CDAC Code Catalog

This lists code that is publicly available from CDAC.

Last revised: 2024-07-12

Table of Contents

• MISC
• ICU
• SLEEP
• DELIRIUM
• ENGINEERING
• EEG

MISC

• cdac_google. No description provided.
• Physionet2018_Challenge_Submission. The code and trained models that were submitted for the official winning entry of the Physionet 2018: You Snooze You Win challenge
• Covid19_Respiration. Code to analyze AirGo and other ICU signals data for Covid-19 patients.
• covid_acuity_score. No description provided.
• NLP_GUI. No description provided.
• tensorizer. No description provided.
• ECG-Philter-DeIdentification. No description provided.
• bdsp-core.github.io. CCNL / BDSP in progress
• plot-ecg. No description provided.
• interrater_analysis. inter rater analysis
• ELUCID. No description provided.
• CCI_SOFA. code to compute CCI and SOFA scores
• mbw-zettelkasten. No description provided.
• Omega. No description provided.
• Noise-in-Diagnosing-Epilepsy. Code and data to reproduce results in our paper about noise in the diagnosis of epilepsy
• Noise_in_Diagnosing_Epilepsy. Code and data to reproduce results in our paper about noise in the diagnosis of epilepsy
• EHR-phenotyping-NAX. No description provided.

ICU

• cdac-burst-suppression-data. Variability in Pharmacologically-induced Coma for Treatment of Refractory Status Epilepticus
• eeg_multitask_embedding. No description provided.
• ICU-Sleep. Code, Datatables, Tools related to ICU-Sleep trial.
• SAH_DCI_Prediction_EEG. The repository contains the implementation for automated prediction of delayed cerebral ischemia after subarachnoid hemorrhage from EEG
• SOFA. computing the Sequential Organ Failure Assessment score
• icare-dl. Predicting Neurological Outcome in Comatose Patients after Cardiac Arrest with Deep Neural Networks
• pkpd-causal-matching. No description provided.
• VE-CAM-S. No description provided.
• IIC_DTR. No description provided.
• time-varying-causal-inference-simulation-tutorial. No description provided.
• VE-ICANS. Code for the VE-ICANS research project
• ICANS-forecasting-after-CAR-T-cell-therapy. MATLAB Code for the CAR-T project
• delirium-nlp-colaboration. No description provided.
• MOCA. This is the repository to store the code related to the MOCA project.
• ABIEE. No description provided.
• Rapid_IIIC_Labeling_GUI. No description provided.
• Rapid_IIIC_Labeling_GUI_MultipleEEGs. GUI for rapid labeling of segments from multiple EEGs, and instructions for preparing data for these labeling tasks
• kimchi_delirium_2019. No description provided.
• ICU_EEG_Neuro_Prognosis. No description provided.
• DeliriumToDementia_CausalSurvivalAnalysis. No description provided.
• MGHNursingCAMsDataset. No description provided.
• IIIC-IRR. Code to reproduce figures in “Interrater Reliability of Expert Electroencephalographers Identifying Seizures and Rhythmic and Periodic Patterns in EEGs”
• icare-dl-lstm. No description provided.
• SOFA-LR. SOFA-LR: a logistic regression based improvement on the SOFA score that accommodates missing data
• E-CAM-S. Code and data to accompany “Physiological Assessment of Delirium Severity: The Electroencephalographic Confusion Assessment Method Severity Score (E-CAM-S)”
• Burst-Suppression-Segmentation. Code to automatically detect periods of suppression in critically ill ICU patients.
• Hypothermia-EEG. No description provided.

