talk 12:24, 22 April 2015 (UTC)

You're the one currently doing the work, so I think that means you get to decide :) Opabinia regalis (talk) 19:01, 22 April 2015 (UTC)

MBOC references[edit]

Article

Genes[1]:2 are numerous[1]:4 and useful[1]:4.1

References

  1. ^ a b c Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. 
Glossary
Ch 2: Cell Chemistry and Biosynthesis
2.1: The Chemical Components of a Cell
Ch 4: DNA and Chromosomes
4.1: The Structure and Function of DNA
4.2: Chromosomal DNA and Its Packaging in the Chromatin Fiber
Ch 6: How Cells Read the Genome: From DNA to Protein
6.1: DNA to RNA
6.2: RNA to Protein
Ch 7: Control of Gene Expression

So {{rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo)talk 01:29, 27 April 2015 (UTC)

I've finished adding MBOC references up to section 3 (gene expression). Also, whoever originally wrote the gene expression section of the article really liked semicolons! T.Shafee(Evo﹠Evo)talk 10:51, 27 April 2015 (UTC)
Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in WP:ACCESSIBILITY so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue. Opabinia regalis (talk) 07:50, 28 April 2015 (UTC)
@Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS." I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view. I tried setting the template parameter expand=true so the box is expanded by default but that made no difference. Maybe better to change to a bulleted or indented list? Adrian J. Hunter(talkcontribs) 10:50, 30 June 2015 (UTC)
@Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in {{Hidden begin}} + {{Hidden end}}, which renders properly on phones (default expanded). T.Shafee(Evo﹠Evo)talk 12:31, 30 June 2015 (UTC)
Yep, that works – thanks! Adrian J. Hunter(talkcontribs) 13:23, 30 June 2015 (UTC)

Reclassification of Cyclopenenone prostaglandins[edit]

Would someone review the Cyclopentenone prostaglandins article for the purpose of reclassifying it? The article has recently been greatly expanded. Although it is categorized as a Pharmacy and Pharmacology article, it is better categorized in the Molecular and Cellular biology section. All of the prostaglandins are so categorized (e.g. see prostaglandin). Also, the article as currently formatted is correctly redirected from 15-deoxy-Δ12,14-prostaglandin J2 (15-d-Δ12,14-PGJ2), a principal cycloentenone prostaglandin. Is it possible to similarly redirect it from other cyclopenentone prostaglandins viz., Δ12-PGJ2, PGJ2, PGA2, and PGA1, discussed in the article (but not given separate Wikipedia pages elsewhere) and, if so, how do I do that? Thanks, (User talk:joflaher). 6 December 2016 (UTC)

Revisit figure of Illumina dye sequencing[edit]

Illumina sequencing is a very important method to know nowadays, as least for anyone working in molecular biotechnology. The figure for the creation of clusters is correct, but could use someone who puts in some love. It was obviously drawn quickly and I think the article deserves more.

https://en.wikipedia.org/wiki/Illumina_dye_sequencing

There are many nice resources to find inspirations, such as the Youtube channel of illumina.

Assessment of class and importance[edit]

Hi. I recently started assessing unassessed articles tagged with WP:MCB. So far I have reduced the backlog from about 1.800 to 1.250. However, since I normally do most of my work on anatomy and medicine related articles I find it very hard to asses importance for MCB articles, so at the moment I am only assessing class and NOT importance. If anybody is interested in helping (so class and importance can be rated simultaneously) I can recommend the Rater gadget and unassessed articles for our project can be found here and if you only would like to rate by importance have a look here. Kind regards JakobSteenberg (talk) 14:53, 13 May 2017 (UTC)

@JakobSteenberg: I'll try to lend a hand this week. I should be able to do a couple of hundred. T.Shafee(Evo&Evo)talk 00:18, 15 May 2017 (UTC)
If anyone else would be happy to tackle a few of these, I'd gladly accept the help. I've got through a few hundred (of the ~2000 total). Most of them are low-importance stub/starts like enzymes and metabolites. Note: Enzymes don't need to be tagged for WP:CHEMS, but metabolites should. T.Shafee(Evo&Evo)talk 14:06, 16 June 2017 (UTC) (Gentle ping Boghog, Seppi333, Adrian J. Hunter, Jytdog, JeanOhm)

