Wikipedia talk:WikiProject Molecular Biology/Biophysics/Archive 1

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

Archive 1

Archive 2

Establishing WP Biophysics

This is the start of WikiProject Biophysics, initially sponsored by the Early Careers Committee, the Education Committee, and the incoming president (Jane Richardson, User:Dcrjsr) of the Biophysical Society and with expert help from User:Phoebe, but hoping to attract much more general and international participation and feedback. Dcrjsr (talk) 18:45, 20 February 2012 (UTC)

WikiProject or task force?

Is this an independent wikiproject? If so, WikiProject Biology is not really a parent but a related wikiproject. RockMagnetist (talk) 01:59, 22 February 2012 (UTC)

It's hoped to be more general than a task force. But Biology already has a number of other WikiProjects underneath it, as true in many but not all other areas. There would seem to be advantages to having such a heirarchy and a home, and most biophysicists consider themselves as primarily biologists rather than primarily physicists. Do others have ideas and opinions on this issue? Dcrjsr (talk) 06:29, 22 February 2012 (UTC)

I think that having a separate wikiproject is fine, especially if more people are coming, even though Biophysics is a part of Biology. My very best wishes (talk) 19:43, 22 February 2012 (UTC)

On second thought, there is no harm - and possibly some good - in listing both biology and physics as parents. I have made a number of adjustments to reinforce this: Category:WikiProject Biophysics is now a subcategory of both projects and I have edited the parent pages as well. RockMagnetist (talk) 21:44, 22 February 2012 (UTC)

Agree. My very best wishes (talk) 02:11, 23 February 2012 (UTC)

Advice for new project

As I've told WP:GLASS in the past, here's a little roadmap you can find useful.

Tagging

There are a bots to help with this task. So to save yourselves some work you should build a list of categories and subcategories that should be tagged with {{WP Biophysics}}. The categories doesn't need to be "100% clean", as long as it contains articles that could be of interest to WP Biophysics. But don't pick something like Category:Books because one in 100 millions will be about a biophysics-related topics. Also decide if you want a taskforce (for example, a biography taskforce, for Biophysicists).

After you do this, you can get bots to tag the articles based on category membership and automatically assess them (for quality, importance remains untouched) based on the already present templates from the other Wikiprojects (if possible). The next step should be to review the assessments (preferably starting with FA, then FL, then A, then GA, then B, etc. in descending order) to make sure that these are actually related to this project, and that the B class articles are actually up to B class standards, etc.

Doing things in this order will save you a lot of work, believe me. Headbomb {talk / contribs / physics / books} 19:41, 27 February 2012 (UTC)

Whats a bot? Can you provide a link? 138.162.8.57 (talk) 20:47, 27 February 2012 (UTC)

Here is an example of one: DodoBot. RockMagnetist (talk) 20:58, 27 February 2012 (UTC)

A bot is a program that automatically edit things, and does tedious or repetitive tasks. For example, instead of you manually adding a list of 250 articles to a category (250 edits, which would take you a few hours), you can get a bot to do it for you. Headbomb {talk / contribs / physics / books} 21:03, 27 February 2012 (UTC)

Thanks, that makes perfect sense. Didn't know they had such a thing here. Anyway it looks like that Dodobot one needs oiled (or whatever). I clicked the User Contribs link and it hasn't done anything since November. If I am reading it right which I probably am not. Is it the only bot that does this type of thing? 138.162.8.57 (talk) 21:06, 27 February 2012 (UTC)

Several of these bots exists (See Category:WikiProject tagging bots). Of course, there are many, many more (Category:All Wikipedia bots). Headbomb {talk / contribs / physics / books} 21:10, 27 February 2012 (UTC)

Interesting, do you recommend one? I looked at the User contribs (thats a neat feature by the way) of 5 and 4 seemed inactive for several months and the other (Anomiebot I think) didn't seem to do this? Of course I didn't check them all. If I am understanding this correctly, these are all programmed by different people? Or are they done by the people that keep the site up? Assuming the first is true (since that is also the way general editing works) and not the latter then they were all done with for reasons, which indicates to me they have different functionality. At least I assume and since you seem to be aware of them perhaps you could offer a recommendation of one that best fits this task? Sorry to keep asking questions, I just don't understand all this yet. 138.162.8.57 (talk) 21:21, 27 February 2012 (UTC)

Personally, I've always liked User:AnomieBOT, and never had problems with the operator understanding exactly what it is I wanted to do. But presumably the other bot operators would be equally fine too. I just got used to AnomieBOT. And don't worry about asking questions, there's no way to learn without asking them. Headbomb {talk / contribs / physics / books} 21:28, 27 February 2012 (UTC)

I hadn't noticed that DodoBot had fallen so fart behind. Ironically, I found out about it from a link in Wikipedia:WikiProject_Council/Guide#Use_bots_to_save_work to User:Xenobot Mk V, which is inactive and recommended DodoBot. The guides are getting a bit stale! How do you use AnomieBOT? RockMagnetist (talk) 21:47, 27 February 2012 (UTC)

