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binnedrubbish · 5 years ago

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5/12/19 Notes

Lab Meeting Prep Pipeline:

(May 2nd, 2019 at 2:38 p.m.)

[ ] Read the Results & Discussion cover to cover

[ ] Complete slides for all figures

[ ] Give a practice presentation

[ ] Read methods

[ ] Complete fluorescence slides

[ ] Decide how to deal with ‘relationship between calcium activity and movement’ section

[ ] Give a practice presentation

[ ] Read supplementary material cover to cover

[ ] Give a practice presentation

Note to self: Relax. Be meticulous. Be disciplined. Keep calm, do your best, trust your team.

——

Advanced Optimization

8 20 905

Live Action Poem, February 2nd, 6:41

Went to Brazil out of spite and saw

stone Jesus, arms open for a hug,

bought street weed, twice, from the same vendor

out of a reckless love for reckless love.

Hoped for a tropical muse and found

a strong handshake from a dangerous man.

Holed up in Rio de Janeiro with piles

of paper money and paced all alone

angry at nothing if only for the moment.

Rain dampened slick stone walkaways,

waiters were too nice and I tipped too much.

One offered to be a bodyguard , violence

hinted in every smirking human moment.

God, I loved being a target, smug,

dumb, flitting away American Dollars.

Jesus Christ looming in stone on a hill top.

Titties and marijuana, iconic primadonna

extravagant flora, dying fauna, fawning

over the climate. I went to Brazil

on an off month. To hole up

safe from my sprawling little lovely life.

To Do 26.1.19

[x] Cristina - Search for Hippocampus Models

[x] Ana G. - Draft e-mail call for interest in “Live Action Science”

[ ]

Data science Club Thursday at 5:00 p.m.

Astavakrasana

laser-scanning photostimulation (LSPS) by UV glutamate uncaging.

12.1.19 Goals

[x] Some Portuguese

[x] Mouse Academy - first read

[ / ] Dynamic mesolithic dopamine

[x] Water rats * SMH

Acorn - tracks impact | BetaWorks | 2 years of money | PitchBook | Social Impact Start Up

Mission Aligned Investors | Metrics | Costumer Acquistion Cost | Clint Corver -> Chain of Contacts -> Who To Talk to (Scope: ~100)

Money Committed || Sparrow || Decision Analysis —> Ulu Ventures [500k] [Budget x ]

Ivan - > IoS Engineering { Bulgarian DevShop }

[market mapping] Metrics -> Shrug

Peter Singer - Academic Advisory Board …

[1 million ]

Product market testing

Foundation Directory Online - Targeted , Do Your Homework

https://www.simonsfoundation.org/2018/11/19/why-neuroscience-needs-data-scientists/

Head-fixed —>

~INHIBITION EXPERIMENT TRAINING PLAN~

STOP MICE: 20th. GIVE WATER: 20th (afternoon) - 30th. DEPRIVE: 31st... (Morning) RESUME: Jan 2nd.

21st - BLEACH/DEEP CLEAN BOXES 1-14 (Diluted bleach; Flush (with needles out) - Open Arduino Sketch with Continuously open Valves - PERFUSE System) *[NOT BOX 11 or 5]*; Run 15 mL of Bleach per syringe; Copious water through valves; Leave dry.

———

http://www.jneurosci.org/content/preparing-manuscript#journalclub

Friday - Dec. 14th, 2018

[x] - Complete 2019 ‘Goals and Blueprint’

[x] - 2-minute Summary ‘Properties of Neuron in External Globus Pallidus Can Support Optimal Action Selection

[ ] MatLab for Neuroscientists :: Basic Bayesian Bearded Terrorist probability plots

[x] Statistics 101: Linear Regression

“Golden Girls” - Devendra Banhart

“King” by Moor - FIREBEAT

Reread - Section 3.3 to

Monday - Apply for DGAV License (MAKE SHORT CV)

SAMPLE: ‘Sal’ From Khan Academy

Make short CV

Tiago - Certificate

MATH:

“We explicitly focus on a gentle introduction here, as it serves our purposes. If you are in

need of a more rigorous or comprehensive treatment, we refer you to Mathematics for Neuroscientists by Gabbiani and Cox. If you want to see what math education could be like, centered on great explanations that build intuition, we recommend Math, Better Explained by Kalid Azad.”

