User talk:Jennifer Rfm

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Hello, Jennifer Rfm, and welcome to Wikipedia! Thank you for your contributions. I hope you like the place and decide to stay. Here are some pages that you might find helpful:

I hope you enjoy editing here and being a Wikipedian! Please sign your name on talk pages using four tildes (~~~~); this will automatically produce your name and the date. If you need help, check out Wikipedia:Questions, ask me on my talk page, or ask your question and then place {{helpme}} before the question on your talk page. Again, welcome!  TimVickers 15:28, 9 May 2007 (UTC)

Welcome to Wikipedia, Jennifer![edit]

Wikipedia is a bright place, especially at the MCB WikiProject.

Hi Jennifer,

Let me be the first to welcome you to our midst! :)

I hope you'll find that Wikipedia everything that you wish for. As you'll no doubt discover, it has its quirks and querky personalities, but it's also filled with well-meaning, well-educated editors who will go the extra mile or two — or twenty. I've found that patience, good humor and gentle strength will carry you far.

Please write if I can help. I've been here only a year, and I'm still awfully clueless, but I'll gladly try. I'm also fond of letters, although you'll have to forgive me straight away for being too talkative. ;)

Looking forward to your contributions to Wikipedia, Willow 12:39, 9 May 2007 (UTC)

Hi there[edit]

It is good to see the recent influx of bioinformaticians, you are most welcome. If you have any questions or think I can help in any way just send me an e-mail or put a note on my talk page. Again, welcome! TimVickers 15:28, 9 May 2007 (UTC)

Help Request[edit]


Hi there, how can I help? Andytalk 10:52, 10 May 2007 (UTC)

I am trying to convert the wikipedia xml into html for displaying on our web site. For various reasons running the mediawiki software/apache server is not straightforward to set up and not supported on our network setup (systems support dont want us to do this). I have been trying to use the Text::MediawikiFormat perl module which works reasonably well but misses a lot of fiddly xml markup. Does anyone know of anything more generic that doesn't require us to run the Apache server -- we did look for a .xslt style sheet in the mediawiki software but couldn't find one. Can you point me in the right direction? Jennifer 10:50, 10 May 2007 (UTC)
Just noticed your above notice which I have moved to here! Just need to clarify what you are asking, You have a wikipedia XML file that you want to use on your website?Andytalk 10:54, 10 May 2007 (UTC)
yes. we are interested in importing and displaying some of the wikipedia entries on our web site. This is to direct our user community to the wikipedia information available for our ncRNA families ( i work on the Rfam database ) and encourage/direct our user community to provide annotation within wikipedia which we will then re-import. Its not worth us donwloading the whole database or running the whole mediawiki software (systems support are not keen on us running Apache). hence we want to download a maximum of ~ 500 entries in xml format and simply strip out the information between the <text....</text> and diplay in on our web page. This information will be clearly labelled as wikipedia and will direct the user back to wikipedia so we have checked there is not a problem regarging copyright/GFDL etc. I simply need some code to correctly convert the xml such as this ( ) to html. does that make sense? Jennifer 11:09, 10 May 2007 (UTC)
Hi there, it looks like you are in capable hands here, but if you need any additional input (many eyes making light work) the main technical help page is at [this page]. Hope this helps. TimVickers 15:25, 10 May 2007 (UTC)

I just happened to learn of a tool that does this sort of thing today after seeing this request; it is here. I have never used it myself and am not a very technical person at all. User:Yann pointed it out to me on a seperate project and he may be the best person to ask for help (or at least be able to direct you to the best person). You may find it quicker to contact him at fr:Discussion Utilisateur:Yann--BirgitteSB 21:18, 10 May 2007 (UTC)

Useful worklist for Wikipedia Rfam articles?[edit]

Hi Jennifer,

I made a worklist for the Wikipedia articles, which vaguely reproduces the index page at Rfam. I thought it might be nice to work from, both to see which families already had a Wikipedia counterpart and to keep track of our progress.

