User talk:ElNando888

From Eterna Wiki

Latest comment: 24 November 2013 by Omei

'sup :)


== Redirects and the Advanced editor ==

Hi ElNando888,

First a quick thanks for fixing the canonical base pairs article, I ran out of time to check on whether AU pair or AU bond existed so I'd left it as AU pair. I notice that the advanced editor doesn't have the option to create a redirect, but I'm fairly familiar with them in wikipedia, so I was trying to work out a solution for people (such as myself) who tend to forget which colour each of the bases are using in Eterna, without thinking I know that red green is very strong, and that blue yellow is medium, with red blue being weak. I also remeber GC is strong, and GU is the one that tends to have player challenges, so it's obviously weak, and thus I can work out that red must be G, guanine.

But sometimes a bit of text is tricky enough (with only A level biology) to mean I get confused. so my plan was to create a series of redirects A redirecting to Yellow redirecting to Adenine and similarly GC pair redirecting to red-green pair redirecting to Guanine Cytosine bond the hope being that the mouseover text would be enough to remind players using the letter or colour system which one was meant, but also clicking either would lead to the correct page. 

I think the advanced editor has put a spanner in the works by automatically adding < p > and < / p> around the #REDIRECT target I'm not 100% sure it would have worked with the mousovers in the same manner as a piped link anyway, but as you seem to be a man of programming skills I thought I'd see if you had the solution.

Also I don't enjoy using the advanced editor having learnt the wikimarkup fairly well, and I've noticed that when you preview a page it kicks in enough to change what you wrote inserting lots of < p > - and it actually automatically killed off the words , < nowiki > and replaced them with p leaving the nonsense string ?UNIQ3d604ae31d52b6c5-nowiki-00000002-QINU? in the middle of the message, I've tried it again this time without preview in the hope it saves correctly. Incidentally I'm now watching this page, so you can reply here. Edward Lane (talk) 06:45, 7 June 2013 (UTC)Reply[reply]


Hi Edward,

And well, welcome to the EteRNA wiki. It actually feels good to actually encounter another soul in this rather desolate and deserted wiki. I could make a short historical account if you're interested some day, but to make it short, this server is a "restart" from a previous effort, and nothing much happened here until I plunged around mid-April.

A number of the current issues in this wiki stem from the early choices of the sysop (how do you prefer to call them? sysop? wiki-admin?), Diana. She thought that a WYSIWYG editor would be easier for newbies... And she chose this extension, which is actually documented as incomplete and breaking some of the natural wiki-formatting.

So, yes, just like me, you had to find a work-around for creating redirects... sigh...

And yes, nowiki doesn't work too well, bullet lists cannot be made normally (the wiki way), it must be done in HTML, etc... sigh again...

About your efforts around the color-coding in use at EteRNA, I was skeptical at first, but I can see the point better now. Still, as documented in the link I placed in the comments of the undo, this (double-redirects) is not supposed to happen in MediaWiki. So I think it would be better to try to think of another way... By the way, I left some comments about the blue and yellow colors being used for other purposes in EteRNA, what do you think? At first, I was about to ask you to modify those redirects, but now that I think a bit more about it, I wonder if we shouldn't petition for other colors when it comes to chemical mapping data. What about the purple+limegreen combo as a replacement for the blue+yellow?

Oh, and about colors, I'm not sure if you noticed, but I created a few templates for displaying sequences: A, U, G, and C. Maybe they can be useful to you too.

-- ElNando888 (talk) 07:19, 7 June 2013 (UTC)Reply[reply]


::I like the templates, and I don't have a preference sysop/Admin/whatever. The what you see is what you get approach is ok, and it seems wikipedia is about to trial such an interface in the hope of retaining/attracting a more diverse editorship. I'm totally happy for you to ammend any/every bit of content I've created on the wiki. It might be worth creating a generic talk page - that lets people work out conventions base pairs rather than base pairs for instance means any article titles being non plural gives you less red links (or at least no need for redirects from single to plural etc). No double redirects is fine -and generally a better idea than my approach. I'm not sure about any obvious blended colour scheme for a pairs - a template:GU pair that looked like GUpair might be cleaner.

Edward Lane (talk) 16:13, 11 June 2013 (UTC)Reply[reply]

== SHAPE entry ==


== Recaptcha ==

I don't know whether they are getting harder or my eyes are getting worse, but it's gotten to the point where I've had to go through trying  as many as four (not counting ones I skipped over) before getting an edit accepted.  Any chance I could be added as a candidate_admin (or a new group specifically for the visually challenged) to be exempted?

Omei (talk) 17:10, 3 November 2013 (UTC)Reply[reply]


Hi Omei, for this type of requests, I have unfortunately no control at all (which is good I think), it's all in Diana's hands.

