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There are many small Wikiprojects within biology (compares to unified WP:Physics or WP:Medicine) with large overlaps in scope. Their efforts could be more efficient if joined into larger projects.
A Possible unification of some of the sub-cellular wikiprojects with large scope overlaps, including:
Initial draft structure:
T.Shafee(Evo&Evo)talk 02:17, 26 May 2019 (UTC)
There's a discussion about a possible User Group for STEM over at Meta:Talk:STEM_Wiki_User_Group. The idea would be to help coordinate, collaborate and network cross-subject, cross-wiki and cross-language to share experience and resources that may be valuable to the relevant wikiprojects. Current discussion includes preferred scope and structure. T.Shafee(Evo&Evo)talk 12:22, 16 June 2019 (UTC)
You are invited to join the discussion at Draft talk:Horizontal transfer of mitochondria#Opinions of subject matter experts sought. Worldbruce (talk) 14:47, 24 June 2019 (UTC)
Just an FYI, our Zika logo above is the cover image of the May/June issue of Laboratory Equipment, which has an article on the intersection of art and science.[1] Congratulations to artist David Goodsell for scoring a cover page. --{{u|Mark viking}} {Talk}
18:39, 26 June 2019 (UTC)
Hello everyone, i am the author of the DNA replication image give or take i made this image arround 2007, i have been asked to modify it to incorporate all the comments and corrections made on the discussion page plus someone left the following request on the Graphics lab on commons:
Now I am an illustrator and by no means expert in this subject so i would really appreciate if someone with the appropriate knowledge could have a look on this Sketch. it isnt yet on its final form but the elements are in the relative position i am hoping them to have (all marked with ? would need some reassuring). also there is like a ton of questions i would really want to have answer if that is ok:
if you would be so kind to answer my questions i could at least have some degree of confidence in remaking the image in a better more accurate state. 大诺史 was kind to offer this article as reference [2]. I look forward to your feedback. and thank you for your time -LadyofHats (talk) 18:58, 5 June 2019 (UTC)
@Prometheus720: and @LadyofHats: First, a couple of important caveats. I am primarily a geneticist rather than a biochemist and I'm happy to be corrected by any of my more biochemically oriented colleagues who may be reading this. It appears to me that you are trying to illustrate eukaryotic DNA replication (at least that's the nomenclature you are using). That's fine, and I've geared my answer with that in mind, but be aware that there are significant difference between eukaryotic and prokaryotic replication (as well as commonalities). Having said that, my answers to your queries (in the order you asked them) are:
I hope that's of some small help. Good luck!Gcopenhaver1 (talk) 18:41, 17 June 2019 (UTC)Gcopenhaver1
Please have a look at this Final draft and let me know if it is ok or in your opinion needs any changes -LadyofHats (talk) 10:31, 28 June 2019 (UTC)
final version is here
-LadyofHats (talk) 21:33, 2 July 2019 (UTC)
@Gcopenhaver1:, do you have any further comments? I may have missed something here. Prometheus720 (talk) 21:50, 2 July 2019 (UTC)
I just noticed that Topoisomerase and DNA Topoisomerase should probably be merged (discussion here). Would anyone be interested in looking through to see if anything is salvageable? T.Shafee(Evo&Evo)talk 11:13, 7 July 2019 (UTC)
One of the achievements of WP:Biophysics back in 2014 was persuading David Goodsell and the PDB to release a whole load of images under CC-BY. I've finished uploading all the released molecular landscape images. Plenty of the Molecule of the Month images are already uploaded, but there are significant gaps (I've renamed them per their series number). If anyone would be happy to help upload some of the missing ones (and the new ones as they come out) it'd be greatly appreciated! T.Shafee(Evo&Evo)talk 01:32, 14 July 2019 (UTC)
I would say that somewhere in the projects and partnerships area we should consider giving some information on other Wikiprojects. If we don't want to do the whole structure of WP:BIOL and its daughter projects, we should at least get WP:BIOL, WP:Micro, WP:Physio, and WP:MED as those projects would likely be of most interest to participants here.
As for discussions, is there a way to hook in the talk pages for those projects until we actually merge them?
And then, as for metrics, I'm thinking that we need to see if we can include something about how those are measured. Maybe a link to the rubric and some information about how we run our assessments (in the future of course). I'd be happy to scrounge that up if you think that sounds good. Also noting the absence of WP:BIOP. Are we going to fold that into the other taskforces, or did you just not include it for some other reason?
Finally, in metrics, I have been bothered for some time about COMBIO's lack of expanded article classes and just chucking everything into NA. Now it also bothers me that the charts are uneven. To me, it is a good thing to be able to keep track of redirects and category pages and so on. What are your thoughts on having a conversation about expanding that? Prometheus720 (talk) 15:58, 28 May 2019 (UTC)
The current draft name is WikiProject Genetic, Molecular and Cellular Biology. I'd be a fan of a shorter name, since even this long name omits developmental biology, microbiology, biochemistry, biophysics, bioinformatics, computational biology etc. My suggestion would be something like WikiProject Molecular Biology or similar, but I'm flexible and happy to wait for more people to contribute to a consensus. T.Shafee(Evo&Evo)talk 07:47, 29 May 2019 (UTC)
The old WP:WikiProject_Molecular_Biology was a redirect to WP:MCB. A discussion to delete it to make space for this wikiproject is here. T.Shafee(Evo&Evo)talk 10:32, 15 June 2019 (UTC)
I've asked about the technical/practical aspects of merging wikiprojects over at the WikiProject_Council talkpage. T.Shafee(Evo&Evo)talk 13:25, 5 June 2019 (UTC)
{{WikiProject Molecular Biology}}
. T.Shafee(Evo&Evo)talk 11:46, 15 June 2019 (UTC)I've done a bit of digging and it seems that Discussions on other WPX projects are populated by User:Reports bot, and that one must somehow subscribe to this bot in order to receive Discussion links. The bot (as well as the Requests system) is maintained by User:Harej who is semi-inactive.