You basically drop a message on AnomieBOT's talk page, and Anomie will review it and take care of everything. Headbomb {talk / contribs / physics / books} 22:01, 27 February 2012 (UTC)

Do you have to give all the categories explicitly, as in your list above? One of the addractions of DodoBot is that you could let the bot crawl through the subcats. RockMagnetist (talk) 22:29, 27 February 2012 (UTC)

Preferably, but it's not technically impossible to do so. What you consider an attractive feature of DodoBot is actually quite the drawback and will bite you in the butt because telling it 'run through everything' means it will actually run through everything. And everything includes lots of things you didn't think of. Headbomb {talk / contribs / physics / books} 22:32, 27 February 2012 (UTC)

Recruiting

Once the basic stuff is dealt with, you should start recruiting some people:

Notify other related projects that the project is set up and that you are looking for members. Encourage to watch Wikipedia:WikiProject Biophysics/Article alerts (users needs to show bot edits) as an alternative to place their name on the member list if they don't want to join 'formally'.
Place a notice on the high profile biophysics-related articles (Talk:Biophysics, ...)
Think of other editors you know that worked on biophysics related articles, or that seemed to know something about biophysics related topics and personally invite them to join the project. If they decline because they don't feel comfortable in joining, invite them at least watch the Article Alerts page. If you don't know that many (or any) such editors, go through the history of biophysics-related articles and look for people who added content. It is my experience that many will ask questions about the benefits and pertinence of joining projects. My usual reply is that it serves as a centralized rally point to discuss biophysics articles and to build a list of "go-to people". Some might know a lot about a particular subfield of biophysics, but don't feel they would "contribute enough" to join, or are not interested by "menial tasks" such as assessment or cleanup. However, many of these people don't mind to place their names on the list to give feedback when requested. And many will agree to at least watch the alert page.
If you know (in real life) people who are knowledgeable (colleges, friends, etc...), invite them to join Wikipedia (or to give it a try, it's intimidating at first, but the community is, as a whole, very supportive).

Headbomb {talk / contribs / physics / books} 19:45, 27 February 2012 (UTC)

I just stumbled onto tis page. I have done a few edits here and there but I have never heard the Wikipedia community being particularly nice to new editors. — Preceding unsigned comment added by 138.162.8.58 (talk) 20:41, 27 February 2012 (UTC)

Keep in mind that people with bad experiences are a lot more likely to complain than those who have good experiences. There's basically two things you need for success. The first is that you need to be able to work in a collaborative environment and able to accept that your opinion on how to improve an article may not reflect consensus, and you'll sometimes need to compromises, or seek alternatives. The second is you need to be able to grasp that conventions do exists. People who say they have bad experiences usually don't work very well with others, or forget that conventions exist for articles. Sure some newcomers will run into rude people, but in science articles, it's pretty rare to get involved in controversy, unless you're trying to push fringe/junk science. Registering is also a good way to establish yourself as a non-idiot, as people will be able to find out if you're here to improve, or here to disrupt.

And if you use Wikiprojects as a way to resolve dispute (or seek help/clarification), you're almost guaranteed to be surrounded by sane people who don't like drama. Headbomb {talk / contribs / physics / books} 20:50, 27 February 2012 (UTC)

Biophysics meeting

Sorry for not taking part in your recruitment event (I had to run to poster session which is the most important part of such meetings). If I had to share my experience and offer some advice for newbies, here is the most important part of it:

If you want to edit on this site, please take it easy. Be a casual contributor. Know exactly what you want to accomplish. Edit few articles, fix a few errors, and return to your normal life. Do not care what may happens later with your edits. Take a long wikibreak if you start thinking about wikipedia business more than about your real life business. This way you can avoid addiction to wikiediting (this is a serious trouble, believe me) and other problems, such as wasting your time in editorial disputes. I have seem many great contributors who became extremely frustrated and even angry after editing on this site. This had happen only because they spent too much time on-wiki and became emotionally invested. You may also wish to read this essay. My very best wishes (talk) 15:20, 1 March 2012 (UTC)

I'll recommend the exact opposite. If you wish to get involved, put as much time in the project as you want (but obviously you shouldn't let it take precedence over real life). Wikipedia needs all the helps it can get, and telling people to contribute the bare minimum is counterproductive advice IMO. The advice mentionned above (in Logan; et al. (2010). "Ten Simple Rules for Editing Wikipedia". PLOS Computational Biology. 6 (9): e1000941. Bibcode:2010PLSCB...6E0941L. doi:10.1371/journal.pcbi.1000941. PMC 2947980. PMID 20941386. {{cite journal}}: Explicit use of et al. in: |author= (help)) is all very sound however.Headbomb {talk / contribs / physics / books} 16:47, 1 March 2012 (UTC)

I think I will stick to editing infrequently but thank you both for the advice. In less than 48 hours of making an edit I was accused of being another user, read several long and disturbing discussions, accused of wasting tax dollars, gotten completely confused with policies and guidelines and heard an earful of stories from my coworkers, most of which, according to them, were "run off" or "chased away" over minor edits, a lack of knowledge about all the policies and an assumption by others that what they were doing was vandalism rather than a good faith attempt to edit. Most didn't last more than a couple days before running into problems. After what I have read, honestly, it seems about right. I'll still make an occassional edit but won't be a regular editor. 138.162.8.57 (talk) 17:25, 1 March 2012 (UTC)

