User talk:Alexbateman/Archive 1

RNA entries
Hi Alex,

Thank you for your kind note. I did have a question about some of the entries. For example Small nucleolar RNA SNORD70 begins "snoRNA HBII-234 belongs to the C/D family of..." is HBII-234 another name for SNORD70? There is a bit of a disconnect here, since the article's subject should be clearly identified in the first sentence. Should these entries be changed to read "snoRNA HBII-234 (SNORD70) belongs to...."? I could use some guidance here as don't really know anything about RNA families (I am an immunologist but I found many of the article to be quite interesting-but they really need to be wikilinked).

A couple of other suggestions I have for the project are: 1) an RNA WikiProject banner for the Talk page, and 2) perhaps a few navigational templates to better link the articles together. A person to contact about creating nav. templates is Arcadian, he is really good at making them. Cheers--DO11.10 16:23, 15 June 2007 (UTC)


 * Hi, SNORD70 is now the official Human Gene Nomenclature Committees name for the RNA. So actually I think that should be the main name. I've now changed that entry round and added a link to the non-coding RNA page. Also added links to relevant databases in the field: SnoRNABase and the HGNC database.


 * Thanks for the suggestions they are indeed good ones. I have added them to Wikiproject RNA/proposals. We really appreciate your help with the WikiProject RNA! Alexbateman 11:28, 16 June 2007 (UTC)

MicroRNA
Thanks for your kind words. Replacing the many links with one certainly makes sense - and if you look closely at the history it was in fact Willow who added the links, not I. I'll be watching your project with interest. Good luck. CheekyMonkey 13:10, 18 June 2007 (UTC)

Making a page for tmRNA
I would like to get started on a page for tmRNA. So far I have removed a redirect on the page TmRNA, but that capitalisation is incorrect. Whenever I try to edit a page called tmRNA I get forwarded to TmRNA. Any ideas? Thanks Alexbateman 13:32, 22 June 2007 (UTC)
 * Wikipedia doesn't distinguish between the case of the first letter of a page name, to help with linking at the start of a sentence. By default, it guesses that a page should start with an uppercase letter. If the correct case of the first letter should be 'always lowercase', place lowercase at the top of the page, and the first character of the name will be made lowercase in the page's title and URL. --ais523 13:41, 22 June 2007 (UTC)

Zasha says...
Hi Alex, thanks for the note. Jeff Barrick mentioned the RNA project. I'm not sure I have that much time for it (my Wikipedia activity has dropped precipitously over the last year or so), but I'll help out here & there. I might finally get around to several edits on the riboswitch page, now that preQ1 is published, and someone conveniently deleted the T-box mention. Zashaw 22:36, 14 July 2007 (UTC)

Academic MCB affiliates
Hi there, I wondered if you wanted your lab homepage to take the first slot in the "Affiliated academic groups" section on the new list of resources and projects at WikiProject Molecular and Cellular Biology/Related projects and resources. I'm trying to improve the Wikiproject's prominence a little. All the best Tim Vickers 19:49, 16 August 2007 (UTC)

Pfam and UniProt
Hi Alex,

I think about a semi-atomatic creation of WP articles using Pfam and UniProt content. How do you think, would that be consistent with their copyright policies? If I understand correctly, this is O'K with Pfam, but UniProt non-derivs policy would require their explicit permission? I am not quite sure how to better approach this. Could you give a piece of advice, please? Thank you. Biophys (talk) 03:00, 24 November 2007 (UTC)

Hi User:Biophys,

I'm not sure about Swiss-Prot but with Pfam it is possible. We are currently running a pilot project using Rfam. We have created 600 WP articles and are seeing how that goes. That has been a lot of work to get them into a suitable shape, so I'd be worried about dumping 10,000 new articles based on Pfam entries into WP currently. But its certainly something that we along with InterPro have thought about.

Cheers Alexbateman (talk) 11:30, 3 January 2008 (UTC)

Tegiap replies
Hi, & thanks for the comments. —— I have only just noticed their existence after having just done some extensive editing in a different direction (adding to refs). I'll now turn to your suggestions, but it might take a day or two for me to take adequate action. — (I do need some sleep!)

(1) Title too long etc. Yes I did have that feeling. It is also divided in what it is trying to say! I'll see what I can do, and that might entail an accompanying reorganization.