I took a look at his contribs to see if he has done any setup before, and found this diff in which it seems he input parameters for a Wikiproject in order to set it up for various WPX things. I believe that this is where we need to go. Due to WP:OWN I don't think it should be a problem for us to just go in and input parameters for GMCB/BIOL/any other projects we redesign--however, after a first glance I'm not entirely sure I understand everything on that page.
@Isarra and Evolution and evolvability: Does this seem correct to both of you? We may have to try emailing Harej soon. Prometheus720 (talk) 17:43, 9 June 2019 (UTC)
I just tried adding myself as a member and the GUI hangs. It's been loading for several minutes. I'll be working on the same module for WP:BIOL soon enough so I may be of some help then. Just thought I would mention it now, though, in case it's an easy fix. Prometheus720 (talk) 18:51, 11 June 2019 (UTC)
{{WPX member box}}
, which creates be calling the link:https://www.search.com.vn/wiki/?action=edit&preload=Template:WikiProjectCard/Preload&editintro=Template:WikiProjectCard/Editintro&summary=Joining+WikiProject&title=Special:MyPage/WikiProjectCards/WikiProject_Molecular_Biology&create=Join+WikiProject
{{Load_WikiProject_Modules}}
so that it can be replicated if needed? I'll also work on adding the documentation of steps that I took in using the template/module. T.Shafee(Evo&Evo)talk 03:29, 20 June 2019 (UTC)There is an additional problem. I used the join feature like a month ago, and I just had to add my card manually. It was my understanding that User:Reports_bot is supposed to do this. I didn't sign us up because I wasn't entirely sure how to do so properly and Harej is very hard to get a hold of. I see that he actually made an edit fairly recently and I will try once again to contact him. If we don't get a response I'm going to go ahead and sign up for reports bot.
As a separate issue, we don't have any members. I am considering collecting have collected a full, organized list of members for the various taskforces and am now considering entering a mass message request to notify all of them and ask them to join the new and improved project. Do you feel ready for that, or would you rather wait? Prometheus720 (talk) 15:27, 6 July 2019 (UTC)
I was editing WP:BIOL's statistics section to have a collapsible bit that showed a table of small stat tables--actually I copied the code from the Metrics section you built here and tweaked it a bit. Thanks for making that!
In the process I found out that WikiProject Ecoregions does not have stats via WP 1.0 bot in order to even generate a table. We will have to deal with that here as well, sooner or later. So I'm gonna link you to the guide at Wikipedia:Version 1.0 Editorial Team/Using the bot#Setting up for the bot. It will not be totally possible to get this working until we have a talk page template here, but it should not be too hard to basically just copy off of similar projects and then tweak to make sure it supports what we do and do not want to support.
One thing that has bothered me about COMBIO for example is that it doesn't support article classes like file, template, redirect, etc. Everything just goes into NA and in a big project like this will be, that is not ok. So I would wish for something more like MCB's, which has pretty much whatever we would need at first glance.
In the mean time I will be setting this up for WP:Ecoregions since they already have most of the stuff they need for the bot to run. If you want I can help set it up here when we are ready, or you can get started yourself. Up to you/your schedule. See ya! Prometheus720 (talk) 20:06, 13 June 2019 (UTC)
Wow, that was something to wake up to! I'm concerned about a lot of broken links and so on. What do we need to do in order to take care of that? Here is the What Links Here on the old redirect. I also notice that Wikipedia:WikiProject_Molecular_Biology/Molecular_and_Cell_Biology did not do so well in the move. The page history doesn't show me what it used to look like, either. What can we do about that?
I haven't looked at BIOP yet but I bet it's in similar shape, only with less stuff in it.
Finally, why didn't you move GEN yet? I know people asked us to wait on COMBIO. Did people ask that for GEN as well? Or are we just doing this bit by bit? Prometheus720 (talk) 16:45, 15 June 2019 (UTC)
We'll want some links to the active (and inactive) taskforces somewhere on the main WP:MOLBIO page, as well as the talkpages on the this page. I'll format up some simple templates asap and we can work out where is the best place to put them (as well as how to best consolidate the archive links, proably something like {{MedTalkheader}}
). After that we can take our time in any formatting changes that would be useful for the taskforces and decide whether the Biophysics taskforce should be marked as inactive. T.Shafee(Evo&Evo)talk 13:02, 16 June 2019 (UTC)
{{MolBioTalkheader}}
and {{MolBioTalkheader/Taskforce}}
to start to clarify the relationships and what should be posted where. Some posts have still been made to multiple taskforce talkpages that might be more sensible to post just this page. The headers should format nicely at any width and I've also added WP:WPMP to the list. Will do a bit of simplification and cleanup on the WP main pages in bits and pieces over the coming weeks. T.Shafee(Evo&Evo)talk 12:37, 6 July 2019 (UTC){{MolBioHeader/Taskforce}}
. Still need to list the taskforces on each of the pages (ideally clear, without being obtrusive, or taking up too much space). T.Shafee(Evo&Evo)talk 12:19, 14 July 2019 (UTC)Hi all,
I would appreciate your input in this strange case: Wikipedia_talk:Copyright_problems#Wikipedia_page_"later"_published_in_scientific_paper:_copyvio?.