SLEEP

• sleep_staging_2000pts. No description provided.
• ecg_respiration_sleep_staging. No description provided.
• SleepBreathing-DL. develop multi-task model that can classify stages, apneas, arousals based on respiration signal.
• AirGo_SleepStaging. Code and Data related to aim ‘Sleep Staging with AirGo’
• noiselight. noise and light in the ICU analysis
• AirGoSleepPyT0-. AirGo repo for PyT0 version
• sleep_research_io. convenient function that format (sleep) biosignals data to common h5 format. used for ICU-Sleep and SleepLab data.
• spindle_detection. No description provided.
• AirGo_ApneaDetection. Detecting Apneas from AirGo (and additional) signals
• BrainAgeExercise. No description provided.
• Undiagnosed_Apnea. Undiagnosed Apnea in the ICU
• self_similarity. Computing self-similarity for high loop gain and central apnea analysis.
• respiratory_event_detection_wearable. This repo contains code, data, and models to detect apnea events from a wearable respiratory band with or without oxygen saturation signals, as described in:
• Auto_PSG_Respiration. automating respiration analysis for PSGs
• CAISR_might_be_junk. Complete AI Sleep Reporting
• ICU-sleep-vitals. This is a repository set up to create plots for vitals of all the patients in the ICU Sleep Cohort.
• sleep_eeg_age_norm. No description provided.
• sleep_general. General functions for sleep data, reserach etc.
• self-similarity-dev. self-similarity code development. For internal use.
• SleepEEGBasedBrainAge. No description provided.
• BrainHealthExercise_Dataset. No description provided.
• sleep_cognition. predict cognitive function from sleep using deep learning
• ecg_respiration_sleep_staging_icu. Repository for “Sleep in the Intensive Care Unit through the Lens of Breathing and Heart Rate Variability: A Cross-Sectional Study”
• Sleep-deidentification. No description provided.
• spindle_optimization. No description provided.
• sleep-outcome-prediction. No description provided.
• sleep_eeg_mri. Code for “Sleep EEG and MRI” project 2022.
• caisr_dev. caisr development, 2022
• CAISR. sleep analysis powered by AI.
• HIV-BAI. No description provided.
• outcome-oriented-sleep-staging. No description provided.
• sleep-conversion. This is the repository to store the code related to EDF to .MAT conversion in the sleep pipeline.
• BCH-Sleep-Step1. This is the repository set up to store all the code related to Step 1 for the BCH sleep pipeline.
• AFib-sleep-cognition. No description provided.
• koges_sleep_staging. No description provided.
• CAISR2. CAISR1+1
• meditation-sleep-brain-age. The code repository for the meditation and sleep EEG-based brain age project.

DELIRIUM

• rass_delirium_eeg_prediction. No description provided.