(2) Brannan...(1990) being first. (I think I got that from Mattick -- perhaps the Sci.Am. article). It is partly an argument over definition. I would have thought that mRNA and tRNA were automatically excluded from being classed as ncRNA. That makes the claim more reasonable, tho it may still be wrong. -- In any case it is very peripheral to what I was trying to say, so it should not be too difficult to rephrase the wording here.

(3) The near-empty "regulators" subsection. True, but (i) I certainly didn't want to re-invent the wheel which follows later, (and in any case that is outside my field) -- yet meanwhile (ii) I did want to contrast the memory/action-use to it, so I needed some way to introduce it. This seemed a tolerable compromise, perhaps leaving scope for others to elaborate if they saw fit. --- OK. I'll have another look at it.

(4) memory-encoding "speculative"? That is actually a very large epistemological question!!! --- I would agree that it is still somewhat hypothetical (and perhaps some of the "regulation" roles are also), but that is a step or two up from being just "speculative". I'll look at it again, but this one might call for more dialogue if you feel it is a major issue.

Kind regards, Tegiap (talk) 16:54, 28 April 2008 (UTC)

Unspecified source/license for Image:Sxy structure.JPG
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Nick Robinson (origami)
Hello Alexbateman. I've replaced the content of the article with the version taken from your userspace, hope you don't mind. See the result of the AfD discussion, your clean up was appreciated. Let me know if you have any concerns. Thanks. Have a good day. --Vejvančický (talk | contribs) 21:11, 26 May 2010 (UTC)

OK thanks Alexbateman (talk) 08:08, 3 June 2010 (UTC)

MEROPS
A MEROPS article already existed at "MEROPS database". I've moved it, and redirected the incoming links, but not changed any content. Rockpock e  t  14:30, 4 June 2010 (UTC)


 * Aha, thanks. THat explains a lot! Alexbateman (talk) 14:34, 4 June 2010 (UTC)

Kelch Motif page introduction
I've removed the nag tag. Cheers --Chuunen Baka (talk  • contribs) 16:57, 22 June 2010 (UTC)

PROSITE vs Prosite
I talked to Boghog2 and the lowercase is now an alternative. Abergabe (talk) 13:33, 24 June 2010 (UTC)
 * That is great. I did look at the template code but got scared.  Actually the edit User:Boghog2 made was the same as I was thinking about :) Alexbateman (talk) 13:45, 24 June 2010 (UTC)

Michael Stratton (scientist)
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Might be of interest to you
Came across this interaction between 2 editors, one being a scientist at University of Nottingham who appears to be having trouble getting to grips with wikipedia rules, I read on your page that you were trying to encourge fellow scientists to use wikipedia and I feel a little biting is going on, so maybe you could drop them a note to help out, if this is of no use to you just disregard best Mo ainm  ~Talk  21:52, 20 July 2010 (UTC)

Alexm1313
Just a note, as I noticed the, on User talk:Alexm1313.  Chzz  ► 19:55, 21 July 2010 (UTC)

Barnstar
Thanks :) Alexbateman (talk) 09:07, 23 July 2010 (UTC)

DUF1220
That's a great idea, I can add some section headings. I also have an image I'd like to upload but because it was published in Science, I can't just upload it to the Commons area. Science Magazine permission for authors states that Jim Sikela (my PI) has permission to reproduce the image since it was his paper, but not permission to let others reproduce it, so I think I have to upload it in a different way. If I understand correctly, it looks like my account needs to be "confirmed" in order to do that. I'm not really sure what that means, but I guess it requires an administrator's approval, so I sent an email asking the "Permissions" department how to do this. Do you happen to know anything about the process of uploading copyrighted material, by any chance? Does it sound like I'm going about this the right way?

Thanks very much for saying hello!

