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.
Proposal
A Possible unification of some of the sub-cellular wikiprojects with large scope overlaps, including:
This was posted in the various WikiProjects just before they were merged as taskforces, so I thought would be useful to repost here.
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)talk12:22, 16 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)
I have always loved his work. I was given his book "The Machinery of Life" a few years back and I can absolutely recommend it as an excellent gift. T.Shafee(Evo&Evo)talk00:49, 27 June 2019 (UTC)
Would you kindly help me with this image
This was posted in WikiProject MCB just before it was merged as a taskforce, so I thought would be useful to repost here.
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:
Pol epsilon should be on the leading strand and attached to the helicase (which should have a ring structure). Pol delta should be on the lagging strand. Pol delta might have some role in leading strand replication (still debated to which extend), but is mostly responsible for lagging strand replication. See also File talk:DNA replication en.svg --大诺史 ()
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:
I have been told that the polymerase that works on the leading strand is attached to the helicase. if so, where do the SSBs (single stranded binding proteins) connect on that side of the fork? also i have seen other diagrams with this polymerase hugging the lagging strand instead sso whicone would be correct?
i made the sliding clamp on the polymerase seem part of the same body, i am aware it is a completely different enzyme is just i thought it would show they both work together and also gives the drawing some directionality which seems to be important in this subject. is this ok?
i am very confused about which polymerase is what greek letter of pol. on the sketch i have made my best guess but i still not sure which is which. Also would it be a problem if a place several polymerases working on different sections of the lagging strand? at the moment the same primase, and polymerase must go round and round backwards to do the job.
on the last image i was asked at least once a month to change the 3'5' notations on the diagram. i have made a little color hook on the primers to show where the 3' end of it would be, and made a image section to explain here is where the polymerase attaches to start working. would this be helpfull or do you think it will make things more confusing?
is it practical to add the Telomerase in the diagram? i am not even sure if it would attach there, would you find it more useful or should i leave it out?
because of space resstrains i placed the RNAse at the same spot than the DNA polymerase that repairs the gap. is this understandable or would they need their own gap?
In many images i have fished out online (excluding those based on my own image) i have found often that enzymes are much bigger than what i have show, and i dont mind that becouse more than scale i am more interested in showing function, but it does worry when i see images like this one where the single strand make strange loops.. is there anything about this i should be aware of?
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)
@LadyofHats: I'm terribly sorry that I am unable to answer most of your questions. I am certainly not an expert on this, and I imagine that you haven't been answered just because people don't know how to help you, not because they haven't seen your post or don't care. What I can say is that I don't think it is necessary for you to include telomerase. In my limited experience, I don't remember it being included in many general diagrams like yours. It would be cool to have it, but I wouldn't think it necessary.
@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:
Pol ε (epsilon) is the primary leading strand polymerase and Pol δ (delta) is the primary lagging strand polymerase. There is some argument about whether each of them “moonlights” in other contexts, but for a baseline model those designations are fine. A complex of proteins comprised of Cdc45-MCM–GINS (called CMG for short) makes up the eukaryotic replicative helicase. There is very good data showing that Pol ε physically interacts with the helicase (https://doi.org/10.1073/pnas.1700530114). SSBs are likely indiscriminate and will bind to any available single-stranded DNA. Since Pol ε physically interacts with the helicase, which will be positioned at the replication fork, there probably isn’t a need to depict it on the leading strand.
Sliding clamps are accessory proteins that increase the efficiency (processivity to be precise) of replication. It is loaded onto the primer-template duplex and then forms physical interactions with its associated polymerase. As such, I would show it as a distinct element that is physically contacts the polymerase.
Pol ε (epsilon) is the leading strand polymerase. Pol δ (delta) is the primary lagging strand polymerase. Pol α (alpha) functions on both the leading and lagging strands to synthesize the first short (roughly 20 nucleotide) stretch of DNA from the RNA primers, then hands off to more processive polymerases (like epsilon or delta), it also fill in the gaps left after primers are removed (see below). Primase is an RNA polymerase that synthesizes the RNA primers used by the DNA polymerases to initiate synthesis. I’m not sure what you mean by the same polymerase going round and round. It is true that the lagging strand is discontinuous – i.e. it proceeds away from the replication fork, synthesizes until it hits the next upstream okazaki fragment and then stops, the fork meanwhile has progressed to reveal more ssDNA and another lagging strand polymerase is loaded and synthesizes another segment (over and over again).
Being clear about the polarity of the nucleic acids (5' and 3') is very important. This is something that learners are generally confused by when trying to tackle the topic and it turns out that once you understand the polarity issue a lot of the rest of the mechanics of replication falls into place. Yes, I think the inset box would help folks. However, I think I would avoid the word “attaches” (this may be confused with some kind of chemical linkage). Instead I would say that the polymerase catalyzes addition of nucleotides at the 3' hydroxyl (OH).
End replication (telomere replication) is a specialized mechanism that involves a whole host of other players. I do not recommend trying to incorporate it into this diagram.