-- ElNando888 (talk) 17:27, 3 November 2013 (UTC)Reply[reply]


Thank you for the warm welcome! My primary goal is to establish a clear issue intake & resolution system so that players understand how to track issues easily. The primary complaints I have seen are:

1) Issues forgotten or lost in the noise of multiple, flooded, and untracked reporting channels.

2) Outcome and redundancy of reported issues unclear.

=> Therefore, I updated the landing wiki page and added a Dev Chat page with a line-item summary of present UI issues as an example to template from for logging and addressing issues. The key feature being to include critical categories of info such as:

a) Location of issue ( name & link to page )

b) Summary of issue ( keywords )

c) Description of issue ( details are important in order for devs to replicate bugs and comprehend feature requests )

d) Solutions for issue ( even if the user cannot diagnose the correct solution per se, knowing a direction to head supplements understanding of the issue; and if it is an easy fix, the devs can find & fix that much faster )

e) Examples of issue ( supplementary to the description and solution, i.e. screenshots, links, mockups, quotes, forum discussions with more granular detail, etc... )

I am hopeful that a more robust tracking system will be implemented, whether the devs permit use of GitHub by players, they branch one out for us, or perhaps we set one up ourselves if they do not have bandwidth to address. Therefore, while the Dev Chat page currently functions as both dev chat agenda and tracking system, ultimately the Dev Chat page would be for presenting and archiving dev chat agenda, notes, and transcripts, however the granular issue tracking itself ought to be migrated to GitHub once approved / set up.

I am not attached to any of this, just trying to help, and I respect that you all have put in a lot of time into the community, therefore if I ever misunderstand or go about things ineffectively, please educate me as to how I can be more useful.

QUESTION: how do you get indents to stick? :D /n00b

Many thanks for all your help!

-- machinelves (talk) 16:30, 14 November 2013 (PST)


Hi machinelves, I'm not sure what today's vandalism on the Main Page was about, but possibly one spammer decided to escalate and test anonymous edits. This may be a reaction to the fact that I started filling up the server's blacklist, which prevents them from posting links to many of their usual 'customers'.

I try to kill fake accounts as soon as I see them, but I would tend to agree that open registration is not really necessary for this wiki. Unfortunately, we tried with Justin and Diana to look into how to link accounts with the main site, and it is not simple at all... Anonymous edits are also in the spirit of wiki in general, but for this specific one, it is questionable if we need to keep this policy...

I'm a sysop, but I'm not an admin on the server, which means I'm limited in what I can do here. In the official dev team, Diana is the one in charge, and you can contact her directly on the wiki, or by PM.

About what happened today: there's no strong reasons to panic, but you're right, we should be watchful, and thanks for your prompt and perfectly adequate reaction (revert), well done :)

-- ElNando888 (talk) 00:09, 17 November 2013 (UTC)Reply[reply]


Hi, guys.  Just wanted to say that I have occasionally made an edit "anonymously".  But it's never on purpose.  It wouldn't cause me any problem to disallow it.

Omei (talk) 01:10, 17 November 2013 (UTC)Reply[reply]


Omei, thanks for sounding in!

Nando, PM

-- machinelves (talk) 18:52, 16 November 2013 (PST)


== Chat Conversation on Disengaged ==

My browser crashed shortly before you went afk today.  Here's the wrap-up I copied from chat.

Omei: Between the new UI and browser crashes, I'm gnashing my teeth right now. [5:14 PM]
Omei: But look at [5:14 PM]
Brourd: Yes, very high error rates Omei :) [5:15 PM]
Omei: The column on the right that says 1.63 says that the best reactivity error for any base in the design was 1.63.  That's terrible. [5:15 PM]
Brourd: Right [5:16 PM]
Omei: My interpretation of that is that so few molecules got sequenced that I wouldn't want to read much into the data. [5:16 PM]
Omei: Rats!  I see that Nando has left! [5:17 PM]
Omei: I'll send him a PM. [5:17 PM]

Unfortunately, Brourd and I continued on to another topic -- designs with higher base error rates than normal, but not so high as 1.63.  If I  logged chat, I would have made a copy of that conversation, too.  But I don't. :-(

Omei (talk) 01:58, 21 November 2013 (UTC)Reply[reply]


Hey, I have 5:12 - 9:53, let me know the time range if you need me to pull from my chat log!

-- machinelves (talk) 00:15, 21 November 2013 (PST)


Yes, I completely agree that in such circumstances, there's very little one can trust, specially at the nucleotide level. You have to remember that for a long time, SHAPE reactivity and reactivity errors were not easily available, if at all, for players. And they would wonder what had happened in those failed designs, possibly thinking that the data had meaning at the nucleotide level. At least, we can classify them clearly as simply failed now, and try to look for explanations for what happened. Unfortunately, it's hard to even formulate a hypothese, in particular for this Disengaged design of mine. 

-- ElNando888 (talk) 08:39, 21 November 2013 (UTC)Reply[reply]


== Continuation of "Disengaged" chat: Tail Interference ==

Here's the continuation, about designs with higher base error rates than normal, but not so high as 1.63.  By base error rate, I mean the minimum (i.e. best) reactivity error reported for any base position in the design.