Jonathon Keeney (talk) 21:25, 5 August 2010 (UTC)
 * Hi Jonathon Keeney. Yes an image will certainly brighten up the page. If you can get hold of the raw drawing file and refactor it by simplifying it then you could upload it to the commons. I think that once you have made a certain numer of edits (say 10) then you can upload images. But don't quote me on that :)  I'll keep my eye on the page and help out where I can. Alexbateman (talk) 08:07, 6 August 2010 (UTC)


 * Hi Alexbateman,
 * Thanks for the advice! I've broken it up by section heading (per Abergabe's advice) and I'm trying to add the image now.  I wasn't really sure how to "refactor" the image, but I was able to get permission from Science, as long as I include the appropriate reference, which they sent me.  So now I just have to upload it!
 * By the way, I wonder if I could ask you about the DUF1220 entry in PFAM. We sent in a critique quite awhile ago regarding the syntax "NBPF domain/repeat," but haven't heard back yet.  Can I send it directly to you?  We never really mentioned exactly what we had in mind in place of what's up there, but I'd be happy to send you that as well.  |  Jonathon Keeney (talk) 06:17, 1 October 2010 (UTC)

Adding link to British Pathe video on RNAS Pulham - advertising issue
I would really like to add a link to one or more of the films held at British Pathe in the RNAS Pulham article. They show some remarkable footage of the station in its heyday. My reservation is that the Pathe website link plays an advert before one views the film. The content is outside of Wikipedia and it could be construed that this is an advertising link:


 * A film from British Pathe showing the R33 taking off from RNAS Pulham

Is there a good way to deal with this issue so that the link could be included in Wikipedia? Could one include a warning of advertising? I'd really appreciate some advice. Thanks. Alexbateman (talk) 09:57, 13 August 2010 (UTC)
 * I think the best way to display any external link would be in it's own section, separate from the main article. Chevy  monte  carlo  10:09, 13 August 2010 (UTC)
 * Many sites around the Internet have advertising, actually it's pretty much all of them. So, I don't think an advertising 'warning' or notice is needed. Chevy  monte  carlo  10:12, 13 August 2010 (UTC)
 * Hi. Yes I agree this would go in a seperate section of external links. My concern is that this advertising is quite invasive, because you have to watch it before you can see the video of the air station. Did you take a look at the video? Alexbateman (talk)

Problems with upload of File:ExamplePDZproteins.jpg
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 * Sigh. For some reason all the authorship and licensing blurb seemed to get lost in the upload. Now fixed. Alexbateman (talk) 15:47, 16 August 2010 (UTC)

DHHC domain
Hi. I've nominated DHHC domain, an article you worked on, for consideration to appear on the Main Page as part of Did you know. You can see the hook for the article here, where you can improve it if you see fit. Rockpock e  t  17:27, 25 August 2010 (UTC)

COSMIC
Hi. I've nominated COSMIC cancer database, an article you worked on, for consideration to appear on the Main Page as part of Did you know. You can see the hook for the article here, where you can improve it if you see fit. Rockpock e  t  17:40, 1 September 2010 (UTC)
 * FYI, the COSMIC DYK will be on the front page on 10th September between 1 and 7pm. Well done. Rockpock  e  t  12:24, 9 September 2010 (UTC)

DYK for DHHC domain
The DYK project (nominate) 06:04, 2 September 2010 (UTC)

New pfambox
Heya, i've added a box on Glutathione S-transferase, Abergabe (talk) 11:18, 13 October 2010 (UTC)

Hello
G'day Alex, I like you shirt. Rockpock e  t  16:14, 9 November 2010 (UTC)
 * You're doing really well!--Paul (talk) 16:16, 9 November 2010 (UTC)
 * I agree. Rockpock  e  t  16:19, 9 November 2010 (UTC)
 * Thanks User:Rockpocket and Paul for all your help with the Wikipedia training for students! Alexbateman (talk) 11:42, 10 November 2010 (UTC)

Thanks
Thanks for the welcome--Hipsc (talk) 12:48, 16 November 2010 (UTC)
 * Best of luck with your editing. Leave me a message if you have any questions. Alexbateman (talk) 12:50, 16 November 2010 (UTC)

Christmas Card


Merry Christmas At this festive time, I would like to say a very special thank you to my fellow editors, and take the time to wish you and your loved ones a very Merry Christmas, and a Happy New Year. And, in case you can't wait until the big day, I've left you each three special presents, click to unwrap :) Acather96 (talk) 10:10, 24 December 2010 (UTC)





File copyright problem with File:Journal.pbio.1000276.g005.png
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Methods to investigate protein–protein interactions
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thanks very much!
hope to be able to contribute here. --Gdreyes (talk) 12:34, 8 March 2011 (UTC)
 * Let me know if you have any questions. Alexbateman (talk) 12:35, 8 March 2011 (UTC)