What a shame. Headbomb {talk / contribs / physics / books} 17:40, 1 March 2012 (UTC)

If you wish to get involved, put as much time in the project as you want ... but obviously you shouldn't let it take precedence over real life. Yes, that is exactly what I am talking about. But unfortunately, there were many good contributors who became addicted to such degree that they kept coming back even after being site-banned or having serious trouble (on-wiki and elsewhere). And it's hard not to become addicted if you are a "regular contributor". People simply do not realize it when they start contributing. My very best wishes (talk) 00:15, 2 March 2012 (UTC)

Sorta ironic we are talking about the Biophyical effects of addiction on this page. 138.162.8.58 (talk) 15:09, 2 March 2012 (UTC)

I am currently active [1]. If new editors have any questions, please do not hesitate to ask. My very best wishes (talk) 04:59, 3 March 2012 (UTC)

Biomembranes subproject

Here is one of previous attempts to create a working group in this area. My very best wishes (talk) 19:15, 3 March 2012 (UTC)

Validation article

Dcrjsr and JeremyBlock are working together on creating a new article on macromolecular structure validation. So far it's just in sandbox territory, but wanted to let other folks know in case they're also interested. Dcrjsr (talk) 02:59, 28 March 2012 (UTC)

I am not sure what Jeremy is trying to accomplish here. He may wish to prepare the text on his PC and then place it to his user subpage (User:JeremyBlock/Sandbox) or just create a new article... When you have a draft, I can help with improvements.My very best wishes (talk) 19:15, 30 March 2012 (UTC)

Our joint work in a non-wikipedia sandbox has now been moved into the draft-article site - hope it now makes more sense.Dcrjsr (talk) 17:11, 5 April 2012 (UTC)

I created the page in main space. Please improve. My very best wishes (talk) 12:57, 6 April 2012 (UTC)

The article is Macromolecular structure validation. RockMagnetist (talk) 14:09, 6 April 2012 (UTC)

We appreciate your feeling it was ready to go live. However, one problem we'd meant to resolve before that was how to rename it to Structure validation (macromolecular), with a hatnote or eventually a disambiguation page. Most people who want this article will search using just "structure validation", and with the current title they don't get there at all directly. But many of the hits are to XML schema validation, which may eventually want its own page, and some are to mechanical engineering. Does anyone have advice on the most robust and feasible way to accomplish this? Dcrjsr (talk) 14:50, 6 April 2012 (UTC)

So, should we move it to Structure validation or Structure validation (macromolecular)? I think simply "Structure validation" is better. My very best wishes (talk) 14:57, 6 April 2012 (UTC)

I wouldn't sweat too much over the name. You could move it to whatever name you think is most appropriate and provide redirects for all the synonyms. You can always change it later. RockMagnetist (talk) 15:01, 6 April 2012 (UTC)

Sure. Done. There is nothing for creating disambig. page right now. My very best wishes (talk) 15:04, 6 April 2012 (UTC)

One reason not to jump the gun in future is that it makes it difficult to nominate articles for DYK. RockMagnetist (talk) 16:08, 6 April 2012 (UTC)

Thanks - this seems good. Dcrjsr (talk) 17:02, 6 April 2012 (UTC)

Yes, it's a shame about DYK. And also, we won't get any credit for the new article. Dcrjsr (talk) 00:26, 14 May 2012 (UTC)

Assessment request for Fred Richards article

I've been extensively rewriting and expanding the biography article on Fred Richards, which was originally in pretty bad shape. Since I have never done any assessment myself, and don't really have any feel at all about what the different quality class descriptions actually mean in practice, I'd really appreciate some feedback from those of you who understand the process better. We'll need such knowledge as the WikiProject goes forward. Thanks in advance for whatever people can do! Dcrjsr (talk) 00:23, 14 May 2012 (UTC)

I have assessed it. RockMagnetist (talk) 13:50, 14 May 2012 (UTC)

Again, thanks - from here as well. The comments were very useful. I've added to the infobox and put in refs for the timeline section, and will work later on a personal biography section.Dcrjsr (talk) 04:14, 15 May 2012 (UTC)

Glad to help! RockMagnetist (talk) 04:51, 15 May 2012 (UTC)

Assessment

Headbomb's request has been filled and we have about 800 automatically rated articles in this project. I have created an Assessment department where you can find the table of article assessments. RockMagnetist (talk) 05:00, 18 March 2012 (UTC)

Upcoming FAC for DNA nanotechnology

I'm going to be submitting DNA nanotechnology for a second FAC in the next couple of days, and I'd appreciate it if you could take a look and let me know if you have any feedback before I start the process. Thanks! Antony–22 (^talk⁄_contribs) 21:45, 19 May 2012 (UTC)

That's a very nice article! The only serious gap I can see on a quick look is the omission of the quite considerable analogous work in RNA structural nanotechnology, where natural RNAs already have selectively-evolved helix junctions that specify 3D relationships that can be used as modular building-blocks. Luc Jaeger's is the work I know best on this, but there are more (I'm on my way to Sicily today, so I can't look anything up now).

