System developer to the Data Science Node in Evolution and Biodiversity (DSN-EB)
About the workplace
Do you want to join us and contribute to developing an organization that, after more than 250 years, remains full of curiosity, and maintains a spirit of discovery and tremendous creativity?
The vision statement for the Swedish Museum of Natural History (NRM), is to be the research museum that leads the way as a platform and forum of exchange among researchers, science, and the public. We offer a dynamic environment where professionals from many disciplines and backgrounds work together and are committed to our responsibility to collect data, produce innovative methods, and provide results, all founded in collections-based research. Our scientific research and environmental monitoring cover different aspects of biodiversity, ranging from individual species to ecosystems, as well as diverse evolutionary patterns and processes, both in Sweden and abroad. At the NRM, the Department of Bioinformatics and Genetics (BIO) consists of 30 employees who conduct research, develop systems and applications, and manage national and international infrastructures. BIO is the home unit for innovative, interdisciplinary research on biodiversity and ecosystems and functions as a critical interface at the NRM for computational, biological, and environmental sciences.
The Swedish Biodiversity Data Infrastructure (SBDI, https://biodiversitydata.se/) is an e-infrastructure established in 2021 with its headquarters at the NRM. It provides data and a wide range of tools for mobilization, visualization and analysis. The SBDI consortium includes eleven research institutions across Sweden in support of open data and open science, that is, transparent, accessible knowledge shared and developed within collaborative networks. In practice, the SBDI provides researchers with unified and open access to biodiversity data guided by FAIR principles (Findable, Accessible, Interoperable, and Reusable). The SBDI is a highly collaborative endeavour, hosting the Swedish node of the Global Biodiversity Information Facility (GBIF), the major global infrastructure for biodiversity research, and developing its technical platform with the Living Atlases community (LA).
SciLifeLab, Science for Life Laboratory, is a national research infrastructure for molecular life sciences and is one of the government’s major investments in research infrastructures in Sweden. SciLifeLab’s overall vision is to enable ground-breaking, multidisciplinary research that would otherwise not be possible in Sweden, and to promote that the research leads to societal utility. SciLifeLab consists of ten technology platforms with activities at eleven different universities across the country. To increase visibility of its role as a national resource, in 2021, the SciLifeLab board established national sites at four universities outside the host universities in the capital region. The SciLifeLab Data Center is responsible for IT issues and research data management for SciLifeLab’s technology platforms and other SciLifeLab-organized programs and activities, such as the National Bioinformatics Infrastructure Sweden (NBIS) and the National Research Program for Data-Driven Life Sciences (DDLS).
The DDLS national program constitutes a 12-year initiative funded with a total of SEK 3.1 billion with the mission to accelerate data-driven research and capabilities within the life sciences. One of the four focus areas of the DDLS program is Evolution and Biodiversity. As part of the DDLS initiative, we are establishing a Data Science Node in Evolution and Biodiversity (DSN-EB), hosted by Uppsala University with staff in Uppsala (UU) and Stockholm (NRM). These staff members will form a central role in further strengthening the aforementioned infrastructures and to form a contact point between research projects and infrastructure accessibility.
We are now looking for a system developer with special expertise in evolution and biodiversity informatics to join the Data Science Node in Evolution and Biodiversity (DSN-EB). This opportunity would allow you to contribute your skills and experience towards enabling research on ecosystems and biodiversity, working on exciting development projects and cutting-edge research within your areas of expertise. This position is a unique opportunity to be part of the larger DDLS framework and to contribute towards establishing an internationally leading role for Sweden in developing data science excellence in biological research. Eventually this will accelerate the development of biological research capabilities in addressing pressing global issues, such as the global biodiversity crisis.
We believe in competence development and competence transfer and here you are offered the opportunity to build technical solutions in biodiversity informatics with Swedish and international colleagues in support of research. Key areas of research will include storage, processing, and availability of biodiversity data from DNA sequencing of natural populations, environmental samples (metagenomics and metabarcoding) and data from automated recording of image, sound, video or sensor data, and large-scale analysis using machine learning.
You will participate in SBDI development in coordination with developer teams. Your colleagues will include researchers, technicians, and a diversity of stakeholders from Sweden and abroad, sharing the mandate to improve infrastructure use and functionality.
You should be prepared to participate in conferences with SBDI and NBIS staff, consortium partners, and collaborators. Within SBDI, primary international collaborators are the Living Atlases (LA) community and the Global Biodiversity Information Facility (GBIF).
We need to reinforce our digital research infrastructure and are therefore looking for a developer experienced in open-source code in distributed environments (e.g., Git and GitHub) and Linux operating systems. You have a university-level education as a computer scientist or as a civil engineer with IT specialization, or you have equivalent knowledge from relevant experience. You should be familiar with Web Services (REST & SOAP), Spring Boot, Hibernate/ORM, JPA, Groovy, Grails, Maven and Gradle.
You have special expertise in evolution and biodiversity and will work closely with the SBDI and NBIS sysdev teams to facilitate interactions. Potential projects will involve integrated analysis of large biodiversity datasets and can include portals to published Swedish genomes and environmental samples, automation of data pipelines for publication of intraspecific biodiversity genomics data and integration to analysis and visualization tools, and development of AI- and ML-based tools for biodiversity data extraction from media files. You need good technical competence with container platforms such as Docker and DevOps, methods such as CI / CD (with tools such as Ansible and Jenkins) and Infrastructure as Code, as well as automation. Experience of system development in Java and JVM-based environments, RDBMS (e.g., MySQL, PostgreSQL), NoSQL databases (e.g., Cassandra, MongoDB) and search indexes (e.g., SOLR, Elasticsearch) is of particular interest.
It is an advantage if you have experience with Python or R, especially when managing data flows, and Agile methods. It is an advantage if you have experience with bioinformatic analysis of biodiversity data (e.g. population genomics or metagenomics).
This position requires a good written and spoken command of both English and Swedish communication in English will be particularly important in many of your interactions.
You are a driven, communicative, and results-oriented person, who can operate as part of a team in order to secure maximum returns on your efforts. This comes, in part, from your ability to respond to challenges in a flexible manner while working independently or within different working groups.
You take the initiative to suggest new working methods or new activities leading towards the desired results, and you have the ability to argue for and explain how the activities could be carried out.
You are able to plan, organize and prioritize your work effectively. The framework and organization schemes in which your work is produced will be readily accessible by team members, and you will be expected to follow established time project frames.
Successful accomplishment of tasks will depend on your ability to respect the perspectives, skills, and work-related objectives of your colleagues, with insight on how to share your knowledge and otherwise support them in ways that benefit the team.
Scope of employment
Form of employment: Permanent employment
Start date: according to mutual agreement.
The position is a full-time permanent appointment with a six-month probationary period.
Please note that the last year of the current funding period for DDLS is 2032.
Last application date: 16/01/2023
Reference number: 2.3.1-727-2022
Number of positions advertised: 1
08-519 551 29
Kevin Holston, Saco-S
08-519 540 92
Mattias Forshage, ST
08-519 540 49
The Swedish Museum of Natural History strives for gender balance and ethnic and
cultural diversity among its staff.