Maybe the first thing to do is to decide on the best names for the Wikipedia pages? I was torn between taking the first and last columns as the Wikipedia name, but I'm sure that you and Alex can think up even better names. I'll upload both and you can see the difference by using the History tab. This is fun; I feel like I'm learning something already! :) Willow 16:28, 10 May 2007 (UTC)

PS. I made a few new categories corresponding to the Type column on the Rfam index page; are they OK?

we apologise for this confusion due to the Type list. Im afraid its not an absolute definition as many of the families have multiple functionalty so beyond the first Type value eg. Cis-reg/Non-coding/ribozyme/silencingRNA we dont think we should subcatagorise the families any more than that at this point Jennifer 12:41, 11 May 2007 (UTC)

PPS. What's in the Rfam.thr file? The last column probably refers to global vs. local alignments, but the others are a mystery to me. Should those numbers be included somehow in the Wikipedia pages? Willow 17:41, 10 May 2007 (UTC)

Hi Willow. this reply is long i hope you have time!.
the work list is great as it gives us a concrete way to keep track of things. two things to discuss : what rfam information we wanted to add and how we go about making new pages.
We have put some thought into how we can integrate Rfam information into wikipedia. Unfortunately we really dont think its relevant to simply auto-generate a family for all of our Rfams. Its important to us that we dont simpy dump Rfam verbatim into Wikipeida--as this would be a waste amd some of our family annotation isnt really stand alone information--instead we want to increase the information available for ncRNA and have the wikipedia compliment the more specific information we have (and abviously encourage users to add..)
I made a mapping of our Rfam families to the most relevant exisiting page in wikipedia and flagging up where we would really need a new page to be made. For example we have 4 families (RF00009, RF00010, RF00011, RF00373) relating to the RNAse_P wikipedia entry and we are happy with that. We dont feel the need at this point for 4 separate wikipedia entries. The links to the 4 Rfam families can be added under the External links in the footer and if at a later date users want to add more then this can be expand. However, we do think it is relevant to autogenerate families for some of the families where there is currently no information for. There will eventually be a lot of these but as I mentioned before we are somewhat tentive about autogenerating them all right now. I have a list of 10 we would like to try out (see below). For these we imagined we would add the image, the curated text, external links and database cross references but not any of the alignments, phylogentic information or the rfam specific information. We would hope the link back to Rfam would allow people to use the Rfam site. There is a lot of functionality in our site that isn't relevant to simply dump into wikipedia.
This answers the question regarding author and the Rfam.thr file. The author info comes under Rfam-specific information which we didnt think was relevant to add to wikipedia. Also the .thr file relates to the thresholds used for the covariance model searches and is only really relevant for using the Rfam flatfiles/INFERNAL for local download and sequence searching.
So I really liked the working list for us to keep track of things. Regarding the names. We essentially liked the use of the DE (description) line information i think as you have it in the second table under 'fullname'. Unfortunately there are a few that we wouldn't use as the wikipedia page name but im afraid its all on a individual basis. Would it be relevant for us to go in and manually correct the names in the working table? could we possibly use an extra column in the table so we can flag up entries that are made or need to be made?
I have a list of the small subset of 'new' entries we wanted to try out. Could you possibly auto_generate them so we can see? (we are excited about this!) I have added this list below but in reality I could do this on the working list? I have also identified several pages that currently exisit as anchors in the ncRNA pages and I was going to make them into main pages ( i finally make some contributions!). I can edit the link under the fullname in the working table to represent this? as you have for tmRNA etc or put this in a new column as mentioned above?
a quick wikipedia general question if you have time: Im curious how wikipeida keeps itself coherent. regarding links in existing pages. eg. Cobalamin_riboswitch we think is relevant to make as a new wikipeida entry for. There is an exisiting page relating to riboswitches with the text 'Cobalamin riboswitch'. I know I could go in and manually add the link from the exisiting page to the new page but If I had missed this, do these type of missed links get put in automatically somehow?
List of 10 new wikipedia entries we wanted to make from Rfam families
RF00030 RNase MRP
RF00013 6S / SsrS RNA
RF00027 let-7 microRNA precursor
RF00052 lin-4 microRNA precursor
RF00012 Small nucleolar RNA U3
RF00016 Small nucleolar RNA SNORD14
RF00019 Y RNA
RF00174 Cobalamin riboswitch
RF00173 Hairpin ribozyme
RF00513 Tryptophan operon leader
For other entries I was planning to expand exisiting entries to be more informative, eg make main pages for Signal_recognition_particle_RNA and tmRNA from the anchors that are in non-coding RNA pages. Does all this seem sensible to you as a way for us to start? We may well end up eventually generating pages for almost all of the Rfams but we wanted to canvas some opinions from the ncRNA user community before we set everything up and wanted to have a small 'example' set to encourage them.
i think i have bombmarded you for now. I realise you are away for a while so may not reply very soon. Thank you again for your valueable interest and help. Hope you are enjoying the graduation :) Jennifer 12:41, 11 May 2007 (UTC)