--Steven Fruitsmaak (Reply) 20:03, 20 July 2019 (UTC)
(RfC link) There's a discussion here about best applying relative due weights to a molbio topic with multiple competing hypotheses that could benefit from the input of some experienced wikipedians. T.Shafee(Evo&Evo)talk 01:52, 24 July 2019 (UTC)
An article that you have been involved in editing—CD64_(biology)—has been proposed for merging with another article. If you are interested, please participate in the merger discussion. Thank you. SCIdude (talk) 14:44, 19 August 2019 (UTC)
There seems to be a whole group of articles on Kuo-Chen Chou and his findings that are highly promotional, hard to understand, almost exclusively reference his own papers, and have been created/expanded by a few editors whose sole editing focus seems to be this topic. I've poked around a bit, but I don't really understand the topic. Does anyone have more familiarity with the topic? Can't tell if these articles just need to be cleaned up, or if some merging/redirecting/deletion might be in order for some of these. Articles I've noticed so far:
Any insight would be helpful. Thanks! Ajpolino (talk) 20:49, 21 August 2019 (UTC)
FYI Portal:Biological warfare is being considered for deletion. --Nessie (talk) 13:43, 28 August 2019 (UTC)
My own amateurish reading of the paper makes it sound like it contradicts itself. Is the variance in same-sex behavior explained by the genetic differences 8-25% or <1%?
Paper here. Note especially the 3 paragraphs between figures 2 and 3.
-Crossroads- (talk) 19:09, 1 September 2019 (UTC)
Hi everyone,
It's my pleasure to announce that entries for the 9th ISCB Wikipedia Competition are open now!
The competition is run annually by the International Society for Computational Biology (ISCB) and the Computational Biology taskforce of WikiProject Molecular Biology. A key component of the ISCB's mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at large. Wikipedia has become an important way to communicate all types of science to the public and the ISCB aims to further its mission by increasing the quality of Wikipedia coverage of computational biology, and by improving accessibility to this information via Wikipedia.
The competition is open to students and trainees at any level, either as individuals or as groups; the competition closes 15 May 2020. Cash prizes and ISCB memberships will be awarded to the best contributions, as judged by a panel of experts. Awards will be presented at the ISMB 2020 conference in Montreal in July 2020.
Please share this call for entries to anyone you think may be interested. More details are available on the competition announcement page; I'm happy to answer any questions as well.
Thanks! Amkilpatrick (talk) 09:06, 6 September 2019 (UTC)
Hi all (and especially those involved in setting up this project), a few project-related questions. It looks like there's a talk page tag for this project at {{WikiProject Molecular Biology}}
, but it's not clear to me if the category system is set up. Do we plan to set up the talk page tag system like other projects have (and presumably then have a bot replace the old project tags with new ones using task force parameters like WP:MED uses, and then setup an assessments table like the old projects have)? If this is just an issue of no one having the time, let me know and I can chip away at it in the next few weeks. If this is intentional, that's fine too. Just not clear to me. Thanks all for your work on this! Ajpolino (talk) 23:11, 6 September 2019 (UTC)
Hi WikiProject Molecular Biology members,
I have made numerous small edits to the ATAC-seq page, a page that is within the purview of your project, to improve its quality. I've also rewritten the whole page to remove promotional and overly-technical content and to add citations and crosslinks. But I have a conflict of interest, so I cannot make the changes myself. I copied my rewrite into the talk page. Could a project member please review my rewrite and use it to replace the content that is there?
Thank you,
cglife.bmarcus (talk) 1:17, 5 September 2019 (UTC)
PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Origin of replication page. Comments and suggestions welcome!
Once again all refs were still using the old {{cite pmid}}
template over at http://topicpageswiki.plos.org as the citoid software hasn't been possible to implement there. If a wikimedia journals sister project is approved, that may solve such problems in future. I'm converting them to {{cite_journal}}
section-by-section (happy for assistance if anyone wants to start at the end and work backwards)! T.Shafee(Evo&Evo)talk 06:07, 14 September 2019 (UTC)
Hello, please consider unifying your article approach, the fact is most articles about genes (human) or proteins (human) or protein families are conflations of all three. Though it is a problem in Wikidata that is solvable (instead of linking to one of the three concepts create a conflation concept in WD that links to all three WD items). Solving it consistently in WD will finally allow automatic infoboxes benefiting from all WD database imports. The first step however is that you demand such conflation concepts in Wikidata. I'm active in the molbio section of WD and would be willing to implement it for already existing articles. So please comment and take the chance.
Of course it does not solve the missing distinction protein/complex/family/complex family here but it's a start. --SCIdude (talk) 07:37, 12 October 2019 (UTC)
Practically with new articles of human genes/proteins, you would have the choice of linking to a Wikidata human gene, human protein, protein family, or conflated concept item. The infobox programmer can then see which of the 4 types the linked WD item is and display the relevant info, accordingly. --SCIdude (talk) 08:08, 12 October 2019 (UTC)
SELECT DISTINCT ?p ?g ?ap ?agWHERE{ ?p wdt:P31 wd:Q8054 . ?p wdt:P352 ?u . ?ap schema:about ?p . ?ap schema:isPartOf <https://en.wikipedia.org/> . ?p wdt:P702 ?g . ?ag schema:about ?g . ?ag schema:isPartOf <https://en.wikipedia.org/> .}
You can see 46 pairs of this kind. I can convert this to a Wiki list, later --SCIdude (talk) 13:59, 12 October 2019 (UTC)
Here it is, maybe on its own page?