Test
Just showing off how talk page messages work. —Tom Morris (talk) 10:56, 28 March 2011 (UTC)
 * Thank for the message.Alexbateman (talk) 10:57, 28 March 2011 (UTC)

Thanks Alex for your latest the message. I will add the Computational Biology WikiProject. 193.62.202.242 (talk) 09:33, 9 June 2011 (UTC)

Thanks for your help! Let me know if you need any help with this. Alexbateman (talk) 09:57, 9 June 2011 (UTC)

Question
Hello, Alex. I kind of get lost here. Do you have any suggestions what should be done with List of glycoside hydrolase families? Should it be split to many separate articles? Best regards, Hodja Nasreddin (talk) 02:30, 12 June 2011 (UTC)
 * Hi Hodja Nasreddin! That is a good question. I think the list article is a useful one to have so I think we should keep it. However we have been thinking about having indiviidual articles for each family as well.  For example Glycosyl hydrolase family 1 has its own linked article in the list linked here. If you are interested in creating some of these articles we have attempted to automatically generate articles for all Pfam families based on InterPro. You can find these in the list of families beginning with G here. Feel free to edit and copy any of them across to WikiPedia space. Alexbateman (talk) 08:11, 13 June 2011 (UTC)
 * Thank you! This is great. Some time ago I generated a wikified file with Pfam families and sent it later to Boghog, but what he does is better. Yes, I would be happy to participate in this as time allows. Biophys (talk) 14:08, 13 June 2011 (UTC)
 * Thanks Biophys! Let me know if you do move any to WikiPedia space. We can then import them into Pfam and you will see them in Pfam like this http://pfam.sanger.ac.uk/family/Glyco_hydro_1 Alexbateman (talk) 14:13, 13 June 2011 (UTC)
 * Yes, I saw this some time ago and like it a lot. It's interesting how different resources can interact and supplement each other. Right now I am busy with finishing my NSF-funded project, writing a new proposal and publishing, but there is always some time to contribute here as well. Thanks, Biophys (talk) 16:13, 13 June 2011 (UTC)
 * Here are several pages I recently edited that need to be properly linked from Pfam.Biophys (talk) 14:24, 14 June 2011 (UTC)
 * Great work! We currently have 932 Pfam families with articles, so this will help us get to 1,000! We'll add the links.  The pages should appear in Pfam in the next couple of days. Thanks again. Alexbateman (talk) 15:40, 14 June 2011 (UTC)

Scope of Wikiproject Computational Biology
The page says:

"Simulation, modelling and analysis of biological systems (as in systems biology) of any scale (molecular structure, gene regulation, metabolism, protein interactions, cell physiology, cell populations, tissue organisation, organ modelling)"

Does-that include computational neurosciences? (I assume it is included in cell physiology, cell populations etc.)Nicolas Le Novere (talk) 21:06, 15 June 2011 (UTC)

Importance of biographies in WikiProject Computational Biology
Hi User:Alexbateman,

You are right. I had a look at the projects evolutionary biology and neurosciences. It seems that very few biography are Top (except Darwin of course). Many are High though. I will reevaluated mine. Still learning :-) Nicolas Le Novere (talk) 11:16, 17 June 2011 (UTC)
 * OK thanks. Yes I still have been revisiting some of my assessments and changing things around as I learn more. Next thing is to try and improve the rather lame Sequence analysis article :) Alexbateman (talk) 11:48, 17 June 2011 (UTC)

Best practice and the use of cite doi/pmid templates
Hi Alex, it's not obvious which way is better for citations (I can't figure it out), please feel free to revert any changes to the UniProt article if you don't like them... Duncan.Hull (talk) 20:33, 28 June 2011 (UTC)

PLoS Comp Biol
Hi Alex, I'm pretty sure you'll know about this but you might want to comment here (first thread here)  Jebus989 ✰ 08:23, 8 September 2011 (UTC)

Interactome
Hi Alex, yeah, I made a few edits on Interactome but there is much left to be done. Will see what I can do! Peter — Preceding unsigned comment added by Peteruetz (talk • contribs) 14:57, 9 January 2012 (UTC)

Protein families
Just letting you know that I resumed contributing in this area. My very best wishes (talk) 18:52, 3 March 2012 (UTC)
 * FYI. My very best wishes (talk) 19:00, 3 March 2012 (UTC)

Speedy deletion nomination of File:HglK dotplot.jpg


A tag has been placed on File:HglK dotplot.jpg requesting that it be speedily deleted from Wikipedia. This has been done under section F2 of the criteria for speedy deletion, because it is an image page for a missing or corrupt image or an empty image description page for a Commons-hosted image.

