Stroklitude Testing Pt. 2

on Monday, July 30th, 2018 1:52 | by

Data 1:

Monica:

Anokhi:

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The Tmaze Experiments : Screen results as on 22-7-18

on Sunday, July 22nd, 2018 6:41 | by

 

Yellow 1 (Positive Control): Gr28bd-G4, TrpA1-G4

Parameters: Light: intensity (500 Lux side, 1000 Lux bottom); frequency = 20Hz; Delay = 1 ms; Duration = 9.9 ms; volts = 6.4

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Experiment Update

on Monday, July 16th, 2018 1:46 | by

> Worked on the ping pong ball machine in the last week.
IMG_2907 (1)

The text file looks something like this: Not very sure how to interpret it because there is no column header.

> Did not find any RU486 fly lines in the Brembs fly stock.
What is RU486 and why are we using it? It is a conditional transactivation method that gets activated when introduced with Mifepristone/RU486 and works on the UAS promoter (Roman et al, 2001).

The genes we are knocking down:
1) SERCA gene
2) Ryr gene

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Overview of Coombe’s Paper

LMC L1 and L2 Paper

(Coombe, P.E., 1986)

ERG

  1. mass electrical response of the eye
  2. waveform consisting of summed extracellular potentials produced by retinula cells and postsynaptic neurons
  3. recorded by electrodes
  4. waveform consists of on transient, negative sustained potential and off transient

L1 and L2

  1. Two main reasons to select study upon these two:
    1. Only lamina neurons which are known electrophysiology
    2. Intracellular waveforms roughly correspond to ERG transients

Vam mutants

  1. Vam = Vacuolar medulla
  2. Semi-dominant mutation (Incomplete dominance)
  3. Characterized by formation of large vacuoles and absence of ERG transients

(Electron Micrographs from the lamina) (ERG)

ERG waveform and LMC degeneration

  1. No wt showed degeneration of LMC
  2. Negative nonlinear relationship between % of LMC degeneration and the size of on/off transients in Vam flies

 

Results

  1. Previous work has shown age-specific degeneration of LMC in the lamina.
  2. Signs of degeneration start to appear in the form of large vacuoles in medulla and lamina.
  3. LMC may be responsible for ERG transients
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Tmaze Exploratory analysis : Middle Flies

on Monday, July 2nd, 2018 2:08 | by

plotting the mean ratio of flies which stay in the middle during experiment.

 

Yellow 1 (Positive Control):  Gr28bd-G4, TrpA1-G4

Parameters:
Light: intensity (500 Lux side, 1000 Lux bottom)

frequency = 20Hz

Delay = 1 ms

Duration = 9.9 ms

volts = 6.4

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T-Maze experiments : screen results as on 25-06-2018

on Monday, June 25th, 2018 1:13 | by

Yellow 1 (Positive Control):  Gr28bd-G4, TrpA1-G4

Parameters:
Light: intensity (500 Lux side, 1000 Lux bottom)

frequency = 20Hz

Delay = 1 ms

Duration = 9.9 ms

volts = 6.4

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Initial screen results

on Monday, June 18th, 2018 1:15 | by

Yellow 1 (Positive Control):  Gr28bd-G4, TrpA1-G4

Light: intensity (500 Lux side, 1000 Lux bottom), frequency (20Hz)

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“Virtual brain” site

on Saturday, March 2nd, 2013 4:00 | by

Arnim Jenett (Janelia Farm Research Campus), Kazunori Shinomiya, Kei Ito (both Tokyo University), and other anatomists made a great site with a 3D-viewer of adult Drosophila brains available. You have the chance to scroll threw a whole mount stack while ticking different brain areas. Those brain areas are listed next to the stack. Different areas are coloured differently, so that you can look at the location of several areas in the same brain. On the main page you can find simply explained tutorials about the usage of the site. It is correlated to the anatomical search engine of the Janelia farm GAL4 collection.
Because it was very helpful to me to learn all the synonyms of relevant areas and because I think it is very helpful to learn more about the structure of the Drosophila brain in general I wanted to advertise the site here.
http://www.virtualflybrain.org/site/vfb_site/overview.htm

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Science and semantic web

on Friday, January 18th, 2013 7:04 | by

I was on a meetup of corporate semantic web last Tuesday. These people are using semantic web technologies (making machine readable content based on ontological terms and relation between these terms) to improve the efficacy of private companies. For instance, they work on ways to improve wiki contents which may be produced in a company. This corresponds at using ontological term to annotate the wiki content and other related technologies. This can be used to find an expert in one category (=somebody who’s posts are rarely corrected on a specific subject).

What is the scientific community (the one which should be leading the way actually) doing during that time: we use text search in “keywords” and titles to find the appropriate literature, that we have to read thouroughly to drive our one conclusions about these different parts… At least, that is what we do 90% of the time, and we all know how inaccurate this can be. Experimental results may be translated into a machine readable content, why aren’t we doing it (it could make everything that much simpler, faster and more accurate)?

The answer: 1. there is no tool nor database where we could do it. 2. Scientists do not have the time to do it, they are over-pressurized to produce data, not to make it reusable or machine readable.
How to push people to use the semantic web technologies, how to ease this use, should it be done by the authors or by the community, pre or post publication, what ontology tool to use,… What can we do? Is anyone asking these questions around? Does a platform like researchgate be a way to introduce this, or should we go for a public solution, inside pubmed for example?

Is any of you asking/answering these questions?

By the way, this post is tagged by none-ontological terms, a shame?

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Trajectory data: database structure

on Thursday, December 20th, 2012 5:16 | by

CeTrAn is our software to analyse trajectory data, written in R it is free and open source . It was designed to analyse data obtained in the Buridan’s experiment setup. I am now trying to have a larger scope and incorporate different type of data:, for instance:

– Buridan’s experiment done with a different tracker

– Walking honeybee tracking in a rectangular arena, with a rewarded target

– Animal (flies/bees) walking on a ball, using open- or closed-loop experiment setup

– trajectory data obtained from the pysolo software (flies)

– larval crawling data

I want to include an automatic depository of the data in a database. Automatic entries in Figshare is for instance possible. (see older posts). My problem is to find a way to treat the data such that:

1. the raw data is uploaded

2. all data is uploaded also if we use only the centroid displacement (in some data file the head position is also given)

3. the data can be reused and data obtained in different lab, animal, setup can be compared. (data should be organized such that it can be searched and queried).

4. probably other elements that I do not think of….

 

My main problem: I have nearly no experience in data management/design, ontology or semantic web. Here is a first draft of a database structure that I have thought of. Every feedback would be welcome:

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