2015.11.06 Michelle's Intro to TB Sensors - Chat Transcript

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mat747: hi hog - how have you been [2:58 PM]

Elves: hi mat & hoglahoo, hey Jen! [2:58 PM]

Jennifer Pearl: still have a couple of minuites untilo official 3pm [2:59 PM]

mat747: hi elves [2:59 PM]

Jennifer Pearl: Hi Elves!!!! [2:59 PM]

Elves: :D hulloooo!  [2:59 PM]

AndrewKae: hi Elves and all [2:59 PM]

Elves: hi Andrew welcome back  [2:59 PM]

mat747: hi andrew [2:59 PM]

hoglahoo: hi mat, long time no see [3:00 PM]

hoglahoo: hi machinelves and all [3:00 PM]

Elves: yeah it's great to see you mat :D [3:00 PM]

mat747: hog - yes I know i`ll been mainstream [3:01 PM]

Jennifer Pearl: @elves gues how much RAM DPAT was using today on my amazon server? [3:02 PM]

Elves: hahaha all of it?? :D [3:03 PM]

Jennifer Pearl: about 14.7GB [3:03 PM]

Elves: but seriously how much?  [3:03 PM]

Elves: o.0 [3:03 PM]

Jennifer Pearl: and 23% of 4 processors [3:03 PM]

Elves: wow, that is super cool actually [3:03 PM]

Jennifer Pearl: its a beast.  [3:03 PM]

Jennifer Pearl: DPAt is aan analysis prgram i have been writing [3:04 PM]

Jennifer Pearl: Dot Plot Analysis Tool(DPAT) [3:04 PM]

whbob: Hi evryone. [3:04 PM]

Elves: hi! [3:04 PM]

Jennifer Pearl: although it is starting to do things outsidde of DotPlots so i will probabily call it RAT (RNA Analysis Tool) soon [3:05 PM]

Elves: how much data were you crunching with that round Jen? [3:05 PM]

AndrewKae: NuPack Rat [3:05 PM]

voyager1: done [3:05 PM]

Jennifer Pearl: all of Exlusion 1 [3:05 PM]

Jennifer Pearl: all aprirng probabilities for teh MFE structure, secondary stucture notation, pairing probability notation and centroid strucure as well [3:06 PM]

Elves: ! omg how long did that take [3:06 PM]

Jennifer Pearl: with 14GB of ram used about 15 -20 minutes [3:06 PM]

Elves: ahahahahaha [3:07 PM]

Elves: *high five* [3:07 PM]

Jennifer Pearl: *high five* [3:07 PM]

Jennifer Pearl: i think it is still trying to runon my server with 8GB of ram [3:07 PM]

mat747: jenn - cool [3:07 PM]

Jennifer Pearl: afgter a few hours [3:07 PM]

Jennifer Pearl: it pulls everything and poutputs an analyis report [3:08 PM]

mat747: jenn - I wish I could code like that [3:08 PM]

Jennifer Pearl: @mat thanks. It is 7000 lines of code [3:09 PM]

Jennifer Pearl: the analysi is 3000 lines [3:09 PM]

mat747: jenn - be great to see one of the reports oneday [3:09 PM]

Elves: mat, you might enjoy some of the graphs of the outputs, Jen made showing clusters of probability of certain stacks to pair in high vs. low scoring designs [3:10 PM]

Jennifer Pearl: https://getsatisfaction.com/eternagame/topics/exclusion-3-design-that-score-in-the-30-or-60-group-structure-in-secondary-structure-pairing-probability-structure-and-centroid [3:10 PM]

Elves: cool link thanks Jen!!  [3:11 PM]

mat747: 7000 wow you are committed [3:11 PM]

voyager1: btw hi everyone [3:11 PM]

Jennifer Pearl: hi voyager [3:12 PM]

Elves: hi voyager! [3:13 PM]

Jennifer Pearl: I have ]posting alot on the forum under analysis [3:13 PM]

Jennifer Pearl: Imve decided to post things as tehy come there adn i will work on a big paper soon about what i have seen and how things work [3:13 PM]

Jennifer Pearl: they best way to get caught up is to folow the bread crumbs [3:13 PM]

