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curl-ier's Introduction

Bernt Popp

🔬 Human Genetics Researcher - Passionate about unraveling the mysteries of genetics and contributing to advancements in medical science.

🌐 Quick Links

📖 Background

I was born in a small Romanian town. My mother is a Transylvanian Saxon, and my father is Romanian. Nature, genetics, and the evolution of DNA, a thread that connects all life on Earth, have always captivated me. My interest in technology and computers began in the late 1990s with a family-owned computer, where I learned to code in Basic. During my medical studies, I discovered the field of human genetics, which provided a way to combine these interests. My journey in this field has been marked by pivotal moments, like securing my first DFG project, being honored with the "GfH-Promotionspreis" 2017, and the SYNLAB-award at EuroDysmorpho 2019, each milestone propelling me further into the exploration of genetic landscapes and bioinformatics.

💼 Professional Experience

  • Currently working at BIH Charité Berlin and LaborBerlin, focusing on rare diseases of neuronal development, rare tumors, and kidney diseases.
  • Senior Physician at Charité – Universitätsmedizin Berlin, Translational Research Area - Research Group "Hypertension and Molecular Biology of Endocrine Tumors" since 07/2022.
  • Previously Senior Physician and Head of the Genetics Outpatient Clinic at MVZ Dresden.
  • Specialist in Human Genetics at the Institute of Human Genetics, University of Leipzig Medical Center, and Deputy Team Leader Genetic Diagnostics - Clinical Genomics.
  • DFG Rotation Position at the Human Genetics Institute of the University Hospital Leipzig, working on the project "Exome Pool-Seq and systems biology approach to identify and characterize genes and networks in neurodevelopmental disorders".
  • Previously Resident and scientific-medical assistant at the Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.

🌱 Other Interests

Nature, science, and technology also play a big role in my personal life. I enjoy freediving, scuba diving, being in nature and I am a passionate photographer. Most recent hobby is finding fossil shark teeth around the world.

I love traveling and experiencing new things, trying to involve in local communities, cultures and citizen science.

🐋 Favorite Animals

Favorite animals: sharks 🦈, whales 🐋, and turtles 🐢.

Whales of Moorea Photographing a baby humpback whale in Moorea, French Polynesia.

Checking of Caretta caretta hatchlings and nests on Kefalonia Checking a nest of loggerhead sea turtles (Caretta caretta) for signs of hatchlings on the island of Kefalonia in Greece.

My first Megalodon tooth in Gainsville Very happy after finding my first Megalodon tooth in Gainsville, Florida.

🏆 Achievements

  • Spearheaded SysNDD, a robust platform for analyzing gene-disease relationships in neurodevelopmental disorders (NDD).
  • Established MorbidGenes, providing a monthly updated list of diagnostically relevant genes to advance genetic diagnostics.
  • Developed HNF1B-db, a dedicated database for HNF1B variant annotations.
  • Contributed to AutoCaSc, an automated variant curation system, showcased in a recent publication in Human Mutation.
  • Involved in Kidney-Genetics, a project dedicated to understanding the genetic underpinnings of kidney diseases, with comprehensive documentation.

👨‍💻 Coding Experience

  • Languages: R, SQL, Bash, Python, JavaScript, HTML, CSS
  • Technologies: Docker, GitHub, Nextflow, SnakeMake

🎓 Academic Background

  • Dissertation Dr. med. at the Institute of Human Genetics, University Hospital Erlangen, Title: "De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females" (summa cum laude), 11/2015 - 02/2013.
  • License as a physician after completing medical studies at the FAU Erlangen-Nuremberg, 11/2012.

📬 Contact

  • 📧 bernt.popp[at]charite.de | bernt.popp.md[at]gmail.com

Disclaimer: Any opinions expressed here are solely my own and do not reflect the views of my employer, funders, or their affiliates.

curl-ier's People

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curl-ier's Issues

Documentation Enhancement

Description

Enhance the documentation for curl-ier.js.

Details

  • Provide detailed explanations of each command-line argument.
  • Include examples covering a range of use cases to assist new users.

Expected Outcome

  • Improved clarity and comprehensiveness of the documentation.
  • Easier adoption and usage by new users.

Rate Limiting

Description

Integrate sophisticated rate-limiting logic in curl-ier.js.

Details

  • Consider scenarios where the script interacts with APIs having rate limits.
  • Implement rate-limiting logic to prevent hitting these limits.