Please see notice at Wikipedia talk:WikiProject Molecular Biology/Genetics#Mendelian inheritance, which in turn relates to several recent threads at Talk:Mendelian inheritance, all initiated by Sciencia58 (talk · contribs) at or since 11:15, 30 September 2019 (UTC). --Redrose64 🌹 (talk) 20:45, 17 October 2019 (UTC)
PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Viral quasispecies page. Comments and suggestions welcome!
The author over at PLOS Genetics has struggled a little to write in a fully encyclopedic style, so there are still tone elements that need updating. However, overall the content is a great expansion and improvement. T.Shafee(Evo&Evo)talk 06:50, 21 October 2019 (UTC)
A nice article on molecular biological info in Wikidata just went up on bioaRxiv:
T.Shafee(Evo&Evo)talk 02:34, 28 October 2019 (UTC)
PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Eukaryote hybrid genome page. The article overall has a very flat heading structure, so that might be worth multi-levelling a little. The refs are all currently using {{citation}}
, so will have to be converted to {{cite journal}}
and {{cite book}}
over the coming days. Comments and suggestions welcome! T.Shafee(Evo&Evo)talk 08:38, 28 November 2019 (UTC)
Per the HGNC CAMP entry (HGNC:1472), UniProt cathelicidin entry, and UniProt "cathelicidin family in Homo sapiens" listing, I rewrote this article and changed the wikidata sitelink to correspond to 1 gene, as the single prepropeptide is cleaved into 2 forms and there's only 1 human gene that belongs to that family. Didn't care to move stuff about a more general protein family in animals out of it. Seppi333 (Insert 2¢) 02:42, 30 November 2019 (UTC)
Hi, I am currently working on improving articles related to T cell signalling. I have noticed that the T-cell receptor activation mechanism is explained incompletely in five different articles, so I am currently adding more detailed information and trying to bring all articles together by creating main and sub-categories. I have written an article about non-catalytic tyrosine-phosphorylated receptors (Draft:Non-catalytic tyrosine-phosphorylated receptors), the receptor family that the T-cell receptor belongs to. In this article I explain the receptor triggering mechanism in more detail such that the mechanism does not have to be explained separately in many different articles. Unfortunately, the article has been waiting to be reviewed for more than 2 weeks. I would greatly appreciate it if someone could have a look at the draft and suggest some improvements. Thanks! Huhny (talk) 13:53, 4 December 2019 (UTC)
Will someone please review this draft to verify whether it should be accepted? My guess is that it should be accepted, but I would like another opinion. Robert McClenon (talk) 18:50, 4 December 2019 (UTC)
{{u|Mark viking}} {Talk}
19:02, 4 December 2019 (UTC)PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Nucleoid page. The article in PLOS Genetics is titled "Architecture of the Escherichia coli nucleoid" as one of the reviewers pointed out that all of the information presented was specific to E. coli. However since the previous Nucleoid article in Wikipedia almost all that is known about nucleoids comes from E. coli. My inclination is that it is still most logical to integrate the info into Nucleoid, since 1) pretty much everything that's known about nucleoids comes from E. coli and 2) the previous start-class article also only discussed E. coli so would be odd for that to be the general Wikipedia page, with separate page on "E. coli nucleoid". However I'd be interested in others' thoughts on this. Some of the figure captions are also pretty long, so could do with a significant trim. T.Shafee(Evo&Evo)talk 00:27, 18 December 2019 (UTC)
I am asking for the advice on improving Draft:Bruno Reversade. He is a developmental biologist and human geneticist, who works as a Director of the Institute of Medical Biology at Agency for Science, Technology and Research (Singapore). Reversade is known for identifying mutated genes that cause Mendelian diseases in humans and for his research on the genetics of identical twins.
This article is a properly stated conflict of interest (COI) contribution. The reviewing editor highlighted WP:NPOV issues that I tried to resolve following advice from 2 senior editors at my talk page. Before submitting the article for the review, I would like to get a second (and professional) opinion to ensure that the issues, indeed, were resolved. Please tell what could/should be improved in the article. --Bbarmadillo (talk) 20:36, 27 December 2019 (UTC)
Does anyone have any knowledge on the "Fractal catalytic model"? It's ringing Fringe science alarm bells for me. I might be flagging false positives, since I'm reading up on the 'anti-helicist' movement for this page. T.Shafee(Evo&Evo)talk 10:36, 27 December 2019 (UTC)links corrected 23:20, 27 December 2019 (UTC)
{{u|Mark viking}} {Talk}
13:01, 27 December 2019 (UTC)Hi, I am new here. I studied molecular biology a long time ago at UC Berkeley, but never progressed to graduate school. I've always stayed interested as a lay person, and think it could be fun to work on this subject on Wikipedia, doing easy tasks, at least to begin. I thought I could begin with "adding pages to the project" by tagging them with the "Wikiproject MCB" tag. My question is, how do I find articles that have not already been tagged? Thanks, --DaringDonna (talk) 20:57, 7 January 2020 (UTC)
{{WikiProject Molecular and Cell Biology}}
template on their talkpages as well as the specific taskforce. T.Shafee(Evo&Evo)talk 05:51, 8 January 2020 (UTC)Is anyone interested in taking on this abandoned draft? I've just saved it from deletion as stale. It looks as if a bit of editing for English might make it suitable for mainspace, but I'm no expert in this area. Regards, Espresso Addict (talk) 03:51, 29 January 2020 (UTC)
Does anyone have access to the paywalled premium content on this website? Seppi333 (Insert 2¢) 09:01, 29 January 2020 (UTC)
I have a technical problem that I mentioned at WT:MCB#Problematic links in the wikitables pertaining to Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology/Human protein-coding genes1 and Human protein-coding genes2, which I am considering moving to the article space. I was wondering if anyone else had a simpler solution than the one I proposed (i.e., building a custom tool and parsing the content of thousands of gene articles). Seppi333 (Insert 2¢) 01:28, 5 November 2019 (UTC)
Approval is now contingent upon the AfD outcome, so this section has become moot. Seppi333 (Insert 2¢) 18:10, 2 January 2020 (UTC) |
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See Wikipedia:Bots/Requests_for_approval/Seppi333Bot#Feedback requested. Seppi333 (Insert 2¢) 05:12, 19 December 2019 (UTC)
|
I figured someone would do this sooner or later. Feel free to weigh in if you have an opinion. Seppi333 (Insert 2¢) 13:18, 2 January 2020 (UTC)
|
Spinning this topic off of this discussion, in which I proposed a help diagram for the short description help page and debated some proposed rules and changes to the contradictory and unnecessarily ambiguous help information. There's been no discussion on short descriptions in this WikiProject yet that I could find.