Jacksonian March seizure (somatosensory)

—

Tara LeGates > D1/D2 Synapses

Scott Thompson

Fabrizio Gabbiani - Biophysics - Sophisticated and reasonable approach

Quote For Neuroscience Paper:

“Every moment happens twice: inside and outside, and they are two different histories.”

— Zadie Smith, White Teeth

Model Animal: Dragonfly? Cats. Alligators.

Ali Farke Toure

Entre as 9 hora e o meio-dia ele trabalha no computador.

Ele volta para o trabalha à uma e meia.

Ele vai as compras depois do trabalho.

A noite, depois do jantar, ele e a mulher veem televisão.

As oito vou de bicicleta para o trabalho. (go)

As oito venho de bicicleta para o trabalho. (come)

A que horas começa a trabalhar?

Eu começo a trabalhar os oito e meia.

Normalmente…

Eu caminho cerca de Lisbon.

É muito triste! Eu faço nada! Talvez, eu caminho cerca de Lisbon. Talvez eu leio um livro. Talvez eu dormi. Eu vai Lx Factory.

Depois de/do (after)

antes de/do (before)

—

Monday -> Mice

MATLAB!

“New ways of thinking about familiar problems.”

~*NOVEMBER GOALS*~

> Permanent MatLab Access [x] -> Tiago has license

> Order Mouse Lines [ ] -> Health report requested… Reach out to Vivarium about FoxP2

-> Mash1 line -> FoxP2 expression?

> Finish ‘First Read Through’ [ ]

> Figure 40 [ ]

SAMPLE : ‘Afraid of Us’ Jonwayne, Zeroh

Monday Nov 5th Goals:

> Attentively watch:

> https://www.youtube.com/watch?v=ba_l8IKoMvU (Distributed RL)

> https://www.youtube.com/watch?v=bsuvM1jO-4w (Distributed RL | The Algorithm)

MatLab License

Practical Sessions at the CCU for the Unknown between 19 - 22 Nov 2018 (provisional programme attached)

Week of November 5th - Handle Bruno’s Animals

Lab Goals -

“Deep Networks - Influence Politics Around the World”

Paton Lab Meeting Archives

Strategy: Read titles/abstracts follow gut on interesting and relevant papers

Goals: Get a general sense of the intellectual history of the lab, thought/project trajectories, researchers and work done in the field and neighboring fields.

Look through a GPe/Arkypallidal lens… what can be revisited with new understanding?

First Read Through

[x] 2011 - (22 meetings || 10/12 - SLAM camera tracking techniques)

[ x] 2012a (18 meetings)

[x] 2012b (15 meetings - sloppy summary sentences)

[ x] 2013a (19 meetings - less sloppy summaries jotted down)

[x] 2013b (17 meetings)

[x] 2014a (21 meetings) (summaries in progress)

[x] 2014b

[x] 2015 (23 meetings)

[ ] 2016 (23 meetings)

Current

—

“I like, I wish, I wonder”

“Only Yesterday” Pretty Lights

retrosplenial dysgranular cx (?)

retrosplenial granular cx, c (?)

fornix (?)

Stringer 2018 arVix

Lowe and Glimpsher

November Goals:

[ ] GPe literature -

[ x ] Dodson & Magill

[ x] Mastro & Gittis

[ ] Chu & Bevan

[x] Modeling (extra credit -Bogacz)

[ ] Principles of Neural Science: Part IV

[ x ] MatLab license… Website program…

Extra credit:

Side projects [/ ] Neuroanatomy 40

[ -> ] ExperiMentor - Riberio, Mainen scripts… Paton! -> LiveAction Science

MACHINE LEARNING

Week of Oct 29th -

Symposium Week!

Wyatt -> John Hopkins -> He got into American University!