Hi Jennifer,

Thanks for your really nice note! I did have a great time at the graduation — my friend and her family are really fun. She's the first person in her family to ever graduate from college, so it's a big deal; you can imagine how proud her parents were! :) They seem to like me, too; I really felt like part of the family. Her dad is in construction and a really good carpenter; since I was interested, he took me under his wing and entertained me with all kinds of interesting things about different construction vehicles, and about how to design woodworking projects. You might be surprised how spellbinding it was; after talking with him, everything wooden seems to be breathing. :)

Daisy composed the Wikipedia files for the 574 Rfam families in about 0.5 seconds. I uploaded the ten you wanted under their "Description" names. Admittedly, Daisy got a little lazy about wiki-linking the main text and making the inline citations for the references, but she can fix the former glitch at least pretty easily. If you have a set of words that you'd think would be good to have wiki-linked, please send them to me, and I'll try to patch that up. Perhaps we might appeal to your colleagues and people at the Molecular and Cellular Biology WikiProject for advice on which terms would be good to wiki-link. I can upload the rest of Daisy's files, or a subset thereof, in the time it takes you to say "knife" — umm, roughly five hundred times. ;)

To tweak the name(s) of the Wikipedia pages however you'd like, please feel free to modify them manually in the worklist. You shouldn't have the least hesitation about it; it won't hurt anything and we can always switch it back. :)

Let's see; what other issues were there? I totally agree that we shouldn't replicate Rfam. We wouldn't even be allowed to do so, under the policy Wikipedia is not a database. I kept the SE (seed alignment) information in the Rfam infobox, but we can remove that if you'd like. Otherwise, I tried to avoid Rfam-specific information.

I'm not sure if I understand your "coherence" question? A phrase like "cobalamin riboswitch" can be wiki-linked by enclosing it in double brackets, e.g., "[[cobalamin riboswitch]]". If the link exists, it appears blue, otherwise it appears red. That's why Wikipedians sometimes exhort each other to "get the red out!" ;) But if the phrase is not enclosed in double brackets, it won't respond to the creation of a page with that name; the connections (the wiki-links) have to be made by hand. Typically, an editor wiki-links only the first occurrence of a phrase/concept in a paragraph. I'm a little over-enthusiastic about wiki-linking, but I try to hold to that standard; however, even that is sometimes considered too often by some Wikipedians.

Thanks for starting me on this, Jennifer; it's fun to collaborate with you and everyone else. :) Willow 21:29, 15 May 2007 (UTC)

Hi Willow, This is great and we are even more positive about getting this all going now we can see our first few stub pages. I've replied about some of this on the MCB proposal page and it essentially relates to us providing a structure to group/catagorise our pages. Should we Rfam just propose what we would like to see and see how MCB responds? But the more we see the more we do think we will generate stubs for all the relevant families and put some work into providing structure/context for the pages Jennifer 13:54, 16 May 2007 (UTC)

Does Alex smoke? Now would be a good time to start having pipe dreams... ;)

The MCB WikiProject is a very encouraging environment, and people are generally happy to work towards the recognized common good. You should feel free to make or suggest any changes that you think would be helpful. Editing is always much more fun when done together with a group of well-meaning and smart people, such as you all at Rfam. :) Sometimes producing an especially fine article feels like a symphony, with each editor playing a distinctive role, like the brass, woodwinds and strings; other times, it's more like a medieval antiphony between one or a few voices and a large chorus.