I could get or make you some more pictures of the models or of 3D crystal structures, if there are others you'd like to include. Also, Thom LaBean, a former student of ours and a local colleague in NC, works in the DNA end (and is a good friend of Eric Winfree, who was also at Duke for a while) - I'll ask him to look at the article.Dcrjsr (talk) 14:24, 30 May 2012 (UTC)

Here are Thom LaBean's comments on the DNA nanotech article, which sound sensible to me:

"The wiki work appears very useful and of nice high quality, with lovely images. On the DNA nanotech page, I have the following comments:

Near the top, where it says "rigid nucleic acid double helix molecules" this sounds like the double helix is one molecule, when of course it is made up of two molecules in a supramolecular complex. I would change it to "rigid nucleic acid double helices" or "rigid nucleic acid double helix complexes".

Again in the caption for the DX tile image: "This double-crossover (DX) molecule consists of five DNA single strands that form two double-helical domains, on the left and the right in this image.", the DX is a supramolecular complex made up of 5 molecules (the strands are each molecules). I know that Ned Seeman always refers to these complexes as molecules, but that is not technically correct and it seems best not to propagate that inaccuracy on the wiki. Also: the two double-helical domains are on the top and bottom, not left and right.

Where it says "DNA nanotechnology use branched nucleic acid structures", it would be more accurate to refer to "topologically branched NA structures" to differentiate this from branched polymer molecules. The NA branch junction structures are made from linear, unbranched DNA polymers.

Where it says "Multiple junctions can also be combined in the same molecule, such as in the widely-used double-crossover (DX) motif,...", swap 'complex' in for 'molecule', as above.

"as deoxyribozymes and ribozymes, which are capable of performing chemical reactions," could be changed to "as deoxyribozymes and ribozymes, which are capable of catalyzing chemical reactions,"

Down in Sequence Design section, "After any of the above approaches are used to design the secondary structure of a target molecule, an actual sequence of nucleotides " i would swap 'complex' in for 'molecule' again. Same thing again a couple of times in the Extended Lattices section. Also the caption to the first figure in Materials and Methods change "DX molecule" to "DX tile" or "DX complex".

The original reference for the image credited to reference 17 is actually:

DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires, Hao Yan, Sung Ha Park, Gleb Finkelstein, John H. Reif, Thomas H. LaBean, Science, 26, 2003, 1882-1884

Reference 17 is a review article that cites this Science paper." - Dcrjsr (talk) 21:11, 31 May 2012 (UTC)

Great to have expert feedback on this! The FAC page is now open so I'd encourage all of you to weigh in on whether you think the article should be promoted or not. Comments from subject matter experts are somewhat hard to come by on articles this technical, and any input would be greatly appreciated.

I've made all but two of the changes suggested above. First, this article focuses on rationally designed structures and so evolved structures wouldn't be within its scope. I'd be happy to collaborate on putting together another article on the evolved RNA structures though. Second, not all (deoxy)ribozymes are catalytic; self-cleaving ribozymes are consumed in the reactions they perform. Antony–22 (^talk⁄_contribs) 22:28, 1 June 2012 (UTC)

Editors with subject domain expertise are cordially invited to comment on the content & other aspects of the article at Wikipedia:Featured article candidates/DNA nanotechnology/archive2 – Ling.Nut (talk) 04:57, 2 June 2012 (UTC)

MfD nomination of Portal:Xray Crystallography

Portal:Xray Crystallography, a portal in which you may be interested, has been nominated for deletion. Your opinions on the matter are welcome; please participate in the discussion by adding your comments at Wikipedia:Miscellany for deletion/Portal:Xray Crystallography and please be sure to sign your comments with four tildes (~~~~). You are free to edit the content of Portal:Xray Crystallography during the discussion but should not remove the miscellany for deletion template from the top of the page; such a removal will not end the deletion discussion. Thank you. ···日本穣^? · 投稿 · Talk to Nihonjoe · Join WP Japan! 17:12, 15 September 2012 (UTC)

WikiProject Biophysics in the Signpost

The WikiProject Report would like to focus on WikiProject Biophysics for a Signpost article. This is an excellent opportunity to draw attention to your efforts and attract new members to the project. Would you be willing to participate in an interview? If so, here are the questions for the interview. Just add your response below each question and feel free to skip any questions that you don't feel comfortable answering. Multiple editors will have an opportunity to respond to the interview questions, so be sure to sign your answers. If you know anyone else who would like to participate in the interview, please share this with them. Have a great day. –Mabeenot (talk) 18:07, 9 April 2013 (UTC)

Is this thing still running?