Belly Full Beat (MadLib album Drive In)

“The human brain produces in 30 seconds as much data as the Hubble Space Telescope has produced in its lifetime.”

Sequence of voltage sensors -> ArcLite -> Quasar -> Asap -> Voltron -> ???

Muscarine -> Glutamate

Ph Sensitive

cAMP

Zinc sensitive

5 ways to calculate delta f

2 main ways

SNR Voltage —

Dimensionality reduction of a data set: When is it spiking?

5 to 10 2-photon microscope open crystal

…Open window to a million neuron…

Week of 10/15/18

Monday: Travel

Tuesday: Rest

Wednesday: Begin rat training. Reorient.

Thursday:

Friday:

|| Software synergistically ||

—————

Beam splitter, Lambda, diacritic

1.6021766208×10−19

‘sparse coding’

Benny Boy get your programming shit together.

Week of Oct. 8th, 2018

10/9/18

[ ] Rat shadowing (9:30 a.m.) -> Pushed to next week

10/8/18

[x] Begin Chapter 13 of Kandel, Schwartz, Jessell

[x] Outline of figure 36

[ ] Read Abdi & Mallet (2015)

DOPE BEAT MATERIAL - Etude 1 (Nico Muhly, Nadia Sirota)

Saturday - Chill [x]

Friday - ExperiMentor … mehhhhh scripts?

Photometry -> Photodiode collects light in form of voltage (GCaMP) (TtdTomate as Baseline… how much fluorescence is based on TdTomatoe, controlling factor always luminesce - GCaMP calcium dependent) :: Collecting from a ‘cone’ or geometric region in the brain. Data stored and plotted over time… Signals must be corrected…

Cell populations are firing or releasing calcium. (GCaMP encoded by virus injection, mice express CRE in a particular cell type).

———————————————

Brain on an Occam’s Razor,

bird on a wire,

synaptic fatalism integrating

consistent spiking;

strange looping: is this me?

Thursday

“We don’t make decisions, so much as our decisions make us.”

“Blind flies don’t like to fly”

[x] 9:00 a.m. Lab Meeting

[x] 12:00 p.m. - Colloquium

“It was demeaning, to borrow a line from the poet A. R. Ammons, to allow one’s Weltanschauung to be noticeably wobbled.”

“You must not fear, hold back, count or be a miser with your thoughts and feelings. It is also true that creation comes from an overflow, so you have to learn to intake, to imbibe, to nourish yourself and not be afraid of fullness. The fullness is like a tidal wave which then carries you, sweeps you into experience and into writing. Permit yourself to flow and overflow, allow for the rise in temperature, all the expansions and intensifications. Something is always born of excess: great art was born of great terrors, great loneliness, great inhibitions, instabilities, and it always balances them. If it seems to you that I move in a world of certitudes, you, par contre, must benefit from the great privilege of youth, which is that you move in a world of mysteries. But both must be ruled by faith.”

Anaïs Nin

[ ] MatLab trial expires in 1 day *

[ ] 3:00 p.m. pictures

“We do not yet know whether Arkys relay Stop decisions from elsewhere, or are actively involved in forming those decisions. This is in part because the input pathways to Arkys remain to be determined.”

These studies prompt an interesting reflection about the benefits and conflicts of labeling and classifying neurons at a relatively grainy level of understanding.

“The authors hypothesize that under normal conditions, hLTP serves an adaptive, homeostatic role to maintain a healthy balance between the hyperdirect and indirect pathway in the STN. However, after dopamine depletion, pathologically elevated cortical input to the STN triggers excessive induction of hLTP at GPe synapses, which becomes maladaptive to circuit function and contributes to or even exacerbates pathological oscillations.”

To Do Week of Oct. 1st - Focus: Big Picture Goals

[ x ] GPe Literature - Hernandez 2015 & Mallet 2016 (Focus on techniques and details)

[ ] MatLab! Lectures 6-7 (Get your hands dirty!)