In your sketch you have RNAse (presumably to remove the RNA primers created by Primase) but this is probably incorrect. Currently it is thought that Pol δ displaces the 5' end of the RNA primer it encounters to create ssRNA flap that is then cleaved by a structure-specific endonuclease called FEN1 (note, removal of primers works by a different mechanism in prokaryotes – in bacteria the lagging strand polymerase, called DNA polymerase I has a 5' to 3' exonuclease).
I’m sure you know much more about illustrating than I do, but as a consumer of illustrations I generally think of two kinds. The first are highly technical depictions of structural studies (like x-ray crystallography) that attempt to accurately display both size and position of the constituent units (bases, amino acids, atoms etc). The second are conceptual models that attempt to depict a set of relationships (physical interactions, or functional partnerships), sometimes as a snapshot in a process (like replication). It seems to me that you’re going for the latter, so I wouldn’t worry too much about relative scales (within reason).
The looping model you point to is arguing for a polymerase dimer mechanism. To my knowledge this is a model in the prokaryotic replication field – and for that you will have to find help from someone who knows far more about prokaryotic biochemistry than I do.
LadyofHats, RNAse is usually spelled with the last two letters lowercase. You also missed an e in exonuclease in that area. Your blurb on topoisomerase should say "unwind." Not all the blurbs are capitalized at the beginning. Pol alpha needs to be spelled with a ph. In the info box, you could add "group" at the end of the blurb, which would likely make it fit perfectly. For ligase, I would clarify which ligase it is. Also, your image makes it look like ligase is "retwisting" the double strand back to its normal state. Your old image left a little room to show that the ligase is joining the two strands, but that the twisting is not due to anything the ligase is doing directly. Could you move the ligases back a few nucleotides to show that ligase does not twist the DNA? I would also say "rejoins strands" or "connects strands" or something like that. "Seals strand" implies that the entire DNA molecule which is being created can be called a strand. That's something that confuses some people. My last gripe is that there are not the same number of nucleotides on the left as on the right. I know that is really hard to show in an image like this, but DNA replication is semi-conservative and we try to hammer that into biology students. It would probably be a lot of work to kink that right molecule around to make it the same as the left side, so if you can't do that, then at least put some kind of note at the bottom.
I'm sorry if I sound really critical--I just want to be careful. I actually think that it's a great diagram and I really like some of the concepts. The box is cool, and so are the arrows on the polymerases. That is a good feature. I think that the more well-researched diagrams there are out there of DNA replication, especially in the public domain, the better. Thanks for doing this! Prometheus720 (talk) 17:00, 28 June 2019 (UTC)
you shouldnt worry to be critical since at this stage of the image creation is the right time to find all posible mistakes. i am out of the city but on Tuesday when i am back i will edit the image and upload it to commons. once again thankyou for all your imput. has been very helpfull-LadyofHats (talk) 23:52, 28 June 2019 (UTC)
Gcopenhaver1, That's looking better! I did notice that the top Pol a text is touching the right strand, and the box text is escaping the box. The only other thing I would say is that alpha is usually spelled as alpha in English, and that the bottom pol a says "fill" and I would change that to "fills." I really like the grayed-out end of the right strand. That is a very good compromise, and I noticed you moved the ligases back as well. I think it's just about ready! Great work!
one of the reasons i like to outline text in my images is because svg tends to move it around, tried to fix it as much as i could-LadyofHats (talk) 23:31, 2 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)talk01:32, 14 July 2019 (UTC)
Initial Startup Discussions
I love it!
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)talk07:47, 29 May 2019 (UTC)
I'm not against the current name. However, I'm not against changing it either. I have toyed around with Cellular and Molecular Biology (CMB) but unfortunately, WP:CMB is already registered as a shortcut. Your idea of Molecular Biology has a shortcut choice of WP:MOL or WP:MOLBIO, of which I would much prefer the latter. So it seems a better choice than trying to register CMB for us. I'd support your name, although I also would like to hear more ideas before we run with it. Prometheus720 (talk) 01:39, 30 May 2019 (UTC)
That WP:CMB is already registered shouldn’t be much of a problem. It isn’t used normally on a single page with the 4 pages where it is used being this discussion, two tables with all three letter shortcuts and the destination page. The page is also tagged as historical so it’s very unlikely it will see more use in the future. Trialpears (talk) 13:28, 5 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.
@Prometheus720: I think that looks right thing to copy. My advice is try it because it can always be undone if it breaks something! Isarra will have to give any further advice on anything more technical than that, since it's well beyond my coding skills! T.Shafee(Evo&Evo)talk12:24, 10 June 2019 (UTC)
@Evolution and evolvability:Turns out that page is protected and I would have to submit an edit request, so I'm trying to work everything out in advance. I'm having some trouble with one of the parameters though. There is a service to send an automated list of missing articles using Wikidata. I looked at WP:WOMSCI for reference, and I really like what their list does--it spits out articles which have entries on other Wikipedias but not on enwiki. That is exactly what I would want for WP:BIOL.
