Flatiron workstation LVM RAID setup

# Dell precision linux setup (T7910)
– Dylan suggested RAID5 XFS on the CENTOS workstation. RAID is managed by LVM (logical volume manager).
– The plan is generate the dataset and run the benchmark on this workstation. When my own linux box is cleared then I could clone the setup.
– Dylan disabled the last access time field, a performance hack.
– Currently generating the test dataset. The RAID is being built but the writing to disk is still possible. He recommended softraid.
– The question about why not using CEPH. read/write variability on the workstation. this is the reason why I want a local RAID. I am dealing with a large file read and write and I want to keep all the processing to local.

# Linux thunderbolt
install sudo apt install bolt
restart and mount
Dell workstation has Thunderbolt port available.

# Memory profiling caveat
In Ubuntu, the memory profiling precision above 20MB (MB is 10^6 whereas MiB is 2^20)

parenting and discipline

Pure freedom is like random noise which knows no direction, no outcome no future. It only leads to a random walk. I am getting concerned about whom my son is becoming. He is getting out of control by yelling, complaining, whining and crying to get his way. The main issue is that I need to get to work on time but my commute often gets delayed by listening to all his demands or my wife’s demands. This is very bad for the future of our family. I have no interest in raising a son whom I would hate to spend time with. Discipline must be balanced with indulgence and many Americans confuse indulgence with happiness. Indulgence is mostly based on material gains or service received by spending money. We need to indulge at times but it must come as reward for work being accomplished, not by accumulating credit card debts. Jordan Petersen said something along the line of “women indulges and man disciplines. Women do as they please and men do what he must”.

I don’t want my son to grow up like a girl. Americans used to be very disciplined people and their hard work changed all of our lives for good. since the civil rights movement the pendulum swung the opposite direction. entitlement and identity politics. disciplines do not matter any more only loud mouth gets what they want. no wonder the country is falling apart. there is no social familial responsibilities. everyone does as they please without thinking of consequences in their near term and far future. the collapse is guaranteed.

I used to be liberal but i can see how the extreme liberalism can destroy individuals families society nation and the whole planet. freedom is a random noise from neuroscience research. it is unpredictable and animal behaviors have been shaped, not perfectly nor completely by the forces of evolution. behavioral flexibility and freedom comes at a cost of suboptimality. micromanaging one’s action is not what i want. i want guidance in everyone’s lives to bring collectively better future. many have tried or at least gave a lip service to this notion. national socialism, international communism, market democracy. market democracy is about choices. females are about choices. shoppers choose. consumers get manipulated by ads and the whole population can be hacked in their brain. what kind of future do i want to live? what do i want my next year to be? am i stuck or am i going somewhere?

don’t be hacked by the social machineries of mass media. news tells half truth half lies. the wise one knows this. the cunning one knows this too. knowledge is power. actionable knowledge is power if i must add. i learned the basic human nature when i restrained by social constructs. it leads to good things in some and terrible outcomes for most people. that’s what an ultimate freedom brings.

I already wasted countless time getting hacked. i am wiser and i will act on the personal experiences i have gained and countless failures i experienced. i am sharing my thoughts to find friends and guide people whom seek advices.

Parenting completes a msn’s destiny. parenting forces me to shape up myself if i managed to be a good dad. what is being a good dad about? i must provide mental and material and emotional supports to my son. i must teach him what he can and cannot eat or play with or touch or act on. i must teach him patience and appreciation for the family and community. i must teach him true strength and warmth of character. i lack many of these but i want my son to be better than me. by helping him to achieve these goals i will become a better man. super man. ubermensh. quiet frankly the future is going to be harder much harder to live in. it would require superhuman qualities to simply survive. i must guide my son to the path toward superhuman. being good is not good enough anymore. being better is not good enough. superhuman intelligence emotional resilience and strength and endurance all of them are required in one person. human being are finally being forced to become complete. we must master our technology not the other way around. we must console machines not the other way around. there are already very few masters and many ignorant mass who live in a flat world. masters live in a tall and narrow spire whom oversees everyone. flatlanders are not even aware of what’s above us. they spend majority of time moving horizontally not vertically.

i need to move vertically and it’s going to require concentrated and directed energy that’s sharply focused toward above.

memory profiling for ironclust

# Goal: expand # channels and durations by tiling and see how the memory use scales per channel and per duration basi

[x] ## 1. expand datasets by tiling.
– cache the original (64ch, 1200s), and tile it