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 * Yes please delete, correct image is here File:HglK dotplot.png Alexbateman (talk) 10:12, 4 April 2012 (UTC)

Alex, I am sorry to have deleted your entries on the 7SK RNA page. I do not have much experience with editing the pages! The 7SK RNA page was not very informative, so I put together some published information. The structure that you show is OK, but not expecially informative. The structure of 7SK has been examaned experimentally by several labs including my own and the figure does not take that experimentally derived information into account as far as I can tell. I am not against keeping the image there, but the resolution is not great enough to see the bases clearly and I can't find the 5' or 3' ends. Can you provide a better quality image? There is general agreement that a region of 7SK sust upstream of the final stem and loop pairs with the 5' end of the RNA. David David H. Price (talk) 17:15, 13 April 2012 (UTC)

Disambiguation link notification for April 15
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Proposal to restore position of title in Infobox protein family template.
A request for comment has been made at the above link. Your input is welcome. Boghog (talk) 19:13, 19 July 2012 (UTC)

Disambiguation link notification for September 10
Hi. Thank you for your recent edits. Wikipedia appreciates your help. We noticed though that when you edited Chris Sander (Scientist), you added a link pointing to the disambiguation page FSSP (check to confirm | fix with Dab solver). Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ* Join us at the DPL WikiProject.

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 * Now fixed. Alexbateman (talk) 13:59, 10 September 2012 (UTC)

Invitation for a Wikimedia UK training event 27-28 October
Hope you are well. Because of your great involvement with Wikipedia training so far and outreach I believe it would be worth sending you a direct invitation to the next training session that Wikimedia UK is organising for our volunteers. Please have a look here. As a thank you we would of course pay all the expenses and organise your accommodation. It's a very highly valued training and a great opportunity to develop your skills! Let me know if you are able to attend - would be great to see you there. Daria Cybulska (WMUK) (talk) 13:07, 15 October 2012 (UTC) (daria.cybulska@undefinedwikimedia.org.uk)

Im making changes to Kinetic Logic
Im currently making changes to the kinetic logic article. Im about to finish with my work. Thanks — Preceding unsigned comment added by Mahumriaz (talk • contribs) 13:50, 10 January 2013 (UTC)

SH3D21
Hello, I am an undergraduate student at the University of Minnesota, Twin Cities, USA. As part of a class on bioinformatics, I was required to study a human gene of unknown function throughout the semester and then draft a Wikipedia article as a portion of my final project. The gene I chose was SH3D21. The page is currently undergoing review for submission. Once this process is complete, if it accepted, I would love for you to provide feedback, if you ever have time.

On an unrelated note, I saw you edited the Wikipedia page on SH3 domains. I've been musing over the presence of the repeated, and relatively well conserved, presence of "Asp-Glu-Leu" in the SH3 domains of human SH3D21. Only one of the domains was found to have the pro-x-x-pro motif. Do you think this is of any relevance? I know "KDEL" is a commonly occurring sequence for protein sorting, but all the data seems to indicate my protein stays in the nucleus.