Expected Outcome

  • Prevention of rate limit breaches when interacting with APIs.
  • More reliable and consistent script behavior under rate-limited conditions.

Refactor sendRequest Function

Description

Refactor the sendRequest function in curl-ier.js to enhance code maintainability and extend functionality.

Details

  • Split sendRequest into two functions, one for GET and another for POST requests, to achieve better separation of concerns.
  • Introduce a parameter or a configuration object to handle different HTTP methods beyond GET and POST.

Expected Outcome

  • Improved code readability and maintainability.
  • Easier extension and support for additional HTTP methods in the future.

Logging Mechanism

Description

Implement a more advanced logging mechanism in curl-ier.js.

Details

  • Explore the integration of logging libraries like winston or pino.
  • Aim for greater control and flexibility in logging levels and outputs.

Expected Outcome

  • Improved logging capabilities.
  • Enhanced control over log management and analysis.

Improve Header Parsing

Description

Improve header parsing in curl-ier.js to handle edge cases more effectively.

Details

  • Modify the header parsing logic to ensure it correctly handles cases where the header string might not have a colon or contains multiple colons.

Expected Outcome

  • More robust and error-resistant header parsing.
  • Prevention of potential runtime errors due to malformed headers.

Error Handling Improvements

Description

Enhance error handling in curl-ier.js, specifically in the shouldRetry function.

Details

  • Expand the range of HTTP status codes in shouldRetry to include 500 series (server errors).
  • Implement a mechanism for error logging and reporting for better monitoring and debugging, especially for production use.

Expected Outcome

  • More robust and reliable error handling.
  • Enhanced monitoring and debugging capabilities.

Feature request: Add Timestamp to Output Filename

Description:
To improve the organization and tracking of output files, it would be useful to include the current timestamp in the filenames. Currently, the output filenames follow the pattern hgmd-genes.ABCA4.html. Enhancing this to a format like hgmd-genes.ABCA4.2024-02-21.html would make it easier to identify when each file was generated, especially in cases of multiple runs or data updates.

Acceptance Criteria:

  1. The output filename should include the current timestamp in a readable format.
  2. The timestamp should be placed between the main filename and the file extension.
  3. The format of the timestamp should be standardized, e.g., YYYY-MM-DD.

Suggested Implementation:

  • Update the filename construction logic in the saveResponse function to include a formatted timestamp.
  • Ensure the timestamp is added before the file extension in the filename.

Feature request: make login optional

Description

Currently, curl-ier.js requires users to login for certain functionalities. This feature request aims to make the login process optional, allowing users to utilize the script without mandatory authentication when not needed.

Motivation:

  • Flexibility: Making login optional enhances the script's flexibility, accommodating a wider range of use cases.
  • User Convenience: Users who only require basic functionalities can skip the login process, simplifying their workflow.
  • Adaptability: The script becomes more adaptable to different scenarios where authentication may or may not be required.

Proposed Change:

  • Introduce a flag or parameter that enables or disables the login process.
  • Modify the script logic to bypass login-related functions when this option is active.
  • Ensure that existing functionalities remain intact and fully operational when the login is bypassed.

Possible Implementation:

  • A command-line argument (e.g., --no-login) could be added to disable the login requirement.
  • Conditional checks within the script to determine whether to execute login-related code based on this argument.

Impact:

  • This feature will not affect existing functionalities for users who require the login process.
  • It will provide a more streamlined experience for users who do not need authentication.

Feature request: Allow Setting Custom File Extension for Output Files

Description:
The curl-ier application currently saves all output files with an .html extension. To enhance flexibility and accommodate various data formats, it would be beneficial to allow users to set custom file extensions, such as .json, .xml, etc. This feature would enable users to specify the format of the data they are expecting in the response, making the tool more versatile.

Acceptance Criteria:

  1. Users should be able to specify the file extension when running the script.
  2. The script should save the output file with the provided extension.
  3. If no extension is specified, the script can default to .html.

Suggested Implementation:

  • Introduce a new command-line option, e.g., --extension or -e, for users to specify the desired file extension.
  • Modify the saveResponse function to use this user-provided extension when constructing the filename.

Use of Environment Variables

Description

Incorporate the use of environment variables in curl-ier.js for managing sensitive or environment-specific data.

Details

  • Utilize environment variables or a configuration file for API endpoints, keys, etc.
  • Ensure sensitive information is securely managed and easily configurable per environment.

Expected Outcome

  • Enhanced security and flexibility in configuration management.
  • Easier adaptation to different environments.

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