[x] ## 2. run the memory benchmark, parameter loop
– parameter loops: {param_set0.prm, param_set1.prm}
try to break the memory limit (256GB in my workstation)
~1MB/chan/min (3.43 MB/chan/min raw, 153GB/380ch/2hrs)

[x] ## 3. plot the scalability benchmark
– memory, speed, accuracy as a function of channels and duration

# Data storage problem on thunderbolt
[x] order thunderbolt enclosure
[ ] migrate
[ ] 18.04 has thunderbolt driver already mounted
do not install sudo apt install bolt
[ ] confirm interoperability between desktop and notebook

In Ubuntu, the memory profiling precision above 20MB (MB is 10^6 whereas MiB is 2^20)
Dell precision (T7919) could have a thunderbolt 2 card installed.
(compare 1.3 GB/s vs 50 MB/s over the network)

# IronClust remaining work
1. documentation
2. benchmark scalability, memory, accuracy, channel count, density, recording duration
3. make it faster using remote slurm interface

# Ironclust result section
## accuracy
– accuracy comparison
– probe layout comparison. density. columns
– drift handling comparison

## scalabiilty
– scalability plot: memory and runtime scaling
– accuracy vs. speed plot
– speed comparison with other software
– speed scalability using multiple computing cores

## usability
-input and output format

debrief global brain 2019

loren frank talk hippocampus theta sequential firing sharp wave ripple during immobility but sequential firing during theta occurs during movement. the difficulty is lack of firing need smaller spikes thus requires spikesorting free decoding and the animal decides left or right that alternates this is the work by kenneth kay et al on biorxiv 2019. hippocampus and forebrain interaction very interesting you can trigger lfp averaring using out of field spikes. looking at the pfc and hippocampus interaction you get to see how the memory can possibly transfer out of the hippocampus. i wonder if the sequences can be selectively disrupted in real time. the flex probe can scale up. they can soon mount 512 channel chips (flip chip bonder) on the flex cable. interconnects are the hardest as expected. spike gadget collaboration with loren’s lab. very innovative solution using flash memory storage. 8 arm choice poster was interesting it scales up the two choice task based on W arm maze.

Time to think early in the morning i rarely get this moment alone since my son was born i need to wake up earlier and devote time to think. this is precious because i need to access my new neuroplasticity and plan the future.

mri q&a with Charles Epstein and Jeremy Magland over lunch

Mark Henkelman
high throughput animal mri
simultaneous fmri and electrophysiology

Coils tuned at
DTI for neuromodulator and neurotransmitter movement tracking
ratiometric measurement of sodium and potassium ions. New receiver coils?

Multimodal imaging worl. MRI, ophys and ephys agreement

Fine-Scale Spatial Organization of Face and Object Selectivity
in the Temporal Lobe: Do Functional Magnetic Resonance
Imaging, Optical Imaging, and Electrophysiology Agree?https://ieeexplore.ieee.org/document/4664427

Integration of EEG/MEG with MRI and fMRI in functional neuroimaging

day 2 global brain

# bernardo sabatini.

fiber photometry and dorsal and ventral striatum behaving differently their dopamine concentrations are different in their time courses.


how is he contributing to the global brain neurotransmitter measurement?

direct and indirect pathways. from striatum.

uchida lab harvard. datta lab.


# carlos brody

calcium imaging. cellular resolution

mouse encoding redundancy.

optimal deciding and encoding directions.

relative angles preserve between linear encoding and decoding vector although the global angles change over time. so there is a stable representation in the brain over time. the updating of the decoding vectors depends on learning reduced set of variables.

global brain talk monday

# misha ahrens: multimodal imaging studies.
five modality imaging
multimodal imaging. gaba voltage glu calcium
Computational correlation framework: optical imaging corelation functional
Radial astrocytes. transition between active and passive behaviral state
glibal imaging Mu cell 2019
noredrenalergic cells. fiber. medula oblongata. glial calcium transients.
Tze Koh from Byron Yu lab.

# Maneesh Sahani. UCL.
population analysis and theory

Gaussian Process Factor Analysis (GPFA) is a method for inferring latent structure that is shared across a population of neurons from single trials [2]. … Thus, inter-trial variability in neural firing that is shared across the population is modelled via the evolution of the latent processes on a given trial.May 27, 2018Temporal alignment and latent Gaussian process … – bioRxiv

temporal variability. time warping. additive varition. point process observation

neuron x time x condition: neuronXfactor, conditionXdrive, factorXdriveXtime. Factorization of regression tensor. Soldado-Magraner

DIstribution representation of neural code
A. averaging.