To do this, you have to input a SPARQL query. I was previously unfamiliar with SPARQL but it's basically just a system to get data out of a database by making simple statements. However, their query doesn't mention anything at all about languages--it seems to just define Wikidata objects that would be of interest to their project, namely women scientists. I don't understand if the code of Reports bot does the languages part for us or what. I'm at a bit of a standstill at the moment. Do you know anything about SPARQL that might help me figure this out?
Finally, I'm taking a look at the metrics section. If you want to set up metrics for GMCB you could probably set it to the default of looking at the talk page banner, but for WP:BIOL we don't use the banner for most of the articles under our scope. For the purpose of metrics I'd probably want to use categories or another SPARQL search to return a list of articles under our subprojects as well. So I have to figure that out as well--somehow I need to represent the larger footprint of WP:BIOL across its subprojects. I don't think I'll have this done for a day or two, but I will let you know when I do so that I can help you set up GMCB to your liking. Hopefully I'll be a pro by then! In the meantime I will continue working on other modules.Prometheus720 (talk) 06:53, 11 June 2019 (UTC)
@Evolution and evolvability: That's a fabulous idea! It has also occurred to me that even if we can't use SPARQL to generate these lists automatically, we might be able to set up something with categories using PetScan and just run the search again every so often. I designed a draft recurring schedule for maintenance like that for WP:BIOL, so that would just be another thing to do monthly or so. I guess I'll give up and try and request a query. Thanks for that link! Prometheus720 (talk) 16:05, 11 June 2019 (UTC)
Well, that's a bit scary, but I'm really glad you guys seem to have figured it out... yeah, I'm helpful. >.> -— Isarra༆18:50, 19 June 2019 (UTC)
Participants list is down
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)
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 collectinghave 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)
Setting up Stats via WP 1.0 bot/talk page banner stuff
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)
@Evolution and evolvability: So I was very confused as to why the table would not work when I called it. Turns out there have been some typos when it was set up. Wikipedia:Version_1.0_Editorial_Team/Ecoregion_articles_by_quality_statistics needed to be moved to say Ecoregions with an s at the end. That page also had a typo calling ANOTHER page, which I could fix. I really do not like that the WP 1.0 bot has to edit so many pages on Wiki to do the same thing. It feels like a very poor way of handling this. So it turned out that all the machinery was already there, I just had to unstick some gears.
However, I do feel like after doing all this I am prepared to set things up for MOLBIO apart from template creation. I do not, at present, know how to do that. Once we have the template, we can go ahead and start tagging our project pages with it, and then I will set up all the stuff we need for WP 1.0 bot. We can also look for a way to transfer all of the MCB tags to MOLBIO tags. If I understand correctly, you want MOLBIO to actually replace MCB, and then you want to put GEN, BIOP, and COMBIO underneath it? So MCB articles should not be in a taskforce at all, they should be our "main" articles, right? In that case, instead of making a new template, what if we just take the MCB talk page template, rename/move it, and all that? Prometheus720 (talk) 18:01, 15 June 2019 (UTC)
Evolution and evolvability, Looks like the request isn't going anywhere for now. Is there anything we can do on our end? I've been going through some of the unassessed articles just to keep everything a bit neater for the move. Should we just go ahead and make a new template? If we can't get a bot request in, it's my understanding that AutoWikiBrowser with the Kingbotk plugin will do page assessment tasks. For the smaller projects, BIOP and CS, we could likely use AWB. Perhaps that would be enough for testing/proof of concept? I could try to apply for permissions. Prometheus720 (talk) 15:12, 6 July 2019 (UTC)
Projects Finally Moved
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)talk13:02, 16 June 2019 (UTC)
I've created initial talkpage headers {{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)talk12:37, 6 July 2019 (UTC)
Evolution and evolvability, Great stuff! And btw, regarding the u --> re fix you did on another page, I'm using Enterprisey's Reply Link script, and that's how it tags people. Anyway, good eye finding WP:WPMP! I'm sorry I have been a bit absent lately--this wikiproject work has been a bit too technical and I felt a bit burned out. But I'm ready to start helping out again! Let me know if you need anything at all! Prometheus720 (talk) 14:58, 6 July 2019 (UTC)
@Prometheus720: No problem at all. The next technical steps will be simplifying the various taskforce main pages, whilst still retaining the important information. Having said that, it's easy to get over-focused on the technical aspects - there's still things like outreach and actual content creation! T.Shafee(Evo&Evo)talk00:32, 7 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)talk01:52, 24 July 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:
Gordon Life Science Institute (previously speedied as copyvio, just recreated which is what brought this to my attention; looks like it has been speedied again. Leaving link in case it comes back)
Kuo-Chen Chou is certainly notable and the 'recognition' section is probably fair. The 'Career' section probably needs a bit of copyediting and cleanup.