[ x ] Kandel Chapters 12 - 13

Tuesday Surgery Induction 10:00 with Andreia

6:00 - 7:30

Portuguese

Digitally reconstructed Neurons: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106405/

To Do Week of, September 24th, 2018

To Do Week of Monday, September 17th, 2018

PRIORITY:

DATA ANALYSIS PROJECT ITI

———— PAUSE. ———————

Talks

[x ] Mainen Lab - Evidence or Value based encoding of World State/Probability - ‘Consecutive failures’ - easy/medium/hard estimate of where the reward will be.

Reading for the Week

[x] Chapter 9 - Propagating Signal | The Action Potential

[/ ] Ligaya et. al (2018) (CCU S.I.?)

[x] Katz & Castillo (1952) Experiment where they describe measurement techniques

[ ] Raiser Chapter 4 - Stimulus Outlasting Calcium Dynamics in Drosophila Kenyon Cells Encode Odor Identity

Video Lectures

[— ] Linear Algebra (Trudge steadily through)

[ — ] Khan Academy Logarithms (Trudge steadily through)

MatLab

[ ] Trudge steadily through www.mathworks.com/help/matlab/learn_matlab

*FIND PROBLEM SET/TEXT BOOK/WORK SHEETS*

Concepts to Grasp

[ / ] Master logarithms!

[ ] Review Kandel Et. Al Part II *Chapters 5-9*

Neuroanatomy

[ x ] Ink Figure 28

Project Planning? Too soon! Too soon! Read some literature on the subject.

17/9/18

1:00 p.m. Meet with Catarina to discuss “CCU Science Illustrated” (WIP) Project

2:30 p.m. Vivarium Induction

_______________________________________________________

| SPCAL Credentials |

| |

| login: |

| PW: |

-————————————————————————

——

NPR:: https://www.npr.org/sections/health-shots/2018/09/11/644992109/can-a-barn-owl-s-brain-explain-why-kids-with-adhd-can-t-stay-focused

9.13.18

[ x ] Pauses in cholinergic interneuron firing exert an inhibitory control on stratal output in vivo (Zucca et. al 2018)

[ x ] Chapter 8 - Local Signaling: Passive Properties of

-> Sub and supra threshold membrane potential (Conceptual)

Monday, Sept. 10th 2018

“Eat the Frog First”

[ N/A ] Review SPCAL Lessons 1-5 (In Library?) CRAM THURSDAY?

-> [/] wait for confirmation from Delores for theoretical test

-> (Out of Office reply from person in charge)

To Do:

[/] Comment Out %PRE_PROCESS_vBeta.m

[x] Change path name and run program in MatLab

[ ] Solve trial.blahblahblah error spkCount? labels?

[ ] Change Epochs and run?

[x] Chapter 7 - Membrane Potential :: Return to Pg. 136-137 Box 7-2 when sharp. ::

[x] Castillo and B. Katz (1954)

[x] 12:00 - Neural Circuits for Vision in Action CCU

[x] 2:30 - THESIS DEFENSE: Mechanisms of Visual Perceptions in the Mouse Visual Cortex

————

Extra-credit

[x] Ink Figure 24

[~ ] Finish “First & Last 2017” (100/127 = 78.74%)

——

Jax Laboratory Tools: https://www.jax.org/jax-mice-and-services/model-generation-services/crispr-cas9

Recommendation for Design and Analysis of In Vivo Electrophysiology Studies

http://www.jneurosci.org/content/38/26/5837

On the Horizon:

Schultz (1997) (Classic, classic, classic)

*[x] 9/7/18 - 6:00 p.m. Flip water for Bruno’s mice *

ITI Data Analysis -> Next step ->….

[ ] (find the sigmoid call) / Poke around preprocessing_beta

Reading

[x] Chapter 6 - Ion Channels

[ / ] Finish Krietzer 2016 —> [ ] write an experiment-by-experiment summary paper

Resource: https://www.youtube.com/watch?v=GPsCVKhNvlA Helpful explanation of ChR2-YFP, NpHR, and general ontogenetic principles.