Thank you, Jkgiesler (talk) 20:21, 9 May 2013 (UTC)
 * Hi Jkgiesler, Its good to see you creating a new article. I'll take some time to look at it soon. One quick point for you to note, though is that the PXXP motif is found in the proteins that SH3 domains bind to and not in the SH3 domain itself.  So you'll want to change that.  When I get more time I'll read through more carefully. Alexbateman (talk) 12:07, 16 May 2013 (UTC)
 * Fixed! I look forward to your future feedback, it will help me a lot. What started as a project has since turned into legitimate curiosity. Thank you Alexbateman. Jkgiesler (talk) 13:09, 16 May 2013 (UTC)
 * Hi Jkgiesler, I've now had a chance to read through the article and it provides a nice summary for the gene and seems to cover what is known about it. But in many ways you have carried out a bit of primary research about the gene as well. Generally Wikipedia is not about including original research, but about verifiable sourced material. To get more information on the Wikipedia guidelines see this page No_original_research. As an example in the protein section you mention the DEL motif found in the three proteins. While this is demonstrably true from the sequence alignment you produced, this is considered original research unless you can cite a paper that describes this fact.  The reader should not have to go through carrying out something like BLAST searches and alignments to verify that this is factually correct.  Now what does that mean for the article?  I think it would be best for you to carefully go through the article and test for the statements you have made whether or not a reader can verify them or not from a primary or secondary source.  Please don't be down heartened by this!  Editing Wikipedia is all about learning the funny rules and regulations, which sometimes seem odd at first, but as you learn more about it you begin to see why they are so useful.  I think the article you have written demonstrates a real flair for writing and carrying out research on proteins. So well done! Let me know if you need any more help or advice.


 * Best wishes Alexbateman (talk) 12:05, 17 May 2013 (UTC)

ISCB contest and assessment
Hi Alexbateman! Thanks for your welcome on my Talk page. I'm actually not participating in the ISCB contest; I am running a subject at the University of Melbourne where we are using the contest for assessment. Several students have signed up to the contest as part of an assignment. I claimed an article as a demonstration (and have since un-claimed it). If there's anywhere it would be good for me to leave a message with my username as the coordinator of this assignment, let me know. Sloc melb (talk) 03:20, 24 September 2013 (UTC)

R2 Element Apology
Dear Alex in 2008 you wrote this on my wall:

"Thanks for your edits on the R2 3'UTR page. I notice from Pubmed that it looks like you were a coauthor on the Kierzek et al. paper in NAR recently. Will you add a section about the 5' structure as well? It would be really cool to include figure 3 from that paper in the R2 element page.  I am pretty sure that the NAR license will allow you to reuse the figure. BTW let me know if you have any questions about wikipedia editing.  I'll be happy to try and help."

I've not done too much wikipedia editing in the last few years and, honestly, I only just saw your message recently. I wanted to apologize for not responding! Please don't think I was being rude or ignoring you. I've become active again, trying to create some new wikipages for RNAs that I've been working on. I'm more serious this time and have been using my "Talk" page. When I saw your note I was so embarrassed! Thank you for your suggestion on the R2 page. I currently have a figure of the R2 5' pseudoknot, Do you still think that Fig. 3 from the NAR paper would be helpful? Sorry and thank you again!

Walternmoss (talk) 23:03, 10 October 2013 (UTC)

categories for species pages
Thank you for your kind comments concerning category listings on pages devoted to plant species.

State categories exist for a reason, i.e., to help people find information on plants reported from the various states. You appear to be suggesting that we should, for example, not list a plant known from Arkansas on the "Flora of Arkansas" list because the species is also found in Kansas or Oklahoma. Leaving the plant off the Arkansas list does not help anyone. Thus a widespread species ends up on the listings of many states. This is just the way they have this set up. — Preceding unsigned comment added by Joseph Laferriere (talk • contribs) 18:11, 6 January 2014 (UTC)

MEROPS numbers in Protease infobox template
Hi, I initially was expanding the page for TEV protease when I noticed that there was no MEROPS number in the protein infobox template. I've raised it on the MCB wikiproject talk page if you have any input on the discussion.T. Shafee (Evo&#38;Evo) (talk) 09:29, 14 January 2014 (UTC)

PA clan request
Hi,

Thank you for the barnstar. I wanted to ask for some extra aid in the PA clan article actually. When I initially put it together, I set it as B class but would really like to improve it. There are no other protein articles on protein superfamilies that are above stub or start class so there's no real template to work to. I've had some peer review feedback but I'd really like to get it up to A class or better as a model for other superfamily pages. Do you have any suggestions or ideas for what to add and expand?