Sufficiently notable: PseAAC and PseKNCr aee rasonably well known (though I couldn't say whether ithey're eing over-emphasised over equivalent methods).
Just a note, a handful of mostly single-purpose accounts has made all of these articles. The currently active one was blocked a few hours ago for being exclusively promotional. Also thanks E&E for your thoughts above! Ajpolino (talk) 14:52, 22 August 2019 (UTC)
Dispute on interpretation of 2019 paper on genetics of homosexuality
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%?
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.
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)
Ah, I see. Thanks for the update. We were able to make the much smaller version of this work when merging WP:WATERFALLS as a taskforce into WP:RIVERS a few months ago. If you'd like a hand with this, let me know and I can try to understand what the folks at your bot request were concerned about, and reach out to some of the folks that helped out with the waterfalls move/merge. Thanks again E&E for your incredible amount of work on this! Ajpolino (talk) 02:59, 9 September 2019 (UTC)
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?
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)talk06:07, 14 September 2019 (UTC)
Wikidata
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)
It's definitely a bit of a mess. I think the ideal would be to merge the articles on proteins and their genes where there are both (though I think many have already been merged) and to have clear distinctions between which sections refer to that protein/gene in humans versus sections on that protein/gene in other organisms. There are a few exge cases where a single gene can code multiple proteins, but those can probably be handled ok on wikidata with a bit of care. For gene/protein families and superfamilies there are different grouping that mostly agree (PFAM, SCOP, CATH, MEROPS, CAZY etc.) That should be the basis for articles where there is sufficient information to warrant an article (e.g. beta defensins). For multi-subunit proteins, we usually have a page for each subunit as well as the complex (e.g. 40S ribosome), but sometimes only a page for the complex as a whole. In general, for permanent complexes, having a page on the complex is probably more useful than for the subunits individually unless there's sufficient information to warrant both. @SCIdude: Is there any wikidata way to list which pages seem to have both as a shortlist for possible manual mergers? The genetics taskforce has several mergers proposed for exactly these sorts of items. T.Shafee(Evo&Evo)talk09:48, 12 October 2019 (UTC)
So you say merging gene and protein would be ideal, that would mean the resp. WD item should be a conflation linking to the resp. gene and protein items. Now consider for example insulin, it's not only about gene and protein but also at least about the ortholog group, and probably also about several families from the databases you mention (which may each have their own WD item), so the WD item linked with the article should also contain these, right? Likewise with protein fragments that are handled in one article, but have all their own WD items (ideally, but I'm working on that). Likewise with complexes---almost never you write about the specific human version, but the family or ortholog group... As to your question, to see which genes with articles encode proteins with articles (or vice versa) use this query:
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)talk06:50, 21 October 2019 (UTC)
@Plantdrew and Redrose64: I think I've now fixed all the broken ref links by checking [3]. It looks as though copying section-by-section caused some citation formatting errors for refs used more than once. The main sections of content overlap are Lethal mutagenesis and Error threshold which will need to be merged. T.Shafee(Evo&Evo)talk00:41, 22 October 2019 (UTC)
Review of mol bio info on Wikidata
A nice article on molecular biological info in Wikidata just went up on bioaRxiv:
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)talk08:38, 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)
I'll admit that the concept seems a little obscure to me. I've seen lots of sources discussing receptors of this type but none that has discussed them as a group. Jo-Jo Eumerus (talk) 19:45, 4 December 2019 (UTC)
I am having a great deal of trouble parsing the title. This should be more precisely defined in the lead sentence. Boghog (talk) 21:37, 4 December 2019 (UTC)
Sorry, after carefully re-reading the lead, I now understand the title, but I still find it a little odd. IMHO, "Src-family kinase-dependent receptors" is less confusing. If there is no loss in accuracy, would favor changing the title to "immunoreceptor" (singular). I have made a few edits to the lead that hopefully clarifies the mechanism. Boghog (talk) 04:42, 5 December 2019 (UTC)
@Huhny: Overall, the organisation and content seems logical and the referencing looks appropriate. Although a relatively niche topic I think it's sufficiently notable, and it's clearly used in the academic literature. As others noted above, the page title might need some consideration. Are "Non-catalytic tyrosine-phosphorylated receptors", "Immunoreceptors" and "Src-family kinase-dependent receptors" strictly synonymous, or just mostly-overlapping concepts? The main source that favours the NTR name is doi:10.1111/imr.12008, but the other terms seem to be more common in the literature as a whole, is there another reason for favouring the NTR name that I'm missing? T.Shafee(Evo&Evo)talk01:59, 5 December 2019 (UTC)