[ / ] Reiser Chapter 3.3.38 - 3.4 (Need to finish 3.4.5, Look up Photoionization detectors, Coherence)

Neuroanatomy

[/] Finish Figure 24 (need to ink)

“Drawing Scientists “

[/] Storyboard for GCAMP6s targeted paper

-> Show Filipe for feedback ->

-> Ask Leopold permission ? Talk to Catarina

[ x] 16:9

[x] Write script and record [ 1:00 ]

Intellectual Roaming

[ / ] Return to Review of Reviews and Review Zoom-In | First & Last |

[/] Explore Digital Mouse Brain Atlas

9/6/18 - Thursday

To Do:

ITI Data Analysis :

[x] Draw data structure on mm paper -> Reach out for help understanding

[ / ] What fields did Asma call? What fields are necessary for a psychometric curve

Reading

[x] Kandel - Chapter 5 | Synthesis and Trafficking of Neuronal Proteins

[ / ] Reiser - Chapter 3 | A High-Bandwidth Dual-Channel Olfactory Stimulator for Studying Temporal Sensitivity of Olfactory Processing (Results complicated)

[/ ] Krietzer 2016 - Cell-Type-Specific Controls of Brainstem Locomotor Circuits by Basal Ganglia

Talks:

[x] 12:00 p.m. - Colloquium - Development of Drosophila Motor Circuit

Tutorials:

~ [x ] MatLab plotting psychometric curves

Neuroanatomy

[ x ] Outline brain for figure 24

———

MatLab

Laser stuff HZ noise, thresholds,

// PCA -> Co-variance ->

// Linear regression | Geometric intuition -> “What is known to the animal during inter-trial? What features can be described by animals history” ===> Construct a history space (axis represent different animals history ex. x-axis previous stimulus, reward, etc.?) Predictive (?)

Plot psychometric functions || PSTH (post stimulation of histogram ) of example neurons -> skills: bin spiking, plot rasters, smoothing (if necessary)

Data:: Access to Dropbox -> /data/TAFC/Combined02/ [3 animals :: Elife]

/data/TAFC/video

Tiago and Flipe know the video data

File Format -> Parser/Transformation (guideline) ||

> MatLab

Access to MatLab -> [/] 28 days!

How can I begin to analysis?

History dependent | Omitted

——

To Do Week of September 3rd

Monday

Administrative

[ x] Check-in with HR (Don’t bombard!): Badge. (Library access?)

[ ] Reach out to SEF?

[x] 2:00 p.m. Meet with Asma - discuss data analysis. Where is it? How do I access it (Tiago?) What has been done and why?

[x] 3:00 p.m. Lab Meeting “Maurico’s Data” - Pay special attention

[x] Finish first read through of Theoretical Laboratory Animal Science PDF Lectures

[ ] Rat Surgery Techniques…

Mouse neuroanatomy project

[/ ] Figure 24

[ ] Figure 28

Math

[x ] L.A. Lecture 2

[ x] L.A. Lecture 3

Read:

[ ] Georg Raiser’s Thesis (Page 22 of 213)

Find time to do at least an hour of quiet focused reading a day. (Place?).

Continue to explore whims, papers, databases, ideas, protocols, that seem interesting.

Develop ‘literature scour’ protocol - (Nature Neuroscience, Neuron, Journal of Neuroscience)

Dates to Remember: September 14th - Laboratory Animal Sciences Theoretical Test!

https://www.sciencedaily.com/releases/2018/08/180827180803.htm:Can these be used for techniques?

https://www.sciencedaily.com/releases/2018/08/180823141038.htm ‘Unexpected’ - Unexpected physical event and unexpected reward or lack of reward (neuronal modeling of external environment)

—

In my first ten minutes at work I’m exposed to a weeks (month/year/decade) worth of interesting information. Going from an intellectual tundra to an intellectual rain forest.

1460 proteins with increased expression in the brain: Human Protein Atlas https://www.proteinatlas.org

Non-profit plasmid repository: https://www.addgene.org

Protein database: https://www.rcsb.org/3d-view/3WLC/1

Started to think at the molecular level.