Thanks, T. Shafee (Evo&#38;Evo) (talk) 07:12, 16 January 2014 (UTC)
 * Hi T. Shafee (Evo&#38;Evo), I would suggest that it would be realistic to go for Good Article status. One protein family article that went all the way to Featured Article was Major urinary proteins, so that might be a good template to work from. I can also ask Neil Rawlings if he can read through and leave you a review of the article. Alexbateman (talk) 09:24, 16 January 2014 (UTC)

Team competition entry
Hi Alex, I can confirm that the competition entry for Point Accepted Mutation was done in partnership with Xelotath19. Best regards, Japefruit (talk) 06:32, 22 January 2014 (UTC)

Contacted you through email
Hello Alex, I just wrote you an email where I identified myself and sent you my student status. Let me know if it reached you already.

Thanks once again. Biohisham (talk) 23:10, 22 January 2014 (UTC)

Notification of automated file description generation
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Wikiproject competition
Dear Alex, I left a message in the wikiproject competition 2013 talk page on 1st April, but I have not received any answer until now. Do you know if a similar competition is being planned for this year? Also, are the winners of 2013 competition already known? If not, when will it be announced? Thank you for you attention. Hope to hear from you soon! JulianaCF (talk) 10:34, 21 May 2014 (UTC)

Changes to WP:COMPBIO landing page
Hi Alex, I've made some changes to the WikiProject landing page. Part of the new page lists the off-wiki collaborations including the ISCB article competition, for which I've named you as a contact — if you object to this please remove it. Similarly feel free to improve the competition text or any other part! Thanks, benmoore 12:47, 21 July 2014 (UTC)

ISCB competition
Hi Alex,

I think the ISCB competition is fantastic and students/trainees have already made some nice additions to several of the articles. However one common problem that I see in several of the additions is that they tend to include instructions for how to use a computational biology program and this conflicts with WP:NOTHOWTO. Also there is a tendency to add material that reads like a text book. While the competition announcement states that "all content ... must adhere to the basic policies and guidelines", I think it would be helpful if the announcement included a caution about these types of common mistakes with a link to Wikipedia is not a manual, guidebook, textbook, or scientific journal. Including this caution hopefully would make the process less frustrating for both the students and fellow Wikipedia editors. Cheers. Boghog (talk) 14:45, 12 September 2014 (UTC)
 * Hi, Thanks for the suggestion. Do you have a specific example of an article I can point to for this? I hadn't really noticed this being an issue before. Alexbateman (talk) 15:02, 12 September 2014 (UTC)
 * Perhaps this is a special case, but one especially problematic example is pharmacogenomics. Boghog (talk) 16:02, 12 September 2014 (UTC)

ISCB competition 2014
Hi Alex. I was wondering if the winners for the ISCB article writing competition 2014 have been declared. Also, if there is any further prospect of having a 2015 edition of the competition. I really loved the idea of this competition and would be really excited to know if it continuing further or not. Thanks. Vivek Rai (talk) 11:30, 29 July 2015 (UTC)
 * Hi Vivek. You can find the results of the 2014 competition here: https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Computational_Biology/ISCB_competition_announcement_2014.
 * We plan to run the competition again this year and would be great if you can participate in some way. Alexbateman (talk) 12:43, 29 July 2015 (UTC)
 * I'd love to. Thank you! Vivek Rai (talk) 03:56, 1 August 2015 (UTC)

Catalytic Triad
Hello again, I'm here to ask if you'd be able to cast your eye over the catalytic triad page. It's been a pet project of mine over the last two years (since it used to be dreadful). I've put it through a Good Article review, but I'm contacting you, Craig Townsend, and Alexander Wlodawer to make sure I've not made any mistakes. Eventually, it'd be great to get it up to Featured Article status T.Shafee(Evo&#65120;Evo)talk 12:10, 21 August 2015 (UTC)

ArbCom elections are now open!
MediaWiki message delivery (talk) 16:37, 23 November 2015 (UTC)

Disambiguation link notification for December 4
Hi. Thank you for your recent edits. Wikipedia appreciates your help. We noticed though that when you edited PhylomeDB, you added a link pointing to the disambiguation page TAIR. Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ* Join us at the DPL WikiProject.