Thanks for your comments. I agree, the many different names of this receptor family are confusing. I prefer the title "Non-catalytic tyrosine-phosphorylated receptors" (or "... receptor family") because "immunoreceptors" can be easily confused with the term "immune receptors" which is often broadly used for every receptor expressed by immune cells. The article doi:10.1111/imr.12008 also states that immunoreceptor is confusing as not all receptors of the family have immunologic functions, while Scr-family dependent receptor is restrictive as other kinases could be involved in the signalling pathway. I have changed the lead, I hope it is clearer now. Huhny (talk) 08:58, 5 December 2019 (UTC)
@Boghog:@T.Shafee:@Jo-Jo Eumerus: Would you mind having another look at the draft? I rearranged and rewritten the introduction, I hope it improved the understandability of the topic. Would it be possible to accept the article? Thanks Huhny (talk) 11:47, 10 December 2019 (UTC)
@Huhny: Much clearer. It might even be worth explicitly adding a History/Etymology section with the info from your comment above to explain the different names, since I suspect that might be of interest to potential readers. I'd support acceptance to mainspace. T.Shafee(Evo&Evo)talk21:07, 10 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)
It might be acceptable an article on an emerging area of nanotechnology. But the medical claims seem out of line for a technology not even in clinical trials yet. I'd want to see MEDRS sources suggesting its fitness for medical purposes. Otherwise discussion of medical applications is non-neutral speculative boosterism for the approach. --{{u|Mark viking}} {Talk}19:02, 4 December 2019 (UTC)
Defnintely notable topic and a very wide-ranging field (though definitions of scope are very variable). Although the topic overall is appropriate, I'd agree with being careful of MEDRS with the medical claims. Also, the sections "Nanorobot", "Nanocell", and "Nano neuro knitting" are merely three examples from a very wide field, so there's a risk of undue weight if they're presented as the only (or even main) developers of these sorts of tech. There are a wide range of polymer- and vesicle- based targeted drug delivery systems that come often under the umbrella of nanomedicine (inc. several in Drug_carrier page), so the "MIT are developing..." angle should probably be toned down a bit. There's quite a bit of editorialising (e.g. "Possibly the most inspiring of these prospects...", but that can be relatively easily cleaned. The link to 'dummies' seems to just go the main website page but not the specific ref. T.Shafee(Evo&Evo)talk02:17, 5 December 2019 (UTC)
@Robert McClenon: The subject is promising, but the article needs significant revision. Is there any way that we can request more editors help us "salvage" this draft? I made edits to the lead paragraph to improve clarity. DA1312 (talk) 13:54, 13 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)talk00:27, 18 December 2019 (UTC)
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)
I think you meant Fractal catalytic model, and yes, that seems fringe neuroscience, albeit from mainstream academia. The idea probably comes from the life at the edge of chaos hypothesis in the complexity/artificial life field. But I don't see any evidence that the idea has caught on in mainstream psychology or neuroscience. On the other hand, there have been lots of wild ideas proposed in the pursuit of understanding cognition, so it might be more charitably thought of as a failed mainstream model. --{{u|Mark viking}} {Talk}13:01, 27 December 2019 (UTC)
Adding pages to the project
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)
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)
Hi. Thanks for the heads up. The draft was in pretty good shape, so I promoted it after a few minor edits to clean up the grammar. Cheers. Boghog (talk) 04:59, 29 January 2020 (UTC)
I'd probably check each link. Or code up a Python script that lists all the links that point to a page w/o {{Infobox gene}} if that is possible, then check each page on that list. Jo-Jo Eumerus (talk) 09:48, 5 November 2019 (UTC)
Not a bad idea. I'll look into coding a tool to implement both your and Boghog's suggestions. It looks like I was right to be worried about that since M195 is one of the links in the table (granted, it's one of the withdrawn entries in the 2nd table as opposed to an approved gene symbol). Seppi333 (Insert 2¢) 19:33, 6 November 2019 (UTC)
Need feedback on the HGNC/UniProt external links and page sizes of the protein-coding gene lists for bot approval
Just FYI: this bot is probably not going to be approved to automate updates to the gene lists unless others indicate they support the current layout. Seppi333 (Insert 2¢) 23:11, 31 December 2019 (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)
I say, be bold and edit them! As you have noted, default SDs have been imposed on WP from the outside, so if you have an improvement, go ahead and override the default. This is what I do. The main use case for an SD is as an aid in mobile device searches by humans. I think SDs can be particularly helpful in this domain, as so many of our gene/protein articles have inscrutable acronyms as titles. For instance, I just boldly added "Human tumor suppressor gene" as an SD to the BRCA1 and BRCA2 articles, which I think would be an improvement upon "mammalian gene found in Homo sapiens" in mobile searches because it is a little less jargonish and gives a hint of what the gene does. If someone comes up with something even better, that is great. --{{u|Mark viking}} {Talk}10:10, 14 January 2020 (UTC)
I agree with improving from just the very generic descriptions. Is there any way to export these back out to Wikidata so that they're standardised across projects? Would editing the wikidata description achieve the same thing? T.Shafee(Evo&Evo)talk11:25, 14 January 2020 (UTC)
To be complete, one would have to write something like:
A protein [or enzyme/transcription factor/etc] coding gene found in homo sapiens and homologs in other species [where certain variations are associated with an increased risk of breast cancer].