“MGSHHHHHHGMASMTGGQQMGRDLYDDDDKDLATMVDSSRRKWNKTGHAVRAIGRLSSLENVYIKADKQKNGIKANFKIR

HNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSVQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGGTGGSMVSK

GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDF

FKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLPDQLTEEQIAEFKEAFSL

FDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKGSYRDTEEEIREAFGVFDKDGNG

YISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK” - CCaMP6m amino acid code.

8/31/18 - (Friday) @12:00 in Meeting Room 25.08

GET USB ! !

[Lisboa Cultura na ru, Lisbon on the streets Com’Out Lisbon - Katie Gurrerirra ]

MatLab -> Chronux Neural Analysis

SEPTEMBER 14th!

Week of August 27th, 2018

“Conserved computational circuitry, perhaps taking different arguments on different locations of Basil Ganglia” - Tuesday

Andrew Barto: http://www-all.cs.umass.edu/~barto/

Basil Ganglia Labs

Okihide Hikosaka Lab: https://irp.nih.gov/pi/okihide-hikosaka

Wilbrecht Lab

Uchida N. (ubiquitous dopamine motivation and reward)

Peter J. Magill

Schultz (Pioneer in the field)

C. Savio Chan

Doya, K. (theory)

Calabresi, P. (muscarinic)

Ana Graybiel (McGovern)

James C. Houk (1994 - Book on Models of Computation in the basal Ganglia)

Evolutionary Conservation of Basil Ganglia type action-selection mechanisms:

https://www.sciencedirect.com/science/article/pii/S0960982211005288

Dopamine D1 - Retinal Signaling https://www.physiology.org/doi/full/10.1152/jn.00855.2017 [Note to self: Too Off Track]

[ ~ ] Flurorphore Library

Official Badge? [ ] Printer Access [ ]?

—

Online Course on Laboratory Animal Science

Monday : 11 [x] 12 [x]

Tuesday : 13 [x] 14 [x]

Wednesday: 15 [x] 16 [/]

Thursday: 17 [x] 18 [x]

Friday: 19 [x] 20 [/]

Lesson 11 - Behavior and Environment, animals must be housed in an environment enriched to maximize their welfare.

Lesson 12 - Rodent and Lagomorph Accommodation and Housing - A more comprehensive guide from the macro environment, facilities i.e. establishments, to the micro environments. Covers health and safety procedures for personnel as well as geometry of housing units (rounded edges to prevent water accumulation). Absolutely essential.

Lesson 13 - Collecting Samples and Administrating Procedures - covers the most common collection techniques and materials collected and stressed the importance of doing as little harm as possible to the animal.

Lesson 14 - Transporting the Animal : Shipper holds most of the responsibility. Major goals are making sure the journey is as stress free as possible, contingency plans are in place, and that all of the logistics have been carefully planned, communicated, and coordinated between various parties responsible in the shipping. Also, animals should be prepared mentally and physically for the journey and should have a period of post-transportation to adjust to the new surroundings and environment. A number of practical issues must be considered such as temperature, availability of food, and access to animals during the journey. Boxes should be properly labelled in whatever languages are necessary.

Lesson 15 - The purpose of feeding and nutrition is to meet the energy needs of the animals, which vary by species, physiological state of animal (growth, maintenance, gestation, and lactation). A number of category of diets exist as well as a variety of specific diets to best fits the needs of the experiment. This chapter covers particulars of nutrition requirements and stresses the importance of avoiding obesity and malnutrition.

Lesson 16 - Anatomy and Physiology of Teleosts (Skip for now: Focus on Rodents and Lagomorphs)

Lesson 17 - Anatomy and Physiology of Rodents and Lagomorphs - General characteristics of the anatomy and physiology of six species, 5 rodents and 1 lagomorph. Mice, rats, guinea pigs, gerbils, and hamsters. Rabbits. It covers particularities of each species and has a quiz asking specific facts, mostly centered on commonalities and distinguishing factors. Worth a close read.