I'm seeing a strong need for this WikiProject to establish a standard practice for gene short descriptions, as I've been seeing how ProteinBoxBot has gone around and added "protein-coding gene in the species Homo sapiens" or some variation ("mammalian protein found in Homo sapiens", "Human gene") to every gene on Wikidata. I've been wanting to import and edit them, but based mainly on the fact no one else has touched the bot's descriptions, I didn't know if the changes I wanted to make would be acceptable. I was thinking they could do with some further disambiguating, i.e. for a notable role like BRCA1 and BRCA2 in cancer or the nature of the gene (e.g., "transcription factor", "enzyme"), which is what the help page emphasises. Also, some of ProteinBoxBot's descriptions are just wrong, like "mammalian protein found in Homo sapiens" on Histidine decarboxylase, which is found in "eukaryotes, as well as gram-negative bacteria". Another thing it's done is add "InterPro domain" to almost every protein domain, so I wanted to know if that need be included in a standard practice established for protein domains (I'd prefer not). SUM1 (talk) 07:47, 14 January 2020 (UTC)
{{u|Mark viking}} {Talk}
10:10, 14 January 2020 (UTC){{u|Mark viking}} {Talk}
18:53, 14 January 2020 (UTC){{u|Mark viking}} {Talk}
03:37, 17 January 2020 (UTC)Hi all, a reminder that the 9th ISCB Wikipedia competition is still open for entries to improve pages relating to computational biology.
All students are welcome to enter; please spread the word and help improve this great resource! Deadline is 15 May. Thanks! Amkilpatrick (talk) 13:27, 7 February 2020 (UTC)
previous discussion from Wikipedia_talk:WikiProject_Molecular_Biology/Archive_1#Kuo-Chen_Chou_et_al |
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There seems to be a whole group of articles on Kuo-Chen Chou and his findings that are highly promotional, hard to understand, almost exclusively reference his own papers, and have been created/expanded by a few editors whose sole editing focus seems to be this topic. I've poked around a bit, but I don't really understand the topic. Does anyone have more familiarity with the topic? Can't tell if these articles just need to be cleaned up, or if some merging/redirecting/deletion might be in order for some of these. Articles I've noticed so far:
Any insight would be helpful. Thanks! Ajpolino (talk) 20:49, 21 August 2019 (UTC)
|
@Evolution and evolvability: It looks like the 2 |-imp=
parameters in the source code of {{WPMOLBIO}}
need to be prefixed with the project title. I'm not sure what pages use this template for those projects, so I'm hesitant to change it. Once you see this, please remove the example project template from the page since it's categorizing this project page as an article. Seppi333 (Insert 2¢) 23:08, 31 December 2019 (UTC)
{{WPMOLBIO|class=stub|importance=Low|biophysics=yes|-imp=Low|computational biology=yes|-imp=Mid}}
produces:
{{WPMOLBIO|class=stub|importance=Low|biophysics=yes|-imp=Low|computational biology=yes|-imp=Mid}}
{{WikiProject_Molecular_Biology}}
to test it's listing of multiple taskforces, e.g. talk:Multiple_sequence_alignment (list). T.Shafee(Evo&Evo)talk 11:05, 9 January 2020 (UTC){{WPMOLBIO}}
; if any are missing, I need to create them. I'll do that today. Seppi333 (Insert 2¢) 01:48, 16 January 2020 (UTC){{WPMOLBIO}}
with task force ratings?Following up on the section above:
I could easily code a bot or use appropriate template wrappers to convert {{WikiProject Molecular and Cell Biology}}
and its template redirects (e.g., {{WPMCB}}
) as follows:
Example template conversion for MCB templates |
---|
Change: {{WikiProject Molecular and Cell Biology | importance=<!--original MCB importance rating--> | class=<!--original MCB class rating-->}} to: {{WikiProject Molecular Biology |importance=<!--Could do one of the following: use the original MCB importance rating, downgrade the MCB importance by 1, or leave it blank for manual input by human editors later on--> |class=<!--use original MCB class rating--> |MCB=yes |MCB-importance=<!--use original MCB importance rating-->}} |
Is this something that others think would be useful?
If so, please state this; it would also be helpful to get feedback on how to assess the importance for the parent project in the 2nd template (see the example options listed above).
NB: I don't need to code a bot if either the original MCB importance rating or no importance rating is used as the importance rating for WikiProject Molecular Biology since all I'd need to do is use the appropriate template wrapper syntax in {{WPMCB}}
(as described here). If I were to downgrade the rating by 1, I'd probably have to use a bot, although I think it might also be possible to implement this without programming a new bot via the use of a switch statement (parser function) in the wrapper template. Would need to get feedback on how to implement that if using a different importance rating is desired.