Which is way longer than the 40 character suggested limit for a description. But it would at least remove the problem of having to explicitly define which phyla the gene is found in. We could sync this description with the Wikidata human gene description that through its homologene link would list the homologs. Boghog (talk) 14:05, 14 January 2020 (UTC)
@Mark viking, Boghog: If you ask me, I would've suggested "Gene known for its role in breast cancer". That is exactly 40 characters and I believe paints the picture clearest to unfamiliar readers. If you don't mind, I'll boldly change it to that myself. SUM1 (talk) 04:31, 15 January 2020 (UTC)
While concise, that definition really troubles me because it implies its only role is to cause cancer. When functioning normally, it is in fact a tumor suppression gene and only certain variants in a minority of the population are associated with breast cancer. Boghog (talk) 04:51, 15 January 2020 (UTC)
"Human (protein/enzyme/TF)-coding gene involved in X, implicated in Y" (e.g., "protein-coding gene involved in tumor suppression, implicated in breast cancer" - 78 characters) doesn't seem like it'd be that long. Key is to be succinct. "Gene known for its role in... " is too verbose IMO. Seppi333 (Insert 2¢) 00:04, 16 January 2020 (UTC)
@Seppi333: Just wanted to point out, you would in that case be basing your statement off of my perception which has had the agreement of 5 other editors so far. Which is fine; I'm glad you also agree. SUM1 (talk) 02:40, 17 January 2020 (UTC)
"Human" is still redundant to me. It's a thousand times more likely to exist in other mammals, vertebrates or even eukaryotes than be specific to humans. The articles mix the protein and gene together (which is logical). Only the verbose protein names are reduced to their human HUGO symbols, but the others aren't, and all of them are about the protein as well, which is usually non-specific to humans. SUM1 (talk) 03:00, 17 January 2020 (UTC)
"Gene known for its role in breast cancer" is not verbose on its own, only in combination with other information. It would fit within all current guidelines on short descriptions on its own. SUM1 (talk) 03:15, 17 January 2020 (UTC)
@Boghog: Then change it. Breast cancer susceptibility is in the title of the protein though. I don't believe anywhere does it suggest its only role is in cancer, especially "causing" it. It just suggests it has a role in the pathology that is breast cancer. Despite being official, I find the term "tumour suppressor" very aversive, as it usually isn't some add-on that only exists to suppress tumours but rather a core part of the cell cycle that is broken when tumours appear. Most "tumour suppressor" genes also lead to congenital developmental diseases when mutated congenitally. SUM1 (talk) 03:00, 17 January 2020 (UTC)
@Mark viking: Thank you. That's all I really needed, a go-signal from other editors to start importing and editing en masse. I've already started replacing examples like "InterPro Family" with "Family of transcription factor genes" or similar. SUM1 (talk) 03:15, 17 January 2020 (UTC)
@SUM1: Is there any way to simply mark a page to use the wikidata description as its short description? Effectively, in stead of importing then editing, editing on wd then cross-wiki transcluding. In most cases improving the wd description would be more useful since it's used in multiple places. It's also avoid drift between wp and wd that'd then need to be manually re-synchronised (e.g. the Gene short description). T.Shafee(Evo&Evo)talk23:03, 22 January 2020 (UTC)
@Evolution and evolvability: Just wanted to correct my explanation: the template adds a Wikidata description that matches the template's one if one doesn't exist yet. Otherwise, by default, it is set to leave the Wikidata description intact but to override it with its own description, however it can be changed in the settings to automatically update the Wikidata description with the template's one or to not touch the Wikidata description at all. All of this can be found in the gadget's settings. · • SUM1 • ·(talk)23:41, 3 February 2020 (UTC)
ISCB Wikipedia Competition
Hi all, a reminder that the 9th ISCB Wikipedia competition is still open for entries to improve pages relating to computational biology.
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:
Gordon Life Science Institute (previously speedied as copyvio, just recreated which is what brought this to my attention; looks like it has been speedied again. Leaving link in case it comes back)
Kuo-Chen Chou is certainly notable and the 'recognition' section is probably fair. The 'Career' section probably needs a bit of copyediting and cleanup.
Sufficiently notable: PseAAC and PseKNCr are reasonably well known (though I couldn't say whether they're being over-emphasised over equivalent methods).