Could you all perhaps could suggest non-specialist "lead in" prose for each of the families? Our chief goal is to produce a good encyclopedia, which means that our chief loyalty is towards our readers, whom are usually assumed to be non-scientists. If there were standard boilerplate for each major family, I could pass that along to Daisy. ;)

We've opened up a list of terms to be wikilinked here, in case you had suggestions for those — thank you, Jennifer! :) Talk to you soon, Willow 19:02, 16 May 2007 (UTC)

Hi Willow. yep we agree this would be a good idea to provide a bit of context for the families. I think we would have slightly different version for the 'gene' and 'cis-reg' types. I will get something together for this.Jennifer 14:33, 18 May 2007 (UTC)

Rfam stub headers and sundry questions[edit]

Hi Willow. sorry its taken a while for me to get back to you. another long one from me..

below is text we thought would be relevant to the header for each stub. The two different 'headers' are relevant to the two main types of RNA : Gene and Cis Reg so the correct header text would need to be added to the correct stub type. Ive left a place holder for the name of the RNA the page title ($name). We also thought it might be useful if the Rfam 'Type' (TP line) information was also used in the stubs. The different catagories can then be linked and allow the reader to get background information. As you are much more experienced at this let us know if the suggested text below is not appropriate and we can have another go :) We also thought adding in the type line information and linking it will also go some way to address the list made by cheekymonkey on the proposals page?

headers text:

The $NAME RNA is the functional product of a gene that is not translated into a protein. Non protein coding RNA molecules usually contain important secondary structure or ligand binding motifs and are involved in many important biological processes in the cell. This stub was generated from a family annotation in the Rfam database.

The $NAME RNA is a region in a larger functional RNA molecule and has an important regulatory function. This is termed a cis-regulatory element. Cis-acting regulatory elements usually contain conserved secondary structures or ligand binding motifs. This stub was generated from a family annotation in the Rfam database.

and for the Type line use the following text:

In the Rfam database this RNA is catagorised as the following type of RNA: <type info in here>

e.g. In the Rfam database this RNA is catagorised as the following type of RNA: Cis-reg; IRES

The relevant links for the RNA types we have are below. There are a couple that there are not pages for yet but we will add them soon. Does this make sense to you?

  • [[Internal_Ribosome_Entry_Sites|IRES]]
  • [[gene|gene]]
  • [[Riboswitch]]
  • [[Antisense_RNA|antisense]]
  • [[MiRNA|miRNA]]
  • [[Ribosomal_RNA|rRNA]]
  • [[Ribozyme|ribozyme]]
  • [[SnRNA|sRNA]]
  • [[Guide_RNA|guide]]
  • [[snRNA]]
  • [[SnRNP|splicing]]
  • [[frameshifting|frameshift_element]]
  • [[tRNA|tRNA]]
  • [[Intron|Intron]]
  • [[Cis-regulatory_element|Cis-reg]]

we would be happy now to just go ahead and make all these stubs for all our families. Would you be happy to go a head and make them for all 574? We have wavered about taking longer about making a template but also sort of feel we should just go ahead and get them made and then see how things take off. btw I was going to go through the work list today and do a quick tidy on the page titles

a couple of questions: If we wanted to add something new/restructure the stubs at a later this possible? Would it also depend if the page had been edited at all? I don't understand how things work when a page/stub already exisits. I know some of the stubs in the test set you made have been edited a little already. Also is it possible/easy to change page titles at a later date or do we need to get it right first time?

Also a bit down the line but something we have talked about: for future releases when we have new/more families. Is there anyway we can deal with generating the new stubs ourselves. Can we use/adapt daisy or another bot? Or are you happy to run daisy for us?. Im concerend you will feel put apon having to do these things for us everytime we find something to improve/change. I guess we would like to feel we could deal with it if you are otherwise busy.

Im going away on saturday to the RNA meeting for a week followed by a bit of holiday so will be a bit silent for the next week or so. I will check up/reply to things but wont be active in doing much!. We have been busy here trying to get the things in place we need here to import the data into our database and get it displayed. After the RNA meeting and we have talked to some of the community we were going to get stuck into setting up the daughter project stuff Ive muted on the proposals page.