And how do I enter competition? Sevendigits (talk) 08:22, 17 May 2013 (UTC)

H-bonds

There is no such things as Tertiary hydrogen bond and Secondary hydrogen bond. There is just Hydrogen bond. Delete both articles? What do you think? My very best wishes (talk) 20:32, 22 February 2012 (UTC)

Better to put in a merge request to merge the two articles with hydrogen bond -- the {{mergeto}} tag on the talk pages of both will notify any current editors of those articles; then any information in them that is useful and isn't already duplicated can be merged into the main article. -- phoebe / (talk to me) 05:47, 23 February 2012 (UTC)

Yes, and this is probably a good way to deal with POV forks in general. I can do it after coming back from the meeting. My very best wishes (talk) 15:54, 23 February 2012 (UTC)

Fixed. No one edits these articles, and all their content has been already included in Hydrogen bond. My very best wishes (talk) 15:10, 24 February 2012 (UTC)

Organismal biomechanics

I discovered that there is a WikiProject Organismal Biomechanics. It's a bit small (covering 241 pages) and might make sense as a task force within this WikiProject. Should we approach them with the idea? RockMagnetist (talk) 18:44, 22 February 2012 (UTC)

This sounds logical. Biomechanics can be considered a part of Biophysics. My very best wishes (talk) 19:43, 22 February 2012 (UTC)

Hi from WikiProject Organismal Biomechanics! Please feel free to help out on any of our pages you can. Hopefully things will move into higher gear soon, as I'm making a pitch to a comparative biomechanics academic society for more faculty involvement (with a cynical eye towards Broader Impacts statements), but any help is always welcome. As far as merging, I'd actually prefer not to in order to keep these articles grouped together for easier tracking and improvement. Plus, at least in my limited experience, the biophysics folks and biomechanics folks don't seem to interact as much as one would think (though I would love for this to change), probably because the former seem focused on the molecular level while the latter tend to be more at the whole organism level. HCA (talk) 15:52, 17 March 2012 (UTC)

Ah, noticed we were plotting your demise, eh? I think I can answer your objections; maybe it is time to open the discussion at your project's talk page. RockMagnetist (talk) 23:56, 17 March 2012 (UTC)

Automated process for article tagging and/or assessing

I would like to submit a request to have DodoBot tag and/or automatically assess articles for our WikiProject, as explained here. Feel free to raise any questions or concerns regarding this suggestion. I will assume there is consensus for the task if there are no objections in a week.RockMagnetist (talk) 02:44, 22 February 2012 (UTC)

This seems like a good idea, since we certainly need automated help. However, the categories are extremely incomplete (didn't include ion channels, for instance, or any structural biology) and "Cryobiology" seems rather a stretch as biophysics. Maybe we should collectively do some work on the categories before letting the bot loose. Other feedback? Offers of more experienced help on the category issue? Dcrjsr (talk) 06:55, 22 February 2012 (UTC)

Let's run it right now, even in "liberal" regime. It will make no harm because this bot only modifies talk pages if I understand this correctly. We can run it again later if needed.My very best wishes (talk) 19:43, 22 February 2012 (UTC)

I've got experiences in setting up taskforces etc... One question that will be important is how will WP:BIOPHYS operate as far as tagging articles go? Will you have your own banners? You currently have {{WP Biophysics}}, but it might not be the best way to handle things. You might want to use {{WikiProject Physics|taskforce=Biophys}}, or perhaps {{WikiProject MCB|taskforce=Biophys}}? Either way is easy enough to implement, but it's best to decide on this early on, and to do so before involving bots. Headbomb {talk / contribs / physics / books} 19:11, 27 February 2012 (UTC)

I think the consensus is that this is an independent wikiproject with Physics and Biology as informal parents (see the comments in the other sections). RockMagnetist (talk) 19:22, 27 February 2012 (UTC)

I have made a DodoBot request to tag all articles in Category:Biophysics. You can see the request here. RockMagnetist (talk) 19:57, 27 February 2012 (UTC)

Categories to tag

Here's a crude list of all the subcategories of Category:Biophysics that could possibly make sense to include. However I'm not a biophysicist, and I didn't pay a lot of attention while build the list, so some review is needed before submitting this list to bots.

Just remove the stuff that doesn't make sense to tag, then you can submit the list to a bot operator. Headbomb {talk / contribs / physics / books} 21:22, 27 February 2012 (UTC)

Maybe not Category:Fictional cryonically preserved characters, Category:Taxes (biology) or Category:Cryonics in fiction? Not sure whats this project looks for but these seem low value to start. Not really my deceision just an opinion. --138.162.8.57 (talk) 21:26, 27 February 2012 (UTC)

It seems that we don't need to worry because it won't look at subcategories. RockMagnetist (talk) 22:43, 27 February 2012 (UTC)

I think that Category:Locomotion needs some work. RockMagnetist (talk) 22:51, 27 February 2012 (UTC)

I have done a lot of tidying of Category:Locomotion and its subcategories, but more could be done. RockMagnetist (talk) 18:51, 28 February 2012 (UTC)

Now obviously I'm not a biophysicist, but some categories still seem a bit out of place (Category:Spinal cord) and maybe a bit too broad to tag by bot (such as the various categories of protein). I've put an asterisk next to all of those I'm a bit unsure about, so if someone could confirm it's a good idea to tag all articles in those categories (or say 90% + of the articles), or if it would be better to be selective about what's tagged. Once that's settled, I can get the bot to tag stuff. Headbomb {talk / contribs / physics / books} 17:04, 1 March 2012 (UTC)