ENGINEERING

• Bedmaster-ICU-tools. Documentation and tools for the Bedmaster ICU project.
• CDAC_Data_Portal. No description provided.
• text-annotator. Annotator app to label freetext
• bedmaster_pipeline_code. pipeline - after deidentification portion
• streaming_pipeline_code. No description provided.
• Bedmaster-Patient-Matching. This is the repository for the Bedmaster Patient Matching Pipeline.
• general-scripts. This is a repository to store all the scripts for use cases that might be useful to many people in the CDAC lab.
• DailyUpdates. This is the repository to store the daily updates for the different pipeline that we are using at CDAC.
• dicom_deidentify. No description provided.
• ECG-deidentification-pipeline. No description provided.
• EEG-Archiving-Pipeline. Copy xltek from multiple xltek archives to LM4
• EEGNormalization. No description provided.
• EEG_Fuzzy_Patient_Matching. No description provided.
• Xltek_Annotation_Extraction. No description provided.
• Persyst_Spike_Detection. Detect annotation
• EEG-deidentification. No description provided.
• BDSPAWSScripts. This is the repository to store all the AWS Scripts related to BDSP.
• LabMeetingDemo. This is a repository that will contain the code for the lab demo.
• bdsp-opendata-registry. No description provided.
• GeneralScripts. This is the repository to store all the scripts that we use for our projects.
• Physionet_build_forked. BDSP Website - adapted from Physionet Website
• ECG_HD5_Plots. No description provided.
• bdsp.io_webapp. No description provided.
• delphi-deidentification. This is the repository to store all the code related to deidentification using Philter+.
• awesome-aws-research. A curated list of awesome Amazon Web Services (AWS) libraries, open source repos, guides, blogs, and other resources for Academic Researchers new to AWS
• bdsp-emr-tools. Tools for extracting EMR data for use in BDSP
• bdsp-license-and-dua. No description provided.
• bdsp-reports-search-web-app. No description provided.
• bdsp-boto3-example. No description provided.
• EEG-Archiving-Pipeline-BIDMC. This is the repository setup to store all the code related to Step 1 of the EEG Pipeline at BIDMC.
• bdsp_aws_athena_db_connection_code. This is the repository for getting started with connecting with AWS Athena.
• Harvard-EEG-Database-Tools. No description provided.
• aws-open-data-registry-browser. A browser for open-data-registry: https://github.com/awslabs/open-data-registry
• bdsp-reports-opensearch. all text reports search using elastic opensearch and deploy in AWS Beanstalk
• BIDS-EEG. No description provided.
• BIDS-Conversion. BIDS-Conversion
• BIDMCDatabase. This is the repository created to share sample code and examples for the Data Science Team to access the BIDMC database.
• BIDS_Conversion. No description provided.
• EEG-Indexing-Pipeline. This is the repository to store the code related to indexing all the EEG’s from MGH and BWH.
• Sleep-Indexing-Pipeline. This is the repository to store the code related to indexing all the Sleep PSG’s from MGH.
• medications_mgh. No description provided.
• philter-plus-deidentification. This is the repository to store the code related to deidentifying unstructured clinical data.
• MGB-Neurology-Reports-Deidentification. This is the repository to store all the code used to deidentify all the MGB Neurology Reports.
• BIDMC-EEG-Reports-Deidentification. This is the repository to store all the code used to deidentify all the BIDMC EEG Reports.
• natus2json. No description provided.
• aws-open-data-registry. A registry of publicly available datasets on AWS
• MGB-Notes-Deidentification. This is the repository to store all the code used to deidentify all the MGB Notes.
• Thunderpack. No description provided.
• IDEA_Platform_MGB. This is the repository to store all the code that I used on the IDEA platform.
• BDSP_BIDS_Conversion_withAnnotationStaging_from_XLTEK_raw. No description provided.
• epilepsy-algolia-sync. Epilepsy.Science
• BIDMC-Notes-Deidentification. This is the repository to store all the code used to deidentify all the BIDMC Notes.
• Imaging-Reports-Deidentification. This is the repository to store all the code used to deidentify all the MGB Imaging Reports.
• PHIlter-deID-pipeline-mbw-modified. modified version of PHIlter+ pipeline – brandon made this initially for ECG report deID
• Thunderpack_WranglingCode. No description provided.
• edfio. convenience function to write edf from python, e.g. from prepared data
• BIDS_EDF_to_BidsFormat_Conversion. No description provided.
• bdsp-sleep-data. general code for handling sleep data on BDSP platform.
• BIDS_Sessions_Creations. No description provided.

EEG

• IIIC_big_map. No description provided.
• AL_IIIC. No description provided.
• EEG_mulitmodal_sedation. No description provided.
• epilepsy-project. This is a repository that will contain all the information regarding the epilepsy project.
• IFCN6. This is a graphical user interface that allows spike annotations.
• EEG-Pipeline. No description provided.
• EEGReportsDeidentification. This is the repository to store the code related to the deidentification for Neurology Reports.
• spike-test-pilot-trial. No description provided.
• IIIC-SPaRCNet. No description provided.
• Seizures-and-Harmful-Brain-Activity. No description provided.
• EEG_Report_Wrangling. No description provided.
• IIIC-Frequency-Analysis. Calculates frequency, spatial extent, location, evolution, and other parameters for rhythmic and periodic EEG patterns
• SpikeNet1. No description provided.
• morgoth. No description provided.
• cyclops. No description provided.

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