Hope this make sense and sorry if Im asking you too many questions Jennifer 11:13, 24 May 2007 (UTC)

Hi Jennifer, I'll be happy to make those stubs for you all. May I offer two suggestions?
  • How about we replace "Type" with "Rfam type" in the box? That would be briefer.
  • Some Wikipedians are pretty finicky about even the appearance of advertising, and Wikipedia is not supposed to be a database. So I'm worried that the sentence "This stub was generated from a family annotation in the Rfam database." would be a red flag for many bullish WPians. ;) So that sentence might not survive long in the main article. On the other hand, we should definitely give credit. I suggest that we put the sentence at the top of each Talk page of the article; stuff should not be deleted from article Talk pages (under the stipulations of the GFDL), so the credit lines would likely survive there.
Are these changes OK with you all?
To address your questions, deleting lots of articles is somewhat hard, but not too onerous especially if only one editor has modified it; there's a special speedy-delete template {{db-author}}. Re-naming pages could also be a little annoying, so we should get the names correct from the beginning. Blanking pages is easy, as is changing them or creating new ones. I'd be happy to make any new pages for you all; it took Daisy less than a second to generate all 574 pages, so adding a few dozen more is the work of a moment. :) As an aside, Daisy is not strictly speaking a bot, since I'm uploading the files personally; instead, she's like a faster and more single-minded version of myself, less prone to distractions. ;) I have a lot of sewing to do today, but I'll try to upload the files by sunset. Wish me luck! :) Willow 12:30, 24 May 2007 (UTC)
Hi Willow. These suggestions you made are absolutely fine. The Rfam database line wasn't meant to be adverstising (more owning up to the source) so yes please make the changes you suggested. Also regarding the problems deleting or changing pages maybe I should ensure the list has the correct names before you make them all. I will get back to you later today so maybe don't load them for the moment? Jennifer 12:45, 24 May 2007 (UTC)
OK Jennifer! I have lots to do today, anyway; please let me know once you're happy with the list of names, and I'll set to work then. As an aside, I'm leaving next week myself to go to another sister's graduation, this time with a Ph.D.! I'll probably stay away even longer this time, maybe for two weeks, so you might not hear from me until the middle of June sometime. That's why I'm trying to get everything done/arranged now. :) Willow 14:17, 24 May 2007 (UTC)

family names[edit]

Hi Willow. Ive edited the list of names in the worklist. I hope the format of the tables is on as I copied the table and did perl replaces on it then pasted it back in...I also wondered if it would set of some huge delete alarm!. didnt know how else to do such global big learning curve of wikiepdia etiquette......

We are curious to see what the reaction to all these pages will be. Some of our Rfam annotations are really not stand alone bits of text so we will see if people want to edit or bin them. Either way a HUGE thank you from all of us here for helping us with this. We all feel like we are learning all the time at the moment and everyone wants to just sit on wikipedia and edit.

Hope the sewing is a pleasant creative project and again, as ever, thank you willow Jennifer 09:39, 25 May 2007 (UTC)

Hi Jennifer, the sewing was fun, but only a little of it was for myself. I'm trying to dash off a new jacket in time for my sister's graduation. It's looking pretty nice so far, which is saying a lot for me; I'm usually more frustrated at this stage of a project. ;)
The Rfam pages were fun; thanks for giving me a brush with cutting-edge science! For my part, it was a pleasure to weave a little magic, and I've high hopes of learning a lot more about RNA, especially as everyone adds more commentary and wiki-links. In the end, I went with the longer name, because that's more customary here (e.g., protein nuclear magnetic resonance spectroscopy) but I'll make re-direct pages for the shorter names. You'll also want to proof-read the pages so far and make the proper wiki-links; I ran out of time yesterday and it was getting too complicated to really do well — sorry! :( Enjoy your vacation, Willow 10:16, 26 May 2007 (UTC)

Rfam glitch[edit]

Hi Jennifer,

Just a little note to let you know that there's a glitch in the Rfam database for RF00255. The reference should read "(MIPF:MIPF0000026)", not "(MIR:MIPF0000026)".