B. Distributed distributional code (DDC). encodes distribution.
– expected value int(p(x)x)
– probablistic computations. beliefe propagation. decidsion making (reward expectation), variational learning (latent statistics expected value)
– so neural firing rate is the coefficient of the basis function

Easy to learn, representative power, …
Helmholtz machine: unsupervised learning by bootstrapping generation and recognition
adversarial? generative and recognition network.
wake phase and sleep phase.

Infrerence in time-postdiction (wenliang & sahani 2019 NIPS) same as NeurIPS
carry belief from the past. dynamical DDC

# Session dinner
Ahrens and Ziquin. voltron imaging.

certain behaviors are phased locked to other behaviors. this is related to the behavioral hierarchy. distributed CPG. this sets the mechanism of multi-timescale behavioral hierarchy (Mark Zimmer)
impute corrupted behavior. probablistic genrative model
Scott Linderman biorxiv, behavioral decoding work.

NeuroPAL. deterministic brainbow. neuralID and connectome.

# Svoboda Mesoscale activity project (MAP)
memory guided flexible mbehavior. Jorge Jaramillo
David Lui. Susu Chen. premotor circuits in the medulla. medulla delay period firing rate increases. ALM and basal ganglia.
in-cage training setup. track localization. ALM projection to either thalamic or medulla projection types. differentiate those two. basal ganglia disinhibition. release movement. disinhibition. movement initiation

# Mante (ETH zurich)
dynamics attractor can be modelled by different combination of potential landscape + input dynamics combination. compare saddle point, line attractor, point attractor types.
compare residuals to compare likelihood of model correctness
eigenvalue, singular values. point attractor is stable. 2D dimensional projeciton. see how the system responds to the perturbation.

# Sussilo
Interpretable neural dynamics: GOLD. goal oriented learning of dynamics
Encoder RNN. stimulus to behavior to Neural. Encoder RNN.
dynamical mechanism.
C. Chandrasekeran. PMd neuropixels task.

# xiao-jing Wang. distributed persistent acivity in multi-regional brain circuits
persistent activity. can’t be stimulated directly.
mouse model whole brain. Allen institute Julie Harris
keeping track of information. mechanism of short term memory.
long firing or firing chain?
sequential activation

Mom’s kidney problem

enoxaparin can damage kidney and CrCl

Over-anticoagulation can occur in patients with moderate (CrCl 30–50 mL/min) to severe renal dysfunction (CrCl <30 mL/min)


Thus, an LMWH with a lower molecular weight are is more dependent on renal clearance and therefore may accumulate in patients with renal dysfunction and may be more pronounced with the smaller LMWH [29].

reduce to 1mg/kg once a day if eGFR < 30mL/min . now she gets 1.5 mg twice a day. 3x of the recommended dose if her CrCl is low.

Cockcroft and Gault equation should be used for low therapeutic index and high-risk drugs. In other cases, eGFR is an adequate estimate of the CrCl.


CKD patients have higher risks of bleeding


Differences between LMWH.

Enoxaparin has 4300 dalton and tin ape run has 5800.

Use of low doses of low‐molecular‐weight heparin (< 3500 anti‐FXa units/d) is associated with equal efficacy and better safety compared with low‐dose unfractionated heparin, whereas use of higher doses of low‐molecular‐weight heparin is associated with significantly greater bleeding (Koch et al, 2001; Mismetti et al, 2001).

action items

1. extent of her kidney damage

2. choice of her anticoagulation regimen

3. her housing situation when discharged

Sep 2 Mon Labor day @ Flatiron

Learning React. why? it ties model view controller framework. Imagine what I can do if I can expose the controls through the web. My work will be completely visible and usable by the users through the web interface. react is the fastest way to get the scientific tools to the users. JSX + react allows easy integration with the python backend. this is why I must learn react. it’s tied to Jeremy’s new visualization effort (reactopya) and it’s a very scalable way to design scientific visualization. Combined with kb-snapshot (model), spikeforest (controller), reactopya (view) it allows full integration of the flatiron pipeline. Now it’s time to build a strong well integrated system.

The ultimate goal is to implement all neural processing routines on the web and work with Jeremy to realize this dream. Break the boundary and make the data available anywhere everywhere. Let the web technology transform the way science is conducted. I bet CZI has similar vision.

Built-in Javascript functions

  • setInterval(fh, milliseconds)
  • new Date().toLocaleTimeString()

Built-in react functions

  • ReactDOM.render(element, document.getElementById(‘root’))
  • const element = (); #declare
  • React.Component doc