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Phil Snyder philerooski

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View change_sharing_scope.R
PROJECT_ID <- "syn12030321"
UDALL_USERS <- "syn18691020"
AT_HOME_PD_USERS <- "syn16786935"
get_users <- function(user_table_id) {
user_table <- as_tibble(synTableQuery(paste(
Compute MD5 hashes of files in a local directory or in an S3 bucket.
Outputs a CSV file with columns `path` and `md5`.
When computing MD5 hashes of objects in an S3 bucket, `path` corresponds
to the S3 URI.
import multiprocessing as mp
import boto3 as boto
import pandas as pd
import pandas as pd
import argparse
import hashlib
import re
import os
def read_args():
parser = argparse.ArgumentParser()
View neurolincs_gaps.csv
Experiment Well ObjectTrackID
AB-CS47iTDP-Survival A1 7
AB-CS47iTDP-Survival A1 11
AB-CS47iTDP-Survival A1 11
AB-CS47iTDP-Survival A10 4
AB-CS47iTDP-Survival A12 8
AB-CS47iTDP-Survival A9 5
AB-CS47iTDP-Survival B10 3
AB-CS47iTDP-Survival B9 7
AB-CS47iTDP-Survival B9 14
View duplicated_indices.csv
Experiment Well ObjectTrackID
AB-CS47iTDP-Survival D1 1
AB-CS47iTDP-Survival D1 2
AB-CS47iTDP-Survival D1 3
AB-CS47iTDP-Survival D1 4
AB-CS47iTDP-Survival D1 5
AB-CS47iTDP-Survival D1 6
AB-CS47iTDP-Survival D1 7
AB-CS47iTDP-Survival D1 8
AB-CS47iTDP-Survival D1 9
View mhealthtools_demo.R
cleaned_sensor_data <- mhealthtools:::preprocess_sensor_data(
window_length = 256,
sampling_rate = 100,
frequency_range = c(1,25),
time_range = c(1,9))
transformation <- transformation_window(
philerooski /
Last active Jun 7, 2018
Get PD Biomarker AUPR scores by task. Requires the original scoring code ``
from __future__ import division, print_function
import synapseclient as sc
import pandas as pd
import numpy as np
import argparse
import LDopaScorer
TRAINING_TABLE = 'syn10495809'
TESTING_TABLE = 'syn10701954'

Mounting an EFS Instance From an External Account

Only First time:

  1. Send Thaneer your AWS account ID and he will add you to the trusted entities for the IAM role that he has created.
  2. If you don't have one already, create an IAM user. Permissions aren't relevant since you will be switching roles as soon as you sign in as the IAM user, but you may want to omit any permissions so that you don't accidentally create an instance before switching roles.

Every time

  1. When you are signed in as an IAM user under your root account, go to this link, enter a display name, (pick your favorite color), and click "Switch Role"

AWS Batch Tips and Tricks

Working with AWS Batch works roughly like this:

​ Compute Environments > Job Queues ⊥ Job Definitions > Jobs

Meaning compute environments and job queues are configured independently of job definitions and jobs — though if you're going to create a job, you're going to need a job definition, and if you're going to create a job queue, it's going to need a compute environment to run within.

Job Definitions > Jobs

philerooski / sf12v2.R
Created Dec 7, 2017
Score a matrix of SF-12v2 responses and store to Synapse
View sf12v2.R
#' SF12v2 questionnaire scoring
healthSurveyId <- "syn10278768"
healthSurvey <- synTableQuery(paste("select * from", healthSurveyId))@values
questionCols <- names(healthSurvey)[12:23]
sf <- healthSurvey[c("recordId", "healthCode", "dataGroups", questionCols)] %>%
filter(dataGroups %in% c("beta_thalassemia", "myelodysplastic_syndrome", "myelofibrosis")) %>% na.omit()
sf12v2 <- function( X = NULL ) {
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