I'll have to leave shortly, unfortunately; I'm starting a new job tonight in a nearby town! :) My new boss is really nice and a wonderfully gifted seamstress with lots of experience in historical costuming; I hope to learn a lot apprenticing under her. I'm also leaving early tomorrow morning for another graduation, so I probably won't be able to write back until next week sometime. But please write if you have any special requests or ideas for the Rfam pages. Pip pip cheerio! ;) Willow 19:11, 10 May 2007 (UTC)

P.S. Oh yes, that reminds me; did you want to include the AU authors in the Wikipedia pages? It'd be nice to give them their due credit, but I'm not sure how to work it in.

thanks for pointing out the error. always appreciated. Jennifer 12:48, 11 May 2007 (UTC)

xml 2 html[edit]

Hello Jennifer,

No I didn't do any such thing. Its is Kelson who works on this. He would much more be able to help you than me. Regards, Yann 18:42, 11 May 2007 (UTC)

Rfam stubs[edit]

Hi Willow

I'm just back from RNA meeting and user community was very positive about the community annotation so I need to get things moving at my end! I was looking at some of the stubs and I noticed the header text we mentioned as a family intro and the TYPE information didn't go into the families. Was there a reason you decided to not to add it? I also noted on your talk pages that you are receiving queries about the page. I hadn't thought about it but suspect you will get a lot of such queries as you will be recorded as creator of the pages. Is this going to be a problem for you? Jennifer 14:39, 5 June 2007 (UTC)

Hi Jennifer,
I'm just getting back today from seeing another sister graduate, this time with a Ph.D! :) It was a lot of fun being together as a family, although we're all such different people. At the various receptions, I went around surreptitiously taking measurements of the ritzier regalia so that I can make a set for my sis so she won't have to buy the outfit. It was surprisingly easy to study the regalia at close range since professors love to talk shop and generally assume that someone scanning them with an eager stare is simply engrossed by their scintillating conversation. ;) In fairness, I did enjoy their conversation, and learned loads about topics ranging from archaeology to criminal justice to infectious diseases to environmental science.
Time was the only reason for not including the other information and for not making the automated wiki-links. I was leaving prontissime and I wanted to have all the articles up and running for you when you got to your RNA conference, so I simply ran out of time to teach Daisy a new song. I'm glad that the articles went over well, and hope that you had fun, too. :)
I'm not worried about getting too many queries about the articles. Wikipedians tend to be an intrepid lot, who figure things out on their own; and Wikipedia is so oceanic an enterprise that the creation of a mere six hundred pages on RNA families — which are cool but admittedly lower profile topics than Paris Hilton or even Vulpix — won't even be noticed. I only hope that the pages receive enough TLC to make them worthy in their own right; I'll try to do my part, albeit piecemeal. :)
Nice to have you back! and nice to be back myself, Willow 16:31, 11 June 2007 (UTC)
Hey welcome back Willow. Very nice to hear from you and also hear your tales from the the graduation. As for surreptitiously measuring up the regalia Im sure you will do a great job of sewing it and I am continually impressed by the range of skills/interests you have :-)
I did assume time was the reason for not having the header etc information in the stubs and we don't think its a problem. We really appreciate you having them generated in time for the RNA meeting. In general we think we could have spent a long time fiddling with stub format but we are happier that the stubs are made and we can just get on with directing our users at them. We will see how they evolve!. I also suspect there is going to be a bit of a lag time in getting the Rfam database front end set up to display the wiki text and to get the ncRNA sister project integrated into the MCB project but its my main priority at the moment so it should happen sooner rather than later. Saying that I will be sloping off on my summer holiday in two weeks time (yes proper a long holiday this time) so Id better get busy. speak to you soon Jennifer 08:54, 12 June 2007 (UTC)

Watch List[edit]


I would like to create a watch list for ~ 500 pages. Can anyone tell me how I can create this watch list from a list of page titles without having to manually enter them under my preferences? I guess I will want to run a script once a week to just flag up the pages that have changed? Jennifer 15:21, 11 June 2007 (UTC)

There's no functionality in the software for adding these directly to your watchlist. One method is to create a page in your userspace (like User:Jennifer Rfm) full of links, like this:
and use its "Related changes" list as a watchlist. If you want the pages added to your main watchlist, there's no feature in the software to do this, but I wrote a Firefox script to do that earlier this week (having a similar problem to deal with); see WikiProject User scripts' script repository). (Installing a script on your Wikipedia account can be complicated, so using a separate page is likely to be easier.) --ais523 15:24, 11 June 2007 (UTC)
thank you fro your help ais523 I will take a look at both Jennifer 15:35, 11 June 2007 (UTC)

Details of Wikipedia article creation[edit]

Hi Jennifer!