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International Molecular Exchange Consortium
I have paraphrased part of your addition to the above article, as it appears to have been copied directly from http://dip.mbi.ucla.edu/dip/page?id=about, a copyright web page. All content you add to Wikipedia must be written in your own words. — Diannaa (talk) 20:23, 15 April 2016 (UTC)

ISMB Editathon
I'd be very happy to help with any newbies! -Kieran (talk) 18:22, 9 July 2016 (UTC)

Facto Post – Issue 1 – 14 June 2017
MediaWiki message delivery (talk) 09:33, 14 June 2017 (UTC)

Welcome to the ISMB/ECCB editathon!
Hi Alexbateman,

Welcome to the ISMB/ECCB Editathon! We hope you find this a useful session, let myself or know if you have any questions. Thank you again for your improvements to computational biology coverage on Wikipedia, and if you're not already a member of WikiProject Computational Biology we encourage you to sign up! Amkilpatrick (talk) 12:23, 23 July 2017 (UTC)

Facto Post – Issue 3 – 11 August 2017
{| style="position: relative; margin-left: 2em; margin-right: 2em; padding: 0.5em 1em; background-color:	#7FFFD4; border: 2px solid #00FFFF; border-color: rgba( 109, 193, 240, 0.75 ); border-radius: 8px; box-shadow: 8px 8px 12px rgba( 0, 0, 0, 0.7 );"
 * Facto Post – Issue 3 – 11 August 2017

 

Wikimania report
Interviewed by Facto Post at the hackathon, Lydia Pintscher of Wikidata said that the most significant recent development is that Wikidata now accounts for one third of Wikimedia edits. And the essential growth of human editing. Impressive development work on Internet-in-a-Box featured in the WikiMedFoundation annual conference on Thursday. Hardware is Raspberry Pi, running Linux and the Kiwix browser. It can operate as a wifi hotspot and support a local intranet in parts of the world lacking phone signal. The medical use case is for those delivering care, who have smartphones but have to function in clinics in just such areas with few reference resources. Wikipedia medical content can be served to their phones, and power supplied by standard lithium battery packages.

Yesterday Katherine Maher unveiled the draft Wikimedia 2030 strategy, featuring a picturesque metaphor, "roads, bridges and villages". Here "bridges" could do with illustration. Perhaps it stands for engineering round or over the obstacles to progress down the obvious highways. Internet-in-a-Box would then do fine as an example.

"Bridging the gap" explains a take on that same metaphor, with its human component. If you are at Wikimania, come talk to WikiFactMine at its stall in the Community Village, just by the 3D-printed display for Bassel Khartabil; come hear talk at 3 pm today in Drummond West, Level 3.

Link

 * Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.

Editor. Please leave feedback for him. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Opted-out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 10:55, 12 August 2017 (UTC)
 * }

Facto Post – Issue 4 – 18 September 2017
{| style="position: relative; margin-left: 2em; margin-right: 2em; padding: 0.5em 1em; background-color:	#7FFFD4; border: 2px solid #00FFFF; border-color: rgba( 109, 193, 240, 0.75 ); border-radius: 8px; box-shadow: 8px 8px 12px rgba( 0, 0, 0, 0.7 );"
 * Facto Post – Issue 4 – 18 September 2017

 

Editorial: Conservation data
The IUCN Red List update of 14 September led with a threat to North American ash trees. The International Union for Conservation of Nature produces authoritative species listings that are peer-reviewed. Examples used as metonyms for loss of species and biodiversity, and |theoretical discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters. Clearly, conservation work depends on decisions about what should be done, and where. While animals, particularly mammals, are photogenic, species numbers run into millions. Plant species lie at the base of typical land-based food chains, and vegetation is key to the habitats of most animals.

ContentMine dictionaries, for example as tabulated at d:Wikidata:WikiFactMine/Dictionary list, enable detailed control of queries about endangered species, in their taxonomic context. To target conservation measures properly, species listings running into the thousands are not what is needed: range maps showing current distribution are. Between the will to act, and effective steps taken, the services of data handling are required. There is now no reason at all why Wikidata should not take up the burden.

Links

 * What Makes a Good Collaborative Knowledge Graph: Group Composition and Quality in Wikidata (paywall)
 * Wikimedia and the free knowledge ecosystem by Maria Cruz
 * Another Year Again: 2017 this time (long), blog by Joe Wass of CrossRef
 * Attack of the 50 Foot Blockchain, blog by User:David Gerard
 * WikiTribune in beta

Editor. Please leave feedback for him. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Opted-out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 14:46, 18 September 2017 (UTC)
 * }