Lesson 18 - Anaesthesia and Analgesia in Rodents and Lagomorphs . Pre anaesthesia techniques, drug combinations, and repeated warning of the importance of choosing the right drugs and technique for the species. Use of a chamber. Methods of anesthesia (IP, IV, Volatile). Endotracheal Intubation for rabbits; the proper use and administration of analgesics; monitoring during the operation (for example - the paw pain reflex disappears in medium to deep anesthesia

Lesson 19 - Animal Welfare and Signs of Disturbance - This chapter repeatedly stresses the importance of the relationship between the caretaker and the animal. It repeats the ideal social, environmental, and nutritional environments for rodents and rabbits and highlights peculiarities of each species. After reading this one should be better suited to detecting stress, disease, or other ailments in a laboratory animal.

Lesson 20 - Fish Psychology and Welfare (Skip for now: Focus on Rodents and Lagomorphs)

Lessons 5, 17, and 20 pertain to fish

TEST SEPTEMBER 14th

—

MIT Open Course Ware:

Linear Algebra

Lecture 2 [/ ] -> Elimination by Matrices, production of elementary matrices, basic computations, and a review of row and column approaches to systems of equations. Introduction to the basic application of the rule of association in linear algebra.

Lecture 3 [ ]

Mouse Neuroanatomy

Ink Figure 16 [x]

Figure 20 [x]

Figure 24 [ ]

Introduction to MatLab: https://www.youtube.com/watch?v=T_ekAD7U-wU [ ]

Math Big Picture: Review Single Variable Calculus! Find reasonable Statistics and Probability Course (Statistical Thinking and Data Analysis? Introduction to Probability and Statistics?) Mine as well review algebra well I’m at it eh.

Breathe in. Breathe out.

—

Data analysis :: Behavioral Analysis

—

Ana Margarida - Lecture 6 - Handling Mice techniques

EuroCircuit can make a piece. Commercial v. DYI version of products.

Dario is the soldering, hardware expert. I.E. skilled technician.

www.dgv.min-agricultura.pt; it is recommended that the entry on Animal Protection and the section on Animals used for experimental purposes be consulted first.

—

Sir Ronald Fisher, stated in 1938 in regards to this matter that “To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of”.

——

Finally, it is time to publish and reveal the results. According to Santiago Ramón y Cajal, scientific writers should govern themselves by the following rules:

Make sure you have something to say; Find a suitable title and sequence to present your ideas; Say it; Stop once it is said.

8/21 Goals

Access ->

:: Champalimaud Private Internet [HR] Printer [HR]

:: Web of Science (?)

:: PubMed (Nature, Journals, etc.?)

———

PRIORITY: Online Course -> Animal Laboratory Sciences PDF’s

20 total -> 4 a day || I can finish by Friday

Monday : 1 [x] 2 [x]

Tuesday : 3 [x] 4 [x ]

Wednesday: 5 [x*] 6 [x]

Thursday: 7 [x* ] 8 [x]es

Friday: 9 [x ] 10 [x ]

Notes:

Lesson 1 - Philosophical and ethical background and the 3 R’s

Lesson 2 - Euthanasia. Recommended, adequate, unacceptable. Physical or chemical. Chemical - inhalable or injectable. Paton Lab uses CO2 and cervical dislocation.

Lecture 3 - Experimental Design. Return to as a starting point for basic design (randomized samples and blocks) Integrate with “Statistical Thinking and Data Analysis”

Lecture 4 - Legislation. Memorize specific laws and acts.

Lecture 5 is highly specific for the care and maintenance of Zebrafish

Lecture 6 - Handling of rodents and mice. A theoretical overview, this material is essentially kinesthetic.

Lecture 7 - Provides a technically detailed account of how genetic manipulations are done and propagated. Deserves a ‘printed’ review and vocabulary cross reference.

Lecture 8 - Health and Safety. Predominantly common sense.

Lecture 9 - Microbiology - contains an appendix with list of common infections that will be eventually be good to know.

Lesson 10 - Anaesthesia pre and post operation techniques, risks of infections etc.