I left you some details on my Talk page about how I made those Rfam pages, which might be useful to your programmers. I'd forgotten that I used both the Rfam flatfile and the family file in making them! Once the article creation is working, I can help you all in uploading them; you just have to make the file names be the same as what you want them to be called on Wikipedia. Hopefully helpful, Willow 20:11, 22 August 2007 (UTC)


Hi Jen, just practising using this talk thing. User:Ppgardne Paul —Preceding unsigned comment added by (talk) 15:44, 12 November 2007 (UTC)

Small nucleolar RNA SNORD113[edit]


This is an automated message from CorenSearchBot. I have performed a web search with the contents of Small nucleolar RNA SNORD113, and it appears to include a substantial copy of For legal reasons, we cannot accept copyrighted text or images borrowed from other web sites or printed material; such additions will be deleted. You may use external websites as a source of information, but not as a source of sentences. See our copyright policy for further details.

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Cyclic di-GMP riboswitch edits[edit]

Hi Jennifer, your recent edits to cyclic di-GMP riboswitch included a box for the SAH switch, and a link to 23S methyl RNA. I assumed this was a mistake, but I've left it for you, since you have the correct data. Zashaw (talk) 19:38, 3 July 2009 (UTC)

aah sorry what a mess. Im fiddling with bot code for updating images and adding boxes. Testing with some hardcoded names and I seem to have got them all mixed up. Will go fix it now. Apologies and thanks for the note.Jennifer_Rfm (talk) 12:16, 6 July 2009 (UTC)

Mg Sensor edits[edit]

Hi Jennifer, I made some edits to the Mg sensor wiki page. The page clearly had confused the Mg-sensing riboswitch (M Box or ykoK element) and the putative magnesium-responsive RNA reported by Groisman's laboratory. I am not certain that my suggested changes would be posted to the Rfam page, so I thought I'd let you know about these edits. Additionally, if the ykoK riboswitch could be changed to include M Box, that would be great. Cedann (talk) 00:37, 27 September 2009 (UTC)

Hi Cedann, sorry to butt in here -- but your comments are probably more appropriate on the Magnesium Sensor discussion page. Do you mind if we take this up there?--Paul (talk) 19:04, 27 September 2009 (UTC)


Hi, I hope you are still around, I found a couple of images that you uploaded (e.g. File:RF00167.jpg) using your bot that would be a lot better if they were svg files rather than jpegs. I just wondered if you might have some files from which these could be converted en masse rather than doing each individually. Good work by the way on the RNA articles :) Smartse (talk) 22:37, 9 November 2009 (UTC)

Hi Smartse sorry for the slow reply -I havent been doing much in the way of editing of late. Im about to do another round of bot updates on the Rfam boxes and images so I will try and deal with this format issue at the same time-thanks :-) Jennifer_Rfm (talk) 10:49, 10 March 2010 (UTC)

Change of bot operator[edit]


I am currently the operator for the Rfambot which the Rfam database uses to contribute to and update pages on ncRNA. I am soon to be leaving the Rfam database and would like to hand over the operation of this bot to another Rfam person Ppgardne. Is it possible to do this? How do I go about it? Do I simply provide him with the source code so he can run it? Thanks for help in advance Jennifer_Rfm (talk) 11:11, 10 March 2010 (UTC)

Wow, you lucked out. I'm on the BAG. My opinion is: get Ppgardne to run a WP:BRfA. While I can't imagine any opposition to the bot or it's task, the third leg of BRfAs is to allow the community to approve operators; generally, they like to see an editor of good standing with an understanding of the editing the bot will be doing and the ability to fix things if they go wrong. Josh Parris 11:42, 10 March 2010 (UTC)
Thanks for the speedy reply - we will do the approval process for user Ppgardne. Jennifer_Rfm (talk) 11:52, 10 March 2010 (UTC)

Nomination for deletion of Template:MiRBase family[edit]

Ambox warning pn.svgTemplate:MiRBase family has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Thank you. — This, that, and the other (talk) 10:19, 14 January 2011 (UTC)