Software Engineering Internships 2018-09-12T11:09:54+00:00

SOFTWARE ENGINEERING INTERNSHIPS

WE AIM HIGH

You are curious, eager to learn, studying as  software engineer, computer scientist or related field. You don’t mind a good discussion on the best solution and are continuously looking for the latest technology and features, all in the interest of the best results. You are a true team player and want to share your knowledge and learn from others.

YOUR ROLE

As a software engineering intern in our team, you will have a chance to work on exciting problems and technologies that can make an impact on a patient’s well-being. You will have the chance to apply Save what you learned in a real-life setting, as well as learn bleeding-edge technologies and platforms.

Multiple positions are/will become available based on your experience and interests, so feel free to apply even if you don’t see a direct fit with the open positions below.

Workflow execution systems for immunogenomics

Starting date: Any time between October 2018 and February 2019

High-throughput DNA sequencing of immune repertoires generates large amounts of data. A life scientist interested in extracting information from this data typically needs to apply several processing and manipulation steps, often involving different software tools chained together in a workflow (sometimes also called a pipeline).

As a relatively new field, there is no established best practice for immunogenomic workflows: in this internship you will investigate and possibly build an efficient and scalable workflow execution system for immunogenomics.

The internship will include the following activities:

  • State-of-the-art survey
  • Hands-on comparison of various workflow management systems on real immunogenomic data
  • Depending on the length of the internship, prototype implementation of an analysis pipeline for high-throughput DNA analysis of immune repertoires

YOUR PROFILE

Required qualifications

  • Working towards a BSc. or MSc. in Computer Science, Software Engineering or related disciplines

  • Familiarity with docker containers

  • Proficiency with an object-oriented programming language, preferably (but not necessarily) Python

Desirable experience

  • Familiarity with workflow execution or management system like Apache Airflow, Nextflow, Snakemake, etc.

Immunogenomic app in BaseSpace cloud platform

Starting date: Any time between October 2018 and February 2019

BaseSpace Sequence Hub is a cloud-based genomics analysis and storage platform that directly integrates with all Illumina sequencers. DNA analyzed with Illumina sequencers can be sent directly to the cloud, where it can be analyzed by a third-party application. The applications in the BaseSpace ecosystem are developed by third-party developers and range from simple visualization apps to computationally intensive data analysis pipelines.

The ImmunoGenomiX Platform contains a variety of modules for the analysis of DNA data related to the immune system, in particular the ImmunoGenomiX Explore module. The aim of the internship is to connect ImmunoGenomiX Explore to BaseSpace.

During this internship you will have the chance to learn about integration with SaaS platforms, authentication mechanisms, multi-tenancy and interaction with RESTful HTTP services.

YOUR PROFILE

Required qualifications

  • Working towards a BSc. in Computer Science, Software Engineering or related disciplines

  • Proficiency with an object-oriented programming language, preferably Python or Java

Desirable experience

  • Familiarity with docker

Dynamic plugins as containerized (micro)services for life science applications.

Starting date: Any time between October 2018 and February 2019

Good data stewardship is key to knowledge discovery and innovation. To generate value for a research community beyond the initial researchers, funding agencies are increasingly setting requirements for proper data stewardship of research data. Beyond proper collection, annotation, and archival, data stewardship includes the ‘long-term care’ of research data, with the goal that they can be found and re-used in downstream studies. To facilitate good data stewardship, a broad community of international stakeholders have developed the FAIR Data principles.

The high-throughput sequencing of immune repertoire, is increasingly applied in the development of tumor biomarkers and immunotherapeutics for cancers. As a relatively new field, most tools for the analysis and sharing of immunogenomic results do not follow FAIR data principles for good data stewardship.

During this internship you will have the chance to learn about FAIR data stewardship in the context of immunogenomics and Adaptive Immune Receptor repertoire (AIRR) sequencing experiments.

