User talk:Edward Lane

From EteRNA WiKi
Jump to: navigation, search

This is my talk page - leave me a message here if it's about stuff in this wiki - and then you can Direct message me in the game to tell me to go log in if its urgent.Edward Lane (talk) 11:35, 30 May 2013 (UTC)

Stuff I also did when I forgot to log in

 

 

Question from Hoglahoo

Should user pages be locked ownership by default to admins and the user the page belongs to? User:Hoglahoo

:Hi Hoglahoo, no I don't think so otherwise no one else would be able to edit this page to ask me a question - unless they were an admin. Edward Lane (talk) 16:46, 11 June 2013 (UTC)

 

Thanks Edward, I guess you're right Hoglahoo (talk) 05:16, 3 July 2013 (UTC)

RMDB and stuff to include

http://rmdb.stanford.edu/repository/

 

http://rmdb.stanford.edu/repository/detail/ETERNA_R70_0000

 


Edward_Lane: I'm looking at this http://eterna.cmu.edu/web/blog/2855177/ [9:15 PM]
Edward_Lane: what do the dark and light bits represent ? is it like a dotplot ? [9:16 PM]
Brourd: @ Edward - they represent the chemical footprint of the RNA [9:16 PM]
Brourd: @ hoglahoo - if you wish to check out the flu RNA, I believe they are in R72 of the RMDB [9:18 PM]
hi529: RMDB? [9:19 PM]
Brourd: I believe the mutate and map technique was used on it [9:19 PM]
Edward_Lane: mutate and map ? [9:19 PM]
hi529: Whats the RMDB [9:19 PM]
Brourd: @ edward - in a sense, you could map the chemical footprint onto a dot plot, however, since dotplots represent paired bases [9:20 PM]
Brourd: it can be rather difficult to determine how exactly the RNA folded [9:20 PM]
Brourd: since each of those bands represent the signal for individual bases [9:20 PM]
Brourd: RMDB - http://rmdb.stanford.edu/repository/ [9:22 PM]
Brourd: @ Edward - signal, reactivity, etc. [9:23 PM]
Brourd: just words meant to represent the estimated measurement of the entire RNA population [9:23 PM]
Brourd: one base at a time [9:24 PM]
Brourd: I'm not entirely sure how long sequencing takes [9:24 PM]
Edward_Lane: ok that makes sense, so a horizontal line is something consistant over the whole population at a particular base ? [9:25 PM]
Brourd: http://rmdb.stanford.edu/repository/detail/ETERNA_R70_0000 [9:25 PM]
Brourd: each cell represents the individual base [9:26 PM]
Brourd: one horizontal line would be the chemical footprint for that RNA when it was sequenced, from bases 1 to 79 [9:27 PM]
Edward_Lane: that looks fascinating if I can get my head around it [9:27 PM]
Edward_Lane: yes I had the axis round the wrong way, vertical line  [9:28 PM]
Brourd: going vertically, it just goes down the list of submitted sequences [9:28 PM]
Brourd: wiith whatever conditions that RNA happened to be sequenced with at that time [9:28 PM]
Brourd: and the chemical modifiers used [9:29 PM]
Edward_Lane: ok and dark is unreactive, thus 'bound' ? [9:30 PM]
Brourd: actually, I believe it is the opposite. They switch it for the game [9:30 PM]
Brourd: yeah, the white cells represent no reactivity, which would be bound, or at least protected from chemical probing [9:32 PM]
Brourd: the darker the cell, the more reactive it would be, or at least open to chemical modification [9:32 PM]


T-rod: what does it mean that it is reactive and non reactive? [9:33 PM]
Brourd: in the game though, as you know, yellow means unpaired and blue means paired ;P [9:34 PM]
Brourd: I guess they figured that was visually the best way for players to distinguish the bases [9:34 PM]
T-rod: does non reactive mean already paired bases, and reactive means unpaired? [9:36 PM]
Edward_Lane: @t-rod that's more or less how I understand it yes [9:37 PM]
T-rod: so, from wich perspective are we waching this RNA then [9:38 PM]
Edward_Lane: but the bonds are all in a state of flux a lot of the time, so the pairedness of a given base varies I think, though that might be across the ensemble [9:38 PM]
T-rod: from the side, or top? [9:38 PM]
Brourd: http://en.wikipedia.org/wiki/Nucleic_acid_structure_determination [9:38 PM]
Edward_Lane: along the line - it's not displayed as a shape [9:39 PM]
T-rod: ah, okay [9:39 PM]
Brourd: you can skip down to chemical methods, unless you wish to learn a littlebit more [9:39 PM]

Personal tools
Main page
Introduction to the Game