Epidemiology & Technology

Blog Archive

Parsing RIS and NBIB reference format files

books, antiquariat, shelf
When working with reference lists, RefMan/RIS and Pubmed NBIB format files cane be seen. RefMan/RIS files can be exported by Zotero and Google Scholar. NBIB has become the format when using "Send To >> Citation Manager" in PubMED. Here's how to parse the files using Pythoon Libraries We will use
October 23, 2024

CVAT Converting Attribute Annotations to CSV – v2

This is an update on my previous post - Version 1 Recently I started working with Glaucoma Images preparation for AI/CV applications. Computer Vision Annotation Tool (CVAT) was deployed locally and fundus images uploaded into an organizational project within CVAT. Each Image is being annotated as follows Exporting the Attribute
October 9, 2024

CVAT Converting Attribute Annotations to CSV

Recently I started working with Glaucoma Images preparation for AI/CV applications. Computer Vision Annotation Tool (CVAT) was deployed locally and fundus images uploaded into an organizational project within CVAT. Each Image is being annotated as follows Exporting the Attrinbute annotations I thought the best format would be the CVAT for
October 3, 2024

ODK Central get list of all projects and total submissions

September 20, 2024

CVAT Install behind Nginx Reverse Proxy and CSRF Mitigation

I recently installed CVAT on a local VM. CVAT uses docker and installs a local Traefik container within the VM. The docs give instructions on how to run it on domain with free SSL by LetsEncrypt, but these docs assume that SSL termination happens on Traefik reverse proxy. However, In
September 10, 2024

Stata and ML resources

ai generated, artificial intelligence, big data
Some links to Stata and ML resources Conference Articles / Presentations / Stata Journal Stata Blog Articles from 2020 Other Resources Seven Steps in developing a prediction model Source: Towards better clinical prediction models: seven steps for development and an ABCD for validation - PMC (nih.gov)
May 20, 2024

ODK Central Backup using Python

We have already seen how to get an access token using Python requests library for ODK central. Now, let us see how we can use that to download our backup file
October 6, 2023

ODK Central API Access using Python

ODK Central provides an API for interacting with the server as described in its docs. Here I will provide some sample code blocks for interacting with the API using pure Python. Logging in and getting an Access Token Logging in and getting an Access Token and using that access token
October 6, 2023

Libraries and packages for Flask Security, Auth etc

Security Plugins
August 31, 2023

Using FastAPI and Pydantic

To rapidly develop an API in python with data models that are validated easily and autogenerated OpenAPI / Swagger / ReDoc documentation, FastAPI its an excellent option. VENV Creation and Installation Creating an FastApi app instance and add HTTP Routes - Main.py Create an instance of FastAPI service. Add a
September 8, 2021