Jennifer Pearl: waiting on a good license to protect it and once that happens the next update will come out [3:14 PM]

johana: http:// youtu.be/OHneJPgpIvo [3:15 PM]

johana: Monthly Eterna Meeting [3:15 PM]

johana: Please join! [3:15 PM]

Jennifer Pearl: nice thanbks [3:16 PM]

Elves: hi Johan! Thanks!! :D [3:16 PM]

Jennifer Pearl: Hi Johan!!! [3:16 PM]

mat747: jenn - what energy modeling is it based on ?? [3:16 PM]

Jennifer Pearl: Vienna 2 with nandos FMN hack [3:16 PM]

Jennifer Pearl: i plan on getting Nupack to work soon since people seams interested in it currenlty [3:17 PM]

mat747: jen - I didn`t like vienna or the other so I made my only system so to spoke [3:18 PM]

mat747: speak [3:19 PM]

hoglahoo: so are any devs here yet? [3:19 PM]

Elves: hogla - monthly das lab meeting  [3:20 PM]

Elves: https:// www.youtube.com/watch?v=OHneJPgpIvo [3:20 PM]

hoglahoo: oh! [3:20 PM]

hoglahoo: ty [3:20 PM]

Elves: np just started :D [3:20 PM]

mat747: where was the link for that ? [3:21 PM]

Jennifer Pearl: you made your own that is cool [3:21 PM]

Elves: Johan posted a moment ago [3:21 PM]

mat747: jenn - don`t tell anyone  [3:22 PM]

Elves: is this expression of genetic material sourced from the infecting organism? i.e. not a result of changing the person's own genetic expression due to infection? [3:30 PM]

voyager1: these puzzles are to hard [3:30 PM]

Elves: is the fluorescence detection something that can be done on site / in the field? for rapid detection, like with the MIT kits and a microscope? or more complex than that? [3:35 PM]

Elves: that is super cool :D :D :D [3:43 PM]

Elves: Thank you for the great presentation Michelle!!! [3:46 PM]

Nando: thanks michelle [3:46 PM]

AndrewKae: nice [3:46 PM]

Elves: and i had one question before that, on source of genetic material being measured [3:47 PM]

Elves: ohhh that's cool [3:47 PM]

Jennifer Pearl: that was  good presentaion [3:48 PM]

Elves: thanks for talking about this, it helps get an introduction to the concept, since it's a steep learning curve [3:48 PM]

Elves: like the A / B genetic expression is from ??? [3:48 PM]

Elves: yes [3:48 PM]

Elves: ahhhh [3:49 PM]

Elves: does this count as epigenetics or not, if it is not permanent? [3:49 PM]

Elves: so that is why it matters that there is diversity in the data you showed at first [3:49 PM]

Elves: so it's a measure of the quantity of particular kinds of RNA  [3:50 PM]

Elves: not a change in the kind of RNA expressed, justa change in the quantity of RNA expressed [3:51 PM]

Elves: as in A and B represent RNAs that pre-exist, and are not changed in structure due to TB, just changed in quantity [3:53 PM]

Elves: thank you very much!! [3:53 PM]

whbob: Thank you! [3:53 PM]

Jennifer Pearl: thanks [3:54 PM]

voyager1: thanks [3:55 PM]

LFP6: Are there any devs on that do GetSaat maintenance? [3:54 PM]

johana: @elves: Yes, A and B are always expressed in the body, but increase in expression when the person is infected with TB.  [3:55 PM]

Elves: thanks Johan! I got confused thinking that expression meant a different kind of RNA was turned on or off based on TB exposure [3:55 PM]

Elves: or got changed somehow [3:55 PM]

Elves: but the RNA itself is the same, just quantities change [3:55 PM]

johana: RNAs are constantly being transcribed and degraded. We don't know the exact structure at this point, just the sequences of these transcripts [3:56 PM]

johana: So when you get infected your immune response turns on transcription such that the levels in the blood increase [3:57 PM]

Elves: oh that's interesting! [3:57 PM]

Elves: thanks for the point on sequence vs structure [3:57 PM]

Jennifer Pearl: cool [3:58 PM]

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