Csaba Halmagyi Email & Phone Number

Cambridge, Cambridgeshire, United Kingdom

I am currently leading the software development team of the European Genome-phenome Archive. My main responsibilities are overseeing the design and implementation of ETL pipelines and APIs for the management, access control, transfer, and analysis of genetic data as well as the prioritisation of software development tasks in the team and providing guidance on technicalimplementations.#SpringBoot #Kubernetes #RabbitMQ

Hinxton, United Kingdom

I worked on the PDX Finder that brings together genomic, histopathological, and drug response data from Patient Derived Xenograft (PDX) models. PDX models are mouse strains engineered to propagate human cancers and are increasingly being used in clinical research to test new chemotherapeutic regimes and study drug resistance mechanisms.PDXFinder is a Spring Boot application that uses a graph database (Neo4j), integrates the National Cancer Institute Thesarus (NCIT) for data harmonization and has an admin interface for mapping and reporting.#Java, #SpringBoot, #Neo4j, #JUnit, #Gradle, #Travis, #Jenkins, #Git, #REST

Hinxton, England, United Kingdom

I was responsible for addressing technical challenges and overseeing the extension of the pdxfinder to include cell line and organoid models. Due to the large volume of the data we were replacing our ETL pipeline with Apache Spark. Our services were containerised and deployed through Kubernetes. https://www.pdxfinder.org#ApacheSpark #Python #Kubernetes #Docker

Cambridge, United Kingdom

I worked as a Clinical IT Integration Specialist for the Department of Haematology, University of Cambridge. My interest was in developing and implementing Open Source systems for Clinical Data Management. My OpenClinica related projects:ODIN: I developed a browser based, open source application that can import subjects, schedule events, do the mapping and import data from a CSV file to a target OpenClinica instance using the OC webservices. The mapping rules will be saved to a mapping file which can be reused. ODIN can also be used to synchronise data between two openclinica instances.Panogram integration: I integrated Panogram, a standalone Pedigree drawing tool based on the Phenotips platform, into OpenClinica CRF to allow clinicians to draw pedigrees online.Camfetch: I developed a custom javascript library to call our custom services such as Panogram or different lookup services. I added SNOMED-CT, Human Phenotype Ontology (HPO), ICD-10, NHS medication and Google Spreadsheet lookup services. Additionally I created usability solutions that suggest phenotypes for selected rare diseases and use the decode function to clinical code your data.Wordpress – CiviCRM – OpenClinica integrator: a wordpress plugin that allowed us to store participant information in a CRM system but store the participant’s clinical data in OpenClinica. Also worked on custom reports and the ability to let participants enter their own clinical data (using a wordpress page where the data points are migrated using the OC metadatas) without logging in to OpenClinica.#PHP, #PostgreSQL, #MySQL, #jQuery, #CiviCRM, #OpenSource

Debrecen, Hungary