Omei: Rats! I see that Nando has left!  [5:17 PM]
Omei: I'll send him a PM.  [5:17 PM]
Brourd: What about Single to Switch attempt 2, by Malcolm?  [5:17 PM]
Brourd: oh, wait, number 3  [5:18 PM]
Omei: Looking.  If you find the (old) lab id before I do, let me know. [5:20 PM]
Brourd: 3396761 [5:21 PM]
Brourd: On the same lab [5:21 PM]
Brourd: As far as I know, malcolm did not purposefully employ any stop sequences, and there is a higher incident of 0's, along with higher error rate. [5:23 PM]
Omei: [5:23 PM]
Omei: So there base error rate is higher, but not so extreme. [5:24 PM]
Brourd: Although, no clue why the RNA population for the creation of the cDNA would be so low. [5:24 PM]
Omei: My first thought on this is that it could be what I am calling tail interference. [5:25 PM]
Omei: Long stems that are close together at their base have a tendency to align antiparallel. ... [5:26 PM]
Omei: And the single strand of the 3' trailer tens to align antiparallel to the barcode. ... [5:26 PM]
fluffy3: perpendicular? [5:26 PM]
Omei: Noo, not perpendicular.  parallel, but pointing away from each other, as oppose to lining up. [5:27 PM]
Omei: When both those conditions hold, the 3' sequence gets juxtaposed with the barcode, where it can form triplexes with the barcode. ... [5:28 PM]
Brourd: Omei, the first thing you should do with the code is make error rates for all residues visible, instead of those that just go over a specific measurement  [5:30 PM]
Brourd: In that particular sequence, without a high % of G-C pairs, would triplexes form? [5:30 PM]
Omei: If the the triplexes are strong enough, it they would interfere with the tail's ability to bind to the library primer that is necessary for reverse transciption.  Hence, fewer molecules end up getting measured, hence higher error rates for all the bases. [5:31 PM]
Omei: I don't know enough about triplex formation strengths to know what is favorable and what isn't.  But a GC triplexed with an A is very common. [5:32 PM]
Omei: No, a triplex describes the condition when a pair bond is joined by a third base, with all three bonded together.  It happens often in nature, but isn't part of the Eterna energy model. [5:33 PM]
Brourd: Do you have any projects where a triplex would form? [5:33 PM]
Brourd: Or should theoretically form? [5:33 PM]
Brourd: by projects, I mean "project ideas" [5:34 PM]
Omei: I have labs where RNA composer predicts triplets, and labs where the SHAPE and error data suggests to me that they ocurred.  And I have labs where I can say that the occurence of these moderately high error rates are highly correlated with the base assignments at the junction of the barcode and neck, which are presumably the ones that most affect their 3D alignment. [5:36 PM]
Brourd: Have you thought of writing that up? [5:36 PM]
Omei: Absolutely.  If I hadn't got sucked into a real-world project, I would at least have a draft for others to read by now. [5:37 PM]
Omei: But i have to say that the evidence isn't definitive.  Although there are lots of correlations, its very hard to know what's actually true and what's experimental noise... [5:39 PM]
Omei: Which brings me to the reproducibility lab data, which I'm also trying to make sense of, despite the numerous obstacles that get thrown up. [5:40 PM]
Brourd: oh? [5:41 PM]
Omei: (End of rant, I think.) [5:41 PM]
Brourd: Or do you mean real life obstacles  [5:41 PM]
Brourd: Did you analyze the "let's break the barcode" data yet? [5:41 PM]
Brourd: After all, that was a large set of identical sequences. [5:42 PM]
Omei: The continually changing UI and unannounced  changes in how data is returned by the server have been obstacals also. [5:43 PM]
Omei: No I haven't.  I didn't even manager to particpate in the last lab round. [5:44 PM]
Omei: And here I am, spending all this time chatting!  [5:44 PM]
Brourd: Must be something really important in real life! [5:44 PM]
Omei: I've just fallen into taking on too much. [5:45 PM]
Omei: It's happened before.  I've learned to live with it. [5:45 PM]
Brourd: naw, communication is imprtant in this project. [5:45 PM]
Brourd: For example, the total number of discussions about the lab this week have increased to 1 thanks to you and Nando  [5:45 PM]
Omei: And he didn't even stick around for the finish! The bum.  [5:46 PM]
Brourd: ha [5:46 PM]
Omei: I really do need to go for now.  I've got a backload of emails I
need to respond to. [5:47 PM]
Brourd: Later omei! [5:47 PM]
Brourd: Thanks for the chat  [5:47 PM]
Omei: But it has been nice to chat with you.  I wish I had more time. [5:47 PM]
Omei: afk for now. [5:47 PM]
Omei (talk) 05:55, 24 November 2013 (UTC)Reply[reply]