There needs to be a consensus in this thread for making this change prior to me proposing a new bot task in the event that I need to go that route. Seppi333 (Insert 2¢) 01:36, 16 January 2020 (UTC)
I'm a member of the team in the Institute of Cancer Research working on canSAR, a public knowledgebase that brings together biological, chemical, pharmacological data.
We have webpages for ~20.000 human genes, with information 3D structure, mutations, drug targets, gene-disease links, etc. We integrate and curate data from multiple sources, but additionally we also include our own druggability and gene-disease assessments as well as compound registration.
I think it would be a valuable addition to Wikipedia gene pages to have a link to a canSAR page. Ideally, a link could be added in the gene page right-hand-side panel, and generated automatically. Do you think this would be possible?
I've seen that there are bots editing automatically gene pages, so I wanted to ask whether we could collaborate to add such links. — Preceding unsigned comment added by Eloy Villasclaras (talk • contribs) 16:17, 26 February 2020 (UTC)
Earlier today, an editor requested a topic expert review the relatively new article MNase-seq and suggested an expert might be found at this WikiProject. davidwr/(talk)/(contribs) 16:02, 27 February 2020 (UTC)
Congratulations on deciding to merge the closely related groups. By way of making that more successful, I offer this unsolicited advice, based almost entirely on my experience with task forces at Wikipedia:WikiProject Medicine:
Good luck, WhatamIdoing (talk) 19:21, 8 March 2020 (UTC)
Requesting input in the page about https://www.search.com.vn/wiki/en/Severe_acute_respiratory_syndrome_coronavirus_2 and https://www.search.com.vn/wiki/en/Coronavirus_disease_2019 especially for elaborating
Regards.
RIT RAJARSHI (talk) 16:24, 24 March 2020 (UTC)
So I recently gained access to all of my brother's WGS and WES datasets and I'm considering using DeepVariant (Google's bioinformatic analysis pipeline for genomic data which utilizes a convolutional neural network for its variant caller algorithm) to analyze them as well as customizing the pipeline by running a different variant caller AI (namely, Clairvoyante) and, assuming I can hack it (pun intended), performing hybrid genome assembly with his Oxford Nanopore, PacBio, and Illumina WGS data.
Now, that's great and all since both variant caller AI can perform variant calling pretty well (i.e., I don't really need to know WTF I'm - or rather the AI I'm using is - doing for that part of the pipeline), but I have limited knowledge of and no experience whatsoever with variant annotation. I intend to apply an algorithmic approach using some python library for that, but I figure I should probably have a good idea of what's going on under the hood, so to speak. I was wondering if anyone here could point me to some resources (e.g., a comprehensive review article, online textbook, or other form of electronic media which goes deeper than SNP annotation and is not limited to just SNPs) I might be able to use as a reference for variant annotation.
The purpose of this little exercise for me isn't to identify novel variants that weren't identified at my brother's hackathon (although, if end up doing that, that'd be pretty cool); it's for me to learn human genome bioinformatics by applying pipelines to human exome and genome datasets sequenced with next-gen short-read (Illumina) and the state-of-the-art third-gen long-read sequencing technologies (PacBio SMRT & Oxford Nanopore Technologies' nanopore sequencing). For various reasons (e.g., HIPAA and the common use of NGS), this isn't something I'd learn from taking a MOOC or university course in bioinformatics, although I imagine some of it would translate to what I'm doing. My motivation for learning this is for applying it − or at least be able to do something useful − at future hackathons, which are all going to be run on Google Cloud Platform. Seppi333 (Insert 2¢) 08:46, 28 March 2020 (UTC)
List of Biological Databases
- Kurop1n (talk) 04:12, 16 April 2020 (UTC)
Hi all, a reminder that the 9th ISCB Wikipedia competition is still open for entries to improve pages relating to computational biology. but only just: the deadline is this Friday, 15 May.
All students are welcome to enter, please spread the word! And if you see editors doing particularly good work in this area, please suggest that they enter. ISCB memberships and cash prizes for the most improved entries! Thanks, Amkilpatrick (talk) 13:14, 9 May 2020 (UTC)
{{Infobox gene}}
Hi all, I noticed the old image at alpha-synuclein (File:Alfa-sinucleina.jpg) was somewhat pixelated, and unclear because the helices were on top of each other. So I made a new one in PyMOL from the same data File:Alpha-synuclein 2005.png. Imagine my surprise when I clicked the edit link at alpha-synuclein and saw only {{Infobox gene}} and no image link. So then I learned that apparently {{Infobox gene}}
takes its image from wikidata, and (as far as I can tell) there's no way to override that with a locally provided image link. So then I'm off to d:Q14862268, where I add the newer image, and refresh the article. Now both images display in the infobox! So I remove the old one (even though it's still perfectly acceptable data for that entry I suppose), now the newer image displays as intended, but it's huge reaching down well past the lead and into the first section. So my questions: (1) Is there any way to make the displayed image smaller? (2) Can we really not override the image with a parameter at the page (e.g. this is done with the {{Automatic taxobox}}
, and is often the only parameter filled out at the page)? (3) Gosh that was a pain in the butt, any way we could make this easier? At a minimum, adding some documentation to the {{Infobox gene}}
page for folks like me who are less familiar with the wikidata system? Happy to hear anyone's thoughts. Ajpolino (talk) 14:57, 11 May 2020 (UTC)
Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.
We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma (talk) 04:24, 27 October 2019 (UTC)
This recently published article may be of interest to educators active in this WikiProject; attempting to promote a closer link between academia and Wikipedia.