There are obviously many overcats here. I am going to remove all sub-cats of Category:Proteins because the entire Category:Proteins belongs to Biophysics. Feel free to correct if needed. My very best wishes (talk) 06:13, 2 March 2012 (UTC)

If we use AnomieBot, you'll need to leave those subcats in because it doesn't look in subcats. RockMagnetist (talk) 06:19, 2 March 2012 (UTC)

But removing obvious sub-cats would not hurt. Right? My very best wishes (talk) 06:25, 2 March 2012 (UTC)

Please do not forget to include Proteins and a lot of other categories that must be included here. I will not do it because you reverted my edits without discussion. Thanks, My very best wishes (talk) 06:30, 2 March 2012 (UTC)

MVBW, I don't think you quite understand how tagging bots usually operates. While in theory it's possible to tell a bot "tag everything in this category and subcategory", many bot operators will not do it because of the risk of chewing something larger than what you meant to chew. Tagging (for example) the entirety of the Category:Proteins would tag many many articles not-very relevant to biophysics, and likewise for many of its subcategories. That's why you want an explicit list of categories that are confirmed to be relatively clean to tag by bot (even if they are subcategories of another category), rather than assume that since a category is related to biophysics, that all the articles in it (and subcategories) are also related to biophysics. Headbomb {talk / contribs / physics / books} 06:27, 2 March 2012 (UTC)

I am sorry, but the entire Proteins belongs to Category:Molecular Biophysics, just as it belongs to Molecular Biology. You asked someone who knows the subject to help. So, here I am. But you reverted my changes right in the process of editing without discussion. That's fine. I have a lot of other things to do. My very best wishes (talk) 06:39, 2 March 2012 (UTC)

No discussion? What do you think my above post is? Headbomb {talk / contribs / physics / books} 06:40, 2 March 2012 (UTC)

You asked someone to help [2]. I came to help, but you reverted my edits right in the process of editing. Frankly, this is something I have never seen in the area of Biology and Chemistry, but only in the area of Politics. Please do not do it. My very best wishes (talk) 06:54, 2 March 2012 (UTC)

"I came to help, but you reverted my edits right in the process of editing." And? That's WP:BRD 101. How about we get back on the topic of tagging articles? Headbomb {talk / contribs / physics / books} 07:02, 2 March 2012 (UTC)

This is very simple. All biomolecules belong to Molecular Biology. They can be studied by chemical methods. Hence they also belong to Biochemistry. They can be studied by physical methods. Hence they also belong to Molecular Biophysics. WP:BRD is not a policy and does not apply to project talk pages. But whatever. My very best wishes (talk) 14:44, 2 March 2012 (UTC)

On a second thought, we certainly do not want to tag all biomolecules for this project. At the same time taging certain types of proteins that are frequently studied by physical methods would be difficult and arbitrary. Maybe we should not run the bot at all. My very best wishes (talk) 16:38, 2 March 2012 (UTC)

Alright, well unless anyone objects, I'm going to send that above list to AnomieBot (minus the starred categories) in the near future, with assessment ratings inherited to save some work. Headbomb {talk / contribs / physics / books} 20:16, 4 March 2012 (UTC)

I have removed the DodoBot request. There doesn't seem to be much chance of it being filled. RockMagnetist (talk) 18:29, 8 March 2012 (UTC)

I agree with My very best wishes that we should not tag all proteins (or all nucleic acids). But I think some of the starred categories for membrane proteins and ion channels should stay, because they're a truly central part of biophysics. The cryopreservation part seems pretty dubious to me, however. The real missing aspect is how we will handle methodology, which is very central, but often the biophysics part of it is a subset of a larger technique (e.g., macromolecular crystallography as a part of x-ray crystallography). I'd suggest that perhaps we could make a clear distinction, with separate pages, underneath a general technique, and then claim, link to, and categorize those subcategories. Does that make sense to people? Dcrjsr (talk) 03:06, 28 March 2012 (UTC)

I'd also drop Category:Lantibiotics, and perhaps Welsh biophysicists (altho I'm completely positive about Alwyn), unless we make subcategories for other major countries.Dcrjsr (talk) 03:12, 28 March 2012 (UTC)

New watchlist

I have added a link on the project page to recent changes to biophysics articles. This link follows changes to any articles listed in Index of biophysics articles (which I just created), so this list should be kept up to date. RockMagnetist (talk) 22:10, 16 May 2012 (UTC)

For the less experienced Wikipedians, I should add that a watchlist like this is a great resource for fighting vandalism. Have a look at it occasionally! RockMagnetist (talk) 22:13, 16 May 2012 (UTC)

Thanks - that's a wonderful addition!Dcrjsr (talk) 14:25, 30 May 2012 (UTC)

Non-helical models of nucleic acid structure

We're doing some heavy discussion on the article Non-helical models of nucleic acid structure, and we'd really appreciate some help from someone familiar with topoisomerases and/or bacterial chromosome replication. Please see Talk:Non-helical models of nucleic acid structure#Balancing information needed. Thanks! Antony–22 (^talk⁄_contribs) 04:49, 2 June 2012 (UTC)

notable women?