Just a note, a handful of mostly single-purpose accounts has made all of these articles. The currently active one was blocked a few hours ago for being exclusively promotional. Also thanks E&E for your thoughts above! Ajpolino (talk) 14:52, 22 August 2019 (UTC)
Because this guy has made it basically impossible to tell which citations to his work are legitimate and which are not, I'd be inclined to redirect most of these to Kuo-Chen Chou rather than fully deleting. But I wouldn't cry if they were nuked. Bueller 007 (talk) 00:18, 12 February 2020 (UTC)
Sorry if I'm doing it wrong here -- I don't generally edit anything on Wiki but after doing a bunch of digging into this guy's Wikipedia vandalism, I felt compelled to leave a comment. If you go through his multiple accounts you find a long trail of him adding himself to quite many Wikipedia articles in a very similar spirit to his academic misconduct, and I don't think any of the mentions of his research fits where he put it. Sometimes the pages he creates are merged into other pages by other users just trying to help, making it even more of a hassle to track down what he's done. But the inclusion of him in each page that he has mentioned himself probably feels like a slap in the face to the hundreds of other researchers who worked on similar things that are being left out while he is putting himself in the spotlight. I honestly think everything he has touched is tainted and mentions of him that he included in pages throughout Wikipedia should be removed -- leaving them there benefits nobody and in fact gives a very skewed picture to anyone who comes across them. His son also seems to have created a Wikipedia article for himself although the train of destruction is much smaller, mostly just contained to him creating his own autobiography (http://en.wiki.x.io/wiki/James_J._Chou) I doubt he meets and of the "reputable" conditions either. Quasilocal (talk) 18:02, 24 February 2020 (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)
Never mind. I noticed the template was quite a bit more broken than this, so I fixed these parameters, the class parameter, and all the project category links. Seppi333 (Insert 2¢) 19:55, 3 January 2020 (UTC)
@Evolution and evolvability: My bad, I didn't notice your reply before posting the sub-section below. There are several ways to implement the template consolidation though. What I've described below also applies for WikiProjects Biophysics, Computational Biology, Genetics, and Gene Wiki (which I've recently added a task force since it was originally a Genetics task force and has its own WikiProject banner templates on a number of pages). Basically, all I need to know is how others would like to set this project's importance rating based upon the original task force's importance rating(s).
I can handle all the template conversions myself (using either template wrappers or a new bot, if necessary) as long as I know how others want it to be implemented. Seppi333 (Insert 2¢) 01:41, 16 January 2020 (UTC)
Addendum: I still need to go through and check that all of the task force's class-rating categories exist for all the acceptable class rating inputs for {{WPMOLBIO}}; if any are missing, I need to create them. I'll do that today. Seppi333 (Insert 2¢) 01:48, 16 January 2020 (UTC)
What do others think about using a bot to convert the task force templates to {{WPMOLBIO}} with task force ratings?
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)
It might be better if people commented on his proposal there, keeping in mind that there are different options on how to rate an article's class/importance for this project, given the sub-project ratings.Seppi333 (Insert 2¢) 02:10, 16 January 2020 (UTC)
Support I have come upon a large number of these article throughout my edits associated with WikiProject Anatomy. Articles are often plastered with a few of these templates simultaneously, and it's clear this is the only active one of those projects. I've previously encountered situations where I wanted to bring an article or articles to a project's attention but it's very confusing without a specific venue and frustrating when there are multiple inactive venues. Additionally I often wonder about the time wasted tagging or updating articles for these wikiproject when it's clear they have a significant overlap and are inactive. It would be very useful to centralise this to a single wikiproject and I think here is a good place. I strongly support a merge into task forces here. Please ping me if there are discussions on other venues as I'd like to contribute there too. --Tom (LT) (talk) 10:49, 21 February 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?
@Davidwr and Omerriya: I've taken a look through this and spot-checked a sample of the refs. All looks in order and well written and appropriately linked. Minor formatting and tone issues, but all very fixable. T.Shafee(Evo&Evo)talk09:01, 28 February 2020 (UTC)
Task forces
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:
If (some or all) the talk pages aren't getting used at all, then consider redirecting them here (say, in a few months). In the meantime, put them all on your watchlists.
Put some effort into tracking down both people who previously participated in the smaller groups and also people who are currently editing articles, and invite them to join you.
The important part isn't getting them to officially sign up. The important part is just getting them to put it on their watchlists, or at least to know that you exist.
@WhatamIdoing: Very good point. Is there an automated way to send a talkpage message to everyone on the taskforce participant lists (example)? Otherwise I'll go through and do them all manually in the coming weeks, but thought I should check for automated solution first! T.Shafee(Evo&Evo)talk10:42, 17 March 2020 (UTC)
Evaluating/Annotating structural and single-nucleotide variants
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)
Eh, seems that there aren't any active Wikipedians with a genome bioinformatics background in this project; figured there were. I guess I'll just see if I can find a comprehensive review on PubMed. I noticed Andrew Su's lab published http://sulab.org/tools/omics-pipe/ though, so I'll probably just ask him if I don't find a useful resource. Seppi333 (Insert 2¢) 06:03, 29 March 2020 (UTC)
Fantastic Databases and where to find them: Web applications for rushed (busy?) researchers
List of Biological Databases
National Center of Biotechnology Information - NCBI [4]
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)
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)
Request for information on WP1.0 web tool
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)
Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles
This recently published article may be of interest to educators active in this WikiProject; attempting to promote a closer link between academia and Wikipedia.