Kilpatrick, Alastair M.; Anjum, Audra; Welch, Lonnie (14 May 2020). "Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles". PLOS Computational Biology. 16 (5): e1007868. Bibcode:2020PLSCB..16E7868K. doi:10.1371/journal.pcbi.1007868. ISSN 1553-7358.
--Amkilpatrick (talk) 13:13, 26 May 2020 (UTC)
I have nominated DNA repair for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. SandyGeorgia (Talk) 22:51, 14 June 2020 (UTC)
What do people think about going to the community-guided conference day at the Bioinformatics Community Conference?
I've drafted a suggestion for some wikidata activities in the communal conference planning document.
Would others be interested in attending? Could be an ideal outreach opportunity to a community with closely aligned goals and interests. T.Shafee(evo&evo) (talk) 12:06, 11 May 2020 (UTC)
PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Holocentric chromosome page. Comments and suggestions welcome! T.Shafee(Evo&Evo)talk 00:32, 31 July 2020 (UTC)
There seems to be dozens of fatty acid images in Wikimedia Commons that have the wrong omega-numbers on the carbons. See for example
The carbons from the end are "ω", "ω−1", "ω−2", etc. Here is a corrected version:
This common mistake makes no difference when locating double bonds, because it happens to be compensated by another common mistake. However, it matters a lot when locating substitutions or enzyme action sites, like "an hdroxyl at position ω−1". See the description of the second image for more details.
All the best, --Jorge Stolfi (talk) 04:08, 1 September 2020 (UTC)
There are uncountable instances, in Wikipedia and on the internet, of the claim "saturated and trans fatty acids are straight, while cis ones are bent". And also "saturated and trans fats have a higher melting point because, being straight, they can pack more compactly"
However, I have been unable to find an authoritative source for these claims — one that is based on experimental determination of the shapes and arrangement of the molecules, rather than being just the inference of the author.
A problem with that theory is that any two parts of the chain separated by a doublesingle bond are free to rotate about it; and the energy barriers for the rotation, that come from repulsion between the H atoms on adjacent carbons, seem to be very small. Thus, one would expect that the molecules of natural fatty acids (with only a few double bonds) will be typically twisted in a random configuration, when they are in the liquid state, or in a solution, or in a complex mixture of solid triglycerides like tallow or butter. And saturated fats should be slightly more crumpled than unsaturated ones; and there should be little difference in the amount of crumpling of cis and trans acids.
For the same reason the three chains of a triglyceride should usually start out in random directions, not neatly parallel.
As for the differences in melting points, I can think of at least two alternative "intuitive" theoretical explanations, other than packing density.
This is "Original Research", of course; but it is offered only to highlight that those claims need to be supported by experiment.
Does anyone have such sources?
Thanks, and all the best, --Jorge Stolfi (talk) 04:37, 1 September 2020 (UTC)
I'm pleased to announce that entries for the 10th ISCB Wikipedia Competition are open now! The competition aims to improve Wikipedia's coverage of computational biology and bioinformatics and represents a great opportunity for students to develop their science communication skills while improving a vital public information resource. Also, cash prizes of up to $500 awarded for the best contributions! More details at the link above.
For those involved with bioinformatics or computational biology in an educational capacity, we encourage you to help your students improve relevant Wikipedia articles as a class activity - see our recent article in PLOS Computational Biology:
Kilpatrick, Alastair M.; Anjum, Audra; Welch, Lonnie (14 May 2020). "Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles". PLOS Computational Biology. 16 (5): e1007868. Bibcode:2020PLSCB..16E7868K. doi:10.1371/journal.pcbi.1007868. PMID 32407308.
Please share! Happy to answer any questions also. Thanks, Amkilpatrick (talk) 12:21, 2 September 2020 (UTC)
Dear Colleagues. I would like to add to the content of Wikipedia's Structural Genomics Consortium (SGC). The changes will be major (under the definition of Wikipedia) and thus I am writing this for advice.
The changes will include a more detailed history of the SGC including the different programs and phases from 2003 to date.
Thank you.
Sincerely,Suzanne — Preceding unsigned comment added by SZAckloo (talk • contribs) 01:28, 30 August 2020 (UTC)
{{ping|Berchanhimez}}
@WikiDan61: @Evolution and evolvability: thank you for your feedback. It has been very helpful so far. (SZAckloo (talk) 14:06, 2 September 2020 (UTC))@Evolution and evolvability: {{ping|Berchanhimez}}
@WikiDan61: What are your thoughts about adding other Open Science initiatives linked to the SGC but that not its core activities? (SZAckloo (talk) 01:49, 11 September 2020 (UTC))
I have nominated Cell nucleus for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. (t · c) buidhe 22:17, 11 September 2020 (UTC)
PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the RNA-directed DNA methylation page. Comments and suggestions welcome! T.Shafee(Evo&Evo)talk 08:56, 9 October 2020 (UTC)
A new editor is expanding this but in the process he is introducing a promotional tone.
I have reverted the edits,[6] but it would be useful to have a subject-matter expert dig through for anything salvageable. davidwr/(talk)/(contribs) 21:55, 26 October 2020 (UTC)
Hi all, I've boldly updated your project's peer review page (Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology/Peer review) by updating the instructions and archiving old reviews.
The new instructions use Wikipedia's general peer review process (WP:PR) to list peer reviews. Your project's reviews are still able to be listed on your local page too.
The benefits of this change is that review requests will get seen by a wider audience and are likely to be attended to in a more timely way (many WikiProject peer reviews remain unanswered after years). The Wikipedia peer review process is also more maintained than most WikiProjects, and this may help save time for your active members.
