MatchMiner: An Open-source Computational platform for Clinical Trials Genomic Matching

MatchMiner: An Open-source Computational platform for Clinical Trials Genomic Matching

The challenge of matching precipitant (patients) for cancer trials is not easy nor simple. The current methods for patient recruitment for clinical trials result in failure [5]. Our topic of the day MatchMiner is designed to help researchers overcome this challenge.

MatchMiner is an open-source computational platform with a specific focus on patient genomic profiles to precision cancer medicine clinical trials. It is intended for researchers with software development skills.

The project is developed by researchers at Dana-Farber Cancer Institute (DFCI) which is known as a comprehensive cancer treatment and research institution in Boston, Massachusetts, United States. It's also an affiliate of Harvard Medical School.

What is Clinical Trial Markup Language (CTML)?

The Clinical Trial Markup Language or (CTML) is a new standard that aims to make a new standard for structured clinical trial data.  

It is introduced by Ethan Siegel in his article "Making Clinical Trial Eligibility Machine Readable". Siegel is also one of the core researchers who developed MatchMiner.

Here are two examples captured from Siegel's article:

How does CTML look like? (src. Making Clinical Trial Eligibility Machine Readable)
How does CTML look like? (src. Making Clinical Trial Eligibility Machine Readable)

MatchMiner is formed of 3 parts:

  1. MatchMiner engine
    The engine is responsible for parsing structured clinical trial data. It follows the Clinical Trial Markup Language (CTML) Standard.
  2. MatchMiner API
    The API is built as an interface for the engine. It is built with Python3.6, uses Eve framework and MongoDB a NoSQL database engine for data storage.
  3. MatchMiner UI
    The MatchMiner UI is a front-end application that is built on top of the API. It's written in JavaScript (NodeJS 10.16.9) and uses AngularJS. It uses Gulp for building and deployment.

    MatchMiner UI offers user authentication, user roles management, and two modes: a clinical trial investigator mode, and oncologist mode.

How does MatchMiner work?

It uses patient records extracted from the electronic medical record (EMR) or electronic health record (EHR) systems and clinical trial data in Clinical Trial Markup Language standard.

The MatchMiner platform matches patient-specific genomic events to clinical trials, and makes the results available to trial investigators and clinicians via a web-based platform.
MatchMiner's mode (src, MatchMiner)
MatchMiner's mode (src, MatchMiner)

Data collection and trial matches with MatchMiner (src, MatchMiner)
Data collection and trial matches with MatchMiner (src, MatchMiner)

Features

  1. Open-source
  2. Complete API support
  3. Developer-friendly
  4. Extensible though plugins and extensions
  5. Well written documentation
  6. Command-line interface
  7. Elasticsearch support

Platforms

MatchMiner can be installed in any platform that has Python and NodeJS.

Technologies used

  • Python3.6
  • NodeJS
  • Eve Rest Framework
  • MongoDB
  • Angular Framework
  • Gulp
  • Docker

License

MatchMiner is released as an open-source project under Apache License 2.0.

Apache License 2.0 (src. GitHub)

Conclusion

Development-wise, MatchMiner follows a good design pattern to ensure a stable and fixable product. Splitting the engine from the user-interface is a good decision as well as proving a headless REST-API on top of the engine which allows developers to integrate it easily in their projects, or build their own applications on top of it.

It's an approach we rarely see from developers with research background as many tend to use old-school approaches to solve their research computational problems.

Resources

  1. Official Website: https://matchminer.org/
  2. MatchMiner: Documentation
  3. https://github.com/dfci/matchminer
  4. https://www.dana-farber.org/
  5. https://medium.com/matchminer/making-clinical-trial-eligibility-machine-readable-3fd3dffb9a8b
  6. https://medium.com/matchminer/clinical-trial-matching-at-the-dana-farber-cancer-institute-f4c57ac18ab0
  7. https://cancerres.aacrjournals.org/content/80/16_Supplement/3382
  8. https://blog.dana-farber.org/insight/2017/01/how-do-i-find-the-right-clinical-trial-for-me/
  9. https://www.hbs.edu/news/releases/Pages/matchmaker-wins-hbs-kraft-challenge.aspx

Photo by Anna Shvets from Pexels




Read more

8 طرق لمساعدة كبار السن على إدارة مرض السكري

8 طرق لمساعدة كبار السن على إدارة مرض السكري

إذا كنت من كبار السن أو كنت مسؤولاً عن رعاية أحد كبار السن المصابين بمرض السكري في نيوجيرسي، فقد يكون من الصعب إدارة الحالة بشكل صحيح. لحسن الحظ، هناك العديد من الطرق التي يمكنك من خلالها الحصول على المساعدة والدعم. 1- قم بإجراء تغييرات غذائية إن تناول نظام غذائي متوازن

By Hazem Abbas
10 نصائح لإدارة مرض السكري لكبار السن

10 نصائح لإدارة مرض السكري لكبار السن

كبار السن لديهم خطر أكبر للإصابة بمضاعفات مرض السكري. تشير تقارير الجمعية الأمريكية للسكري إلى أن واحدا من كل أربعة أشخاص يبلغون من العمر 65 عاما أو أكثر مصابون بمرض السكري من النوع الأول أو النوع الثاني مقارنة بمن تقل أعمارهم عن 65 عاما. ومن ناحية أخرى، قد تشكل إدارة

By Hazem Abbas
10 فوائد للبرمجة للأطفال: لماذا نتعلم البرمجة في سن مبكرة؟

10 فوائد للبرمجة للأطفال: لماذا نتعلم البرمجة في سن مبكرة؟

البرمجة هي نشاط ممتع متعدد التخصصات يشرك العقل ويحمل الكثير من الفوائد الضخمة للأطفال. على سبيل المثال، هل تعلم أنه يدعم إبداعهم وتفكيرهم المنطقي بالإضافة إلى قدرتهم على التركيز؟ فيما يلي قائمتنا المختصرة التي تضم أهم 10 فوائد للبرمجة للأطفال، بناءً على تجربتنا التجريبية والنتائج العلمية المتاحة. في جميع أنحاء

By Hazem Abbas



Open-source Apps

9,500+

Medical Apps

500+

Lists

450+

Dev. Resources

900+