Recently, a picture of Rosalind Franklin was removed from List of biophysicists because copyright restrictions only allow it to be used in her article. I tried to replace her picture with another of a female biophysicist, only to discover that she is the only woman the list. Are there any Wikipedia articles on women that should be in the list? Ae there any female biophysicists that should have articles and don't? RockMagnetist (talk) 18:45, 31 July 2012 (UTC)

I'd suggest Janet Thornton - there's a very nice picture on her page (I haven't checked it's permissions, tho). Isabella Karle & Helen Berman have pictures; Louise Johnson doesn't. There's a picture on my page (Jane Richardson), but it would be entirely inappropriate to feature me. If Janet doesn't work, I'll think of some more. And I'm sure there are indeed some women (and men) who should have a page and don't. We may have a subcategory problem, since Janet & Louise are categorized as "British biophysicists" and Qwerty has been changing "Biophysicists" to "American biophysicists" in many articles. Presumably the "List of biophysicsts" is not automatically updated from the categories.

So I've added some of these women to the list, and put in Janet's picture, which is CC BY. Dcrjsr (talk) 23:14, 3 August 2012 (UTC)

You developed the ribbon diagram! I'm impressed. It is certainly appropriate to put your name in the list, and I have done that. The permissions for Janet Thornton look fine to me. RockMagnetist (talk) 23:51, 3 August 2012 (UTC)

Hal Anger

The article on Hal Anger is provided with several good sources, but very little use is made of them. Instead, there is a lot of information on patenting of a device that is given undue weight (see also Hal Anger#Unbalanced). This would make a good project for someone. RockMagnetist (talk) 17:49, 26 September 2012 (UTC)

Ariel Fernandez

The article on Ariel Fernandez has been tagged for possible conflict of interest. It is written by employees of a company run by Fernandez, and lacks independent sources. The main contributor has already removed the tags once and I have restored them (see User_talk:Arifer#Notices in Ariel Fernandez). If anyone independent of Fernandez can add appropriate sources, they would help to address both issues. RockMagnetist (talk) 16:46, 27 September 2012 (UTC)

Actually, the vast majority of the edits are by User:Ariel Fernandez(talk) or User:Arifer(talk) (an obvious contraction of Ariel Fernandez). I think he actually is notable, but the article is full of puffery, especially the word "pioneering". The COI and BLP sources tags have already been removed by an IP editor after providing sources for a couple of awards and one statement about the significance of his research. RockMagnetist (talk) 16:20, 28 September 2012 (UTC)

I have launched a sockpuppet investigation of the user Arifer. This mainly applies to the articles on Ariel Fernandez and Dehydron. RockMagnetist (talk) 00:24, 1 October 2012 (UTC)

The result was that several accounts and IP's were identified as sockpuppets or meatpuppets. A lot of the content of Ariel Fernandez and Dehydron has been deleted because it was promotional. RockMagnetist (talk) 17:28, 8 October 2012 (UTC)

Biographies needed

I'd like to reduce the number of redlinks in the Foresight Institute Feynman Prize in Nanotechnology awardees list. Being that there's a biophysics editing contest coming up here, I've listed the more biophysics-related awardees below, in case any of you are looking for suggesions for articles to write.

Thanks! Antony–22 (^talk⁄_contribs) 20:59, 12 January 2013 (UTC)

Do genes belong in this project?

Do specific genes belong in this project? For example, the biophysics content in CLCN5 seems limited to the fact that it encodes an ion channel. Is that enough to merit inclusion in this project? RockMagnetist (talk) 05:19, 23 April 2013 (UTC)

Good question. On some WP articles there seems to be some confusion between genes and proteins. Genes, as sets of sequences of DNA or RNA, are firmly in biology territory. There are people who look at the physics of DNA and RNA, but typically the focus is not on the physics of a particular sequence. Proteins are the end result of multiple steps of transcription and post processing. There is a rough identification of genes and proteins, but it is not 1-1 in all cases. Things like channel proteins can be of interest to biophysicists, but it is not clear that all such proteins have been of biophysical interest. If the protein has been of biophysical interest and the only article we have on it is on the genetic sequence it is based on, it makes sense to me to include it in a biophysics category. But I wouldn't slap a biophysics category on every gene article in general. --Mark viking (talk) 15:06, 23 April 2013 (UTC)

Alas, we already have slapped them with a bot. They make up a large fraction of the unassessed articles. I think a lot of them come from Category:Ion channels. RockMagnetist (talk) 15:18, 23 April 2013 (UTC)

It's probably hard to exclude the ion-channel genes from "ion channels", which is certainly one of our important categories. Does anyone know either how to do that, or how to mark the gene-only ones as unimportant for us? Dcrjsr (talk) 12:36, 24 April 2013 (UTC)

All we need to do is remove the {{WikiProject Biophysics}} templates from the talk pages. RockMagnetist (talk) 14:59, 24 April 2013 (UTC)

OK - that makes sense. We can do that as a background project. Dcrjsr (talk) 00:34, 25 April 2013 (UTC)