AfD notification[edit]

Sorry, me again. This time its an AfD of Chronic cellular dehydration, here. Thoughts and comments from interested parties would be appreciated. Thanks! Ajpolino (talk) 16:56, 7 June 2017 (UTC)

Facto Post – Issue 1 – 14 June 2017[edit]

Facto Post – Issue 1 – 14 June 2017
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Editorial

This newsletter starts with the motto "common endeavour for 21st century content". To unpack that slogan somewhat, we are particularly interested in the new, post-Wikidata collection of techniques that are flourishing under the Wikimedia collaborative umbrella. To linked data, SPARQL queries and WikiCite, add gamified participation, text mining and new holding areas, with bots, tech and humans working harmoniously.

Scientists, librarians and Wikimedians are coming together and providing a more unified view of an emerging area. Further integration of both its community and its technical aspects can be anticipated.

While Wikipedia will remain the discursive heart of Wikimedia, data-rich and semantic content will support it. We'll aim to be both broad and selective in our coverage. This publication Facto Post (the very opposite of retroactive) and call to action are brought to you monthly by ContentMine.

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Transfer "Light-independent reactions" to another project?[edit]

Hello. I started a discussion at Talk:Light-independent reactions about transferring the whole article "Light-independent reactions" to a sister project, like either Wikiversity or Wikibooks. I realized that whoever would request an importation on the whole article should work on the article. Because I can't be the one working on it or requesting a transfer, I hope that someone else interested can go to v:Wikiversity:Import and/or b:Wikibooks:Requests for import and work on an imported copy at either Wikiversity or Wikibooks. Anyone interested? Thanks. --George Ho (talk) 16:46, 28 June 2017 (UTC)

brcaexchange.org[edit]

Do folks feel like brcaexchange.org is a valuable addition to the 3 BRCA articles? An IP keeps trying to force it into WP. I have been removing it, and also cleaned the ELs on those articles today as they had become all crufted over. Jytdog (talk) 19:36, 11 July 2017 (UTC)

I think it is probably appropriate for BRCA mutation as a database of variants. I don't really know the difference between that database and e.g. the universal mutation database or the brca database. For BRCA1 and BRCA2, I'd probably leave the cancer.gov link too. In general, I think that a long article can supprt 4-8 external links if they are distinct from one another (e.g. scientific database, patient information, etc). T.Shafee(Evo&Evo)talk 00:43, 12 July 2017 (UTC)

Facto Post – Issue 2 – 13 July 2017[edit]

Facto Post – Issue 2 – 13 July 2017
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Editorial: Core models and topics[edit]

Wikimedians interest themselves in everything under the sun — and then some. Discussion on "core topics" may, oddly, be a fringe activity, and was popular here a decade ago.

The situation on Wikidata today does resemble the halcyon days of 2006 of the English Wikipedia. The growth is there, and the reliability and stylistic issues are not yet pressing in on the project. Its Berlin conference at the end of October will have five years of achievement to celebrate. Think Wikimania Frankfurt 2005.

Progress must be made, however, on referencing "core facts". This has two parts: replacing "imported from Wikipedia" in referencing by external authorities; and picking out statements, such as dates and family relationships, that must not only be reliable but be seen to be reliable.

In addition, there are many properties on Wikidata lacking a clear data model. An emerging consensus may push to the front key sourcing and biomedical properties as requiring urgent attention. Wikidata's "manual of style" is currently distributed over thousands of discussions. To make it coalesce, work on such a core is needed.

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Tris[edit]

Could someone fix this part of the Tris page?

I can't tell what it's trying to say!

Thanks DemandAmbition (talk) 09:53, 21 July 2017 (UTC)

I've had a go. Hopefully the wording is a little clearer now. T.Shafee(Evo&Evo)talk 11:24, 21 July 2017 (UTC)