// http://ec.europa.eu/environment/chemicals/lab_animals/member_states_stats_reports_en.htm

http://ec.europa.eu/environment/chemicals/lab_animals/news_en.htm -> General European News regarding

http://www.ahwla.org.uk/site/tutorials/RP/RP01-Title.html -> Recognizing pain in animals

Week of 8/20/18 To Do:

Tiago/Team -> Whats the most important priority?

Get Arduino Machine working again [?]

Jupiter/Python Notebook Up [ ]

Bruno MatLab Access [… ]

- Get documents to HR

- Animal Lab certified?

- Logistical/Certificate/Etc.

- Start discussing personal project:

> (Rat colony) Wet Lab

> (Machine Learning) Electric Lab

> Statistics project

- Reacquaint with Lab Technology/Protocols

- Review papers - Engage back with the science

Project Print: Screen shots

[ ] collect

“Do the job. Do it engaged. Engage -> Not just execute the best you can, understand the experiment.

Why? Alternative designs? Control experiments needed to interpret the data? Positive controls and negative controls? What do you need to do to get crisp. Totally engage.

How it fits into other experiments?

“Engage with the science as if it were your baby.”

Execute beautifully… Ask --- et. al. What does ideal execution look like

Extra time: allocate time. Technicians : Freedom to do other things, work with other things, other technical things, giving people independent project to carry out. Project --- has in mind? Design. Hands on education of how science works then reading. Spend time focused on a problem and in the ideal become the world’s foremost expert on whatever ‘mundane’ aspect of what ever problem you are working on.

Computational in the context of a problem. Learn to use. Defining “problems I want to solve.” As an operating scientist, the technology can change very quickly. Capable of learning, understanding, and applying.

Answer questions in a robust way. Thinking of technology in context of problem. Deep domain knowledge; focus on experimental more than book reading.

Realistic path -> Research fellow to PhD. program. Industry… Strong head’s up to do research. First-rate OHSU? Excellent. IF: Remember that it is narrow, broader with neuroscience as a component. Biology < > Neurology. Real neuroscience computational ->

Juxtasuposed: Engineering, CS, A.I., and all that…

Label in broad ways: Molecular, cellular, systems, cognitive, psychology. Borders are so fuzzy — as to be

Domain bias. In general -> other than P.I. protected from funding. Publication, the life of the business. Metric of success is the science they publish. Work that contributes to being an author = more engaged, more independent. Evolved to an independent project.

So incredibly broad -> CRISPR, GFP, Optogenetics, with higher level systems problems. 100 years = absurd. Look back -> Could we have conceived whats going on today.

Foremost expert on something how-ever limited. Grow from there. Grown from a particular expertise.

Molecular biologist || Do what a 3 year old is taught to do. How? How? How? How does that work. Quantum physics. Ask questions. Be open.

Go to seminars -> Go to every talk. Take every note. Primary literature fundamentally different. Always learn in context. Don’t dilute too much (ignore title, abstract, discussion). Look at figures and tables and derive for yourself what they say. Look for THE FIGURE or THE TABLE that is the crux and look for the control experiment. Understand the critical assessment, are the facts valid and warranted? Infinite amount to learn, don’t spread yourself infinitely thin. “

To Do: Develop Independent Machine Learning Project

Gain Access to Web of Science

————

Paton Learning Lab

Personal Learning Goals

September 1st - December 1st

Major Goals

[ ] Read Principles of Neuroscience 5th Edition

[ ] Complete CSS 229

[ ] Deep read 12 papers (Write summary || Practice peer review)

Administrative

[ ] Reactivate

[ / ] Figure out Residence Permit/Visa

Lifestyle

[ x ] Purchase commuter bicycle

[ / ] Purchase waterproof computer/messenger bag

Language

[x] …. Focused practice minimum 20 minutes daily …?

[ ] Find language partner

[ ] Portuguese film/television/music

UPCOMING

Phone conversation with --------

Tuesday, August 7th 9:00 a.m. EST (10:00 a.m.

0 notes