I've done this boldly as it seems your peer review page is pretty inactive and I am working through around 90 such similar peer review pages. Please feel free to discuss below - please ping me ({{u|Tom (LT)}}) in your response.
Cheers and hope you are well, Tom (LT) (talk) 22:52, 12 November 2020 (UTC)
Immune system has been proposed to run TFA on the mainpage as the COVID vaccine is launched: please see Wikipedia:WikiProject Medicine/Collaboration of the Month#Immune system. SandyGeorgia (Talk) 17:35, 20 November 2020 (UTC)
00:21, 26 October 2020 2601:985:380:afe0:575:447d:240d:24aa made a very specific addition to the introducing chapter of Assay. I think it is good will, but i do not think that it really improves the article. If the information is of encyclopedic relevance, i think it should be transferred to a more specific place. --Himbeerbläuling (talk) 12:52, 22 November 2020 (UTC)
I watch both, but I'm not sure why someone would post on one rather than the other. Perhaps we discussed this in the past during the big merger, but should we just archive the rest of the contents at Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology and redirect that talk page here so there's just one place for folks to talk about molecular biology? Ajpolino (talk) 03:41, 13 November 2020 (UTC)
Extended content |
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Anyone have a moderate-advanced working knowledge with at least some applied experience in this area? Have some questions pertaining to a protocol we've developed. Just looking for some additional feedback. @DGG: I have a sufficient understanding of this subject area to expand that article now. Will do so after we get past certain milestones sometime within the next 4-8 months. Seppi333 (Insert 2¢) 05:19, 26 November 2020 (UTC)
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Hi members, I am requesting here for a DYK review of Template:Did you know nominations/Nucleoside-modified messenger RNA if anyone interested. I am posting the request regarding modRNA DYK as COVID-19 vaccine BNT162b2 has been approved for EUA in Great Britain, Bahrain whereas mRNA-1273 is also expected to get approval soon in US, Europe and both are based on Nucleoside-modified messenger RNA (modRNA) technology. The DYK can be scheduled for early weeks of December 2020 if passed. I have also notified the same at Wikipedia talk:WikiProject COVID-19. Thank you — Amkgp 💬 09:41, 9 December 2020 (UTC)
Enzyme inhibitor has turned into quite a wreck since Tim Vickers stopped editing; unless someone is able to bring it to WP:WIAFA standard (and fix the image layout mess, too), the article should be submitted to WP:Featured article review. It was last reviewed in 2006, and is the oldest article from this Project at Wikipedia:Unreviewed featured articles/2020. Please place notes for article improvements needed at Talk:Enzyme inhibitor#WP:URFA/2020. SandyGeorgia (Talk) 20:56, 13 December 2020 (UTC)
Similar for Talk:Enzyme kinetics#WP:URFA/2020 SandyGeorgia (Talk) 21:04, 13 December 2020 (UTC)
With this edit on ISRIB, I saw that someone had converted the [[eIF2α]] redlink (as of 2020-12-29T01:42:45) to [[EIF2S1|eIF2α]]. I thought that I would create a eIF2α redirect to EIF2S1, but when I searched on eIF2α, I noticed Integrated stress response#eIF2α among the results.
Two things I think:
This is not my area of expertise, hence the reason I bring this here. I am hoping someone with more knowledge than I have about eIF2α, EIF2S1, & integrated stress response will infer the correct solution. Peaceray (talk) 22:00, 29 December 2020 (UTC)
![]() | Sandbox Organiser A place to help you organise your work |
Hi all
I've been working on a tool for the past few months that you may find useful. Wikipedia:Sandbox organiser is a set of tools to help you better organise your draft articles and other pages in your userspace. It also includes areas to keep your to do lists, bookmarks, list of tools. You can customise your sandbox organiser to add new features and sections. Once created you can access it simply by clicking the sandbox link at the top of the page. You can create and then customise your own sandbox organiser just by clicking the button on the page. All ideas for improvements and other versions would be really appreciated.
Huge thanks to PrimeHunter and NavinoEvans for their work on the technical parts, without them it wouldn't have happened.
John Cummings (talk) 11:09, 6 February 2021 (UTC)
Dear all, a reminder that entries for the 10th ISCB Wikipedia Competition are still open (deadline 14th May). The competition aims to improve Wikipedia's coverage of computational biology and bioinformatics and represents a great opportunity for students to develop their science communication skills while improving a vital public information resource. Also, cash prizes of up to $500 awarded for the best contributions! More details at the link above.
For those involved with bioinformatics or computational biology in an educational capacity: please share this link with your students! We also encourage educators to help students improve relevant Wikipedia articles as a class activity - see our recent article in PLOS Computational Biology:
Kilpatrick, Alastair M.; Anjum, Audra; Welch, Lonnie (14 May 2020). "Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles". PLOS Computational Biology. 16 (5): e1007868. Bibcode:2020PLSCB..16E7868K. doi:10.1371/journal.pcbi.1007868. PMID 32407308.
Please share! Happy to answer any questions also. Thanks, Amkilpatrick (talk) 12:28, 16 February 2021 (UTC)
Neoblast is being reviewed as a GA. Can someone point me to the criteria in this project for formating a Molecular Biology article? Thank you. --Akrasia25 (talk) 13:49, 18 February 2021 (UTC)
The problem that Wikipedia articles cover multiple Wikidata concepts will get a solution with the possibility to associate Wikidata concepts with Wikipedia Redirect pages. This is in the process of implementation right now.
Maybe you want to think already about how to use this. Obviously, articles covering gene + protein + protein family would ideally have separate paragraphs for each of these, and redirect pages linking to these sections. --SCIdude (talk) 10:47, 19 February 2021 (UTC)