The internship will include the following activities:

  • Literature survey
  • Review of existing ontologies for immune repertoire sequencing data
  • Creation of an ontology for Adaptive Immune Receptor repertoire (AIRR) sequencing experiments
  • Construction of a FAIR data exporter for the analysis results of AIRR experiments

YOUR PROFILE

Required qualifications

  • Working towards a MSc. in Computer Science, Software Engineering or related disciplines

  • Familiarity with docker containers

  • Proficiency with an object-oriented programming language, preferably (but not necessarily) Python

Desirable experience

  • Familiarity with Service Oriented Architectures and microservices

FAIR data stewardship in immunogenomics

Starting date: Any time between October 2018 and February 2019

Good data stewardship is key to knowledge discovery and innovation. To generate value for a research community beyond the initial researchers, funding agencies are increasingly setting requirements for proper data stewardship of research data. Beyond proper collection, annotation, and archival, data stewardship includes the ‘long-term care’ of research data, with the goal that they can be found and re-used in downstream studies. To facilitate good data stewardship, a broad community of international stakeholders have developed the FAIR Data principles.

The high-throughput sequencing of immune repertoire, is increasingly applied in the development of tumor biomarkers and immunotherapeutics for cancers. As a relatively new field, most tools for the analysis and sharing of immunogenomic results do not follow FAIR data principles for good data stewardship.

During this internship you will have the chance to learn about FAIR data stewardship in the context of immunogenomics and Adaptive Immune Receptor repertoire (AIRR) sequencing experiments.

YOUR PROFILE

Required qualifications

  • Working towards a MSc. in Computer Science, Software Engineering, Bioinformatics or related disciplines

  • Ability to read and understand scientific publications

  • Familiarity with semantic web technologies

Desirable experience

  • Proficiency with an object-oriented programming language, preferably (but not necessarily) running on the JVM (e.g. Java, Scala, Kotlin)

Open Application

Starting date: To be agreed with the student

Good data stewardship is key to knowledge discovery and innovation. To generate value for a research community beyond the initial researchers, funding agencies are increasingly setting requirements for proper data stewardship of research data. Beyond proper collection, annotation, and archival, data stewardship includes the ‘long-term care’ of research data, with the goal that they can be found and re-used in downstream studies. To facilitate good data stewardship, a broad community of international stakeholders have developed the FAIR Data principles.

The high-throughput sequencing of immune repertoire, is increasingly applied in the development of tumor biomarkers and immunotherapeutics for cancers. As a relatively new field, most tools for the analysis and sharing of immunogenomic results do not follow FAIR data principles for good data stewardship.

During this internship you will have the chance to learn about FAIR data stewardship in the context of immunogenomics and Adaptive Immune Receptor repertoire (AIRR) sequencing experiments.

YOUR PROFILE

Required qualifications

  • Working towards a BSc. or MSc. in Computer Science, Software Engineering, Bioinformatics or related disciplines

  • A curious, inquisitive mind

  • A proactive attitude, and willingness to learn new technologies

  • Proficiency with an object-oriented programming language, preferably Python or Java

Desirable experience

  • Familiarity with docker

LOCATION

INTERESTED?

If you need more information about this job opportunity or are already excited to get on board, mail or call Alvise Trevisan (Chief Technology Officer) at a.trevisan@enpicom.com or +31 6 149 64 730. We look forward to hearing from you.

ENPICOM is a young, dynamic and expanding biomedical software development company. We use computational biology to build solutions that truly matter and improve people’s lives and health.

Originally setup in 2015 to create tailored computational solutions for life science, but since 2017 also on a mission to bring innovative products to the market in support of the development, guidance and monitoring of immunotherapies. Our first product under development is a T-cell receptor and B-cell receptor repertoire analysis platform.

ENPICOM has a strong focus on developing bleeding edge technology, combined with a passion for the well-being of people. Quality, creativity and self-development are our top priorities. We believe in a good work-life balance. We offer flexible working hours, flexibility in organizing your work and an employee stock ownership plan.