Cleanup listing

Hi. I'm currently working on an bot that creates on-wiki copies of Svick's cleanup lists. I've been using your project's list for testing, so I'm curious what you think of it. The list can be found at User:HhhipBot/Cleanup listing/Biophysics. The main motivation for having this list on-wiki is that it can be watchlisted and that article links are internal (that is, protocol-neutral). Additional features are that each section can be individually transcluded, and several ways to find new or recently resolved issues. Comments or suggestions are welcome! — HHHIPPO 12:18, 16 June 2013 (UTC)

I like the idea of an in-wiki cleanup listing, and your version has an attractive layout. I'd like to see the importance rating for each article - when I use a cleanup listing I prefer to work on the highest priority articles first. RockMagnetist (talk) 21:25, 16 June 2013 (UTC)

You mean, like this? I added a short marker giving the importance for each listed article (and there will be a legend somewhere). One could also think of sorting by importance, for the projects that have these ratings, but then there's so many sort options, we should probably stick to one for the wiki version and use the original tool for the rest. — HHHIPPO 18:50, 17 June 2013 (UTC)

Yes, there is something to be said for two tools with different advantages. I think the markers are a little cryptic; without some explanation at the top, most people would probably not guess why there is an [M] or [?] after a listing. You could add an explanation at the top, use something like the {{Classicon}} template, or expand the markers to read something like [Top]. RockMagnetist (talk) 02:00, 19 June 2013 (UTC)

Yea, I considered those options, too. There seems to be no established set of icons for importance ratings, and I think [Top], [Unknown] etc. might still be cryptic on first sight, so I went for the option with compact labels plus legend. I added the legend to the top of the page now, together with some more description and links. I couldn't find a good general description of importance ratings, the ones at WP:1.0 are somewhat focused on preparing offline releases, which is not why we want the ratings here.

Feel free to further tweak the introduction text, I plan on teaching the bot to leave the lead section alone before I run it again, so that can be customized by each project. — HHHIPPO 18:44, 20 June 2013 (UTC)

Archived a few threads

I've archived some inactive threads to subsections which were notifications about discussions that have since been closed. — Cirt (talk) 22:00, 8 February 2014 (UTC)

Wikipedia session at Biophysical Society meeting

The notes from the session are available at Wikipedia:WikiProject Biophysics/Biophysics wiki-edit contest/BPS 2014 session. -- Daniel Mietchen (talk) 01:29, 17 February 2014 (UTC)

Royal Society journals - subscription offer for one year

I'm delighted to say that the Royal Society, the UK’s National Academy for science, is offering 24 Wikipedians free access for one year to its prestigious range of scientific journals. Please note that much of the content of these journals is already freely available online, the details varying slightly between the journals – see the Royal Society Publishing webpages. For the purposes of this offer the Royal Society's journals are divided into 3 groups: Biological sciences, Physical sciences and history of science. For full details and signing-up, please see the applications page. Initial applications will close on 25 May 2014, but later applications will go on the waiting list. Wiki at Royal Society John (talk) 03:13, 29 April 2014 (UTC)

Outline of biophysics

FYI, "Outline of biophysics" has been requested to be renamed to Biophysical techniques; for the discussion, see talk:Outline of biophysics -- 65.94.169.222 (talk) 08:49, 27 July 2014 (UTC)

Comment on the WikiProject X proposal

Hello there! As you may already know, most WikiProjects here on Wikipedia struggle to stay active after they've been founded. I believe there is a lot of potential for WikiProjects to facilitate collaboration across subject areas, so I have submitted a grant proposal with the Wikimedia Foundation for the "WikiProject X" project. WikiProject X will study what makes WikiProjects succeed in retaining editors and then design a prototype WikiProject system that will recruit contributors to WikiProjects and help them run effectively. Please review the proposal here and leave feedback. If you have any questions, you can ask on the proposal page or leave a message on my talk page. Thank you for your time! (Also, sorry about the posting mistake earlier. If someone already moved my message to the talk page, feel free to remove this posting.) Harej (talk) 22:47, 1 October 2014 (UTC)

WikiProject X is live!

Hello everyone!

You may have received a message from me earlier asking you to comment on my WikiProject X proposal. The good news is that WikiProject X is now live! In our first phase, we are focusing on research. At this time, we are looking for people to share their experiences with WikiProjects: good, bad, or neutral. We are also looking for WikiProjects that may be interested in trying out new tools and layouts that will make participating easier and projects easier to maintain. If you or your WikiProject are interested, check us out! Note that this is an opt-in program; no WikiProject will be required to change anything against its wishes. Please let me know if you have any questions. Thank you!

Note: To receive additional notifications about WikiProject X on this talk page, please add this page to Wikipedia:WikiProject X/Newsletter. Otherwise, this will be the last notification sent about WikiProject X.

Harej (talk) 16:56, 14 January 2015 (UTC)

WikiProject X newsletters

We were subscribed to WikiProject X newsletters by someone who is not listed as a participant of this WikiProject. I have taken the liberty of unsubscribing us and removing the newsletters. However, they can easily be restored if participants want them. RockMagnetist(talk) 23:04, 17 August 2015 (UTC)