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)
I'll aim to have a look through some sections. It's been a while since I did an FAR. Would definitely value the assistance of others on this! T.Shafee(Evo&Evo)talk03:13, 15 June 2020 (UTC)
Wikidata at the Bioinformatics Community Conference 2020?
There seems to be dozens of fatty acid images in Wikimedia Commons that have the wrong omega-numbers on the carbons. See for example
File:Fatty acid numbering.png
The carbons from the end are "ω", "ω−1", "ω−2", etc. Here is a corrected version:
File:Fatty acid carbon numbering.svg
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)
Conformation of fatty acid and trigliceride molecules
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)
Jorge Stolfi I don't understand "any two parts of the chain separated by a double bond are free to rotate about it" – wouldn't this imply that, for example, the cis monounsaturated oleic acid would not be in practice separable from its trans isomer, elaidic acid? Our articles report different melting points, suggesting they really are different compounds. Though I note we report a higher density for the cis isomer, which seems to count against the idea of better packing of the trans isomer. Adrian J. Hunter(talk•contribs)07:57, 1 September 2020 (UTC)
10th ISCB Wikipedia Competition: entries open now!
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:
Editing 'Structural Genomics Consortium' Wikipedia page
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.
@SZAckloo: Go for it. The Structural_Genomics_Consortium page is definitely in need of improvement. I think the current Publication overviews section would either be better integrated into the Highlight publications section or replaced with a history/milestones section that just covers the major achievements with the references themselves included inline. Does anyone know of a good exemplar page for a similar not-for-profit consortium? Some of the genome projects (e.g. HGP) might give useful ideas for additional info to include. T.Shafee(Evo&Evo)talk03:49, 30 August 2020 (UTC)
@Szackloo: I have reverted your changes, which, in essentially doubling the size of the prior article, went well beyond the scope of the discussion here. Also, I believe that the changes failed to maintain the proper neutral point of view, and introduced numerous stylistic and citation errors. I would prefer to see a more extensive discussion before engaging in what amounts to a top-to-bottom rewrite of the article. WikiDan61ChatMe!ReadMe!!20:04, 31 August 2020 (UTC)
@WikiDan61: I have made some changes to the entry since we last communicated. For some of the historical information, I wondered what the community thought about using an infographic. The community's opinions are very much appreciated. (I have to admit that it is not easy to use Wikipedia. For example, I did not realize there is/was a way to continue the thread and I completely agree that I should have done so.) (SZAckloo (talk) 12:36, 1 September 2020 (UTC))
@SZAckloo: No problem. Some general editing tutorial information that might be useful can be found here. I tend to mainly use visualeditor since I find it easier, but there's advice for editing the source code as well. T.Shafee(Evo&Evo)talk11:47, 4 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) buidhe22:17, 11 September 2020 (UTC)
In retrospect, it does seem rather inappropriate for me to have posted what DGG deleted in this section, so I wanted to apologize to those here (re this discussion: User talk:Seppi333#October 2020). My bad. I hope everyone can forgive my lack of forethought and stupidity for committing a faux pas. Seppi333 (Insert 2¢) 07:43, 15 October 2020 (UTC)
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.
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)
@Ajpolino: I support archiving and redirecting the MCB discussion page. One of the aims of this page was to move towards greater consolidation of the pages listed as taskforces so continuing that centralisation is useful. I actually think the same is true for the other WP:MOLBIO taskforce talkpages to this page and also the move new participants to in stead join this list. T.Shafee(Evo&Evo)talk06:56, 14 November 2020 (UTC)
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)
Just as an open question, are there any microbial taxa that are hard to lyse besides gram-positive bacteria, yeast, and spore-forming bacteria? Primarily asking in relation to protozoa and viruses. Seppi333 (Insert 2¢) 05:28, 26 November 2020 (UTC)
@Amkgp: I can help out with the image if I've a few examples to work from (it's pretty outside my core area). Is something like the right hand side of this diagram the sort of thing that's be useful? Most available diagrams, like this one, are just for unmodified RNA vaccines. Is the process especially different, or is the process the same? In the #Applications section, it should be made clear what the significance is of the modified nucleosides in the mRNA vaccine. Is it just stability, or do they affect its interactions? T.Shafee(Evo&Evo)talk22:29, 9 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.
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)
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.
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:
Part of the problem you'll no doubt find is that relatively few editors are currently around who work on molecular biology articles. So you may find that many of the GAs/FAs were reviewed and promoted in the distant past. That said, there are still a few of us here. So if there's any way we can help, please do reach out. All the best, Ajpolino (talk) 01:34, 19 February 2021 (UTC)
Solution to annoying Wikidata problem in sight
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)
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)
Moved from WT:MCB § Cathelicidin
.svg)
File:Fatty acid numbering.png
File:Fatty acid carbon numbering.svg
Seppi333 (Insert 2¢) 07:43, 15 October 2020 (UTC)
Done For MCB.Ajpolino (talk) 17:35, 22 November 2020 (UTC)
Resolved
