Data Centre

The SciLifeLab Data Centre provides the SciLifeLab platforms with services for IT and data management. We also work to facilitate the communication between SciLifeLab platforms, their users, and the research community, and develop databases and tools. The purpose is to maximize the scientific impact of SciLifeLab generated data and provide a good helpful IT environment for the SciLifeLab platforms and their users. The Data Centre strives to follow the principles of Open Science and to make the data generated at SciLifeLab FAIR.

Services: Systems for facility operations | Collaboration and communication systems | Facility IT planning meetings
Human data | Workshops and events | Contact Data Centre

Services

We have a number of services available to facilities, and some things are in development. Our aim is to provide better services for the facilities, and produce a supportive environment for you to be able to help your users. All our services are currently provided for free for facilities. Email us at datacentre@scilifelab.se for access.

Systems for facility operations

ORDER PORTAL

A web based system for facility communication with prospective users. We can provide you with an instance configured according to your own specific requirements. Try out a demo instance at orderportal.scilifelab.se, contact us or Per Kraulis directly.

PUBLICATIONS DATABASE

The Data Centre built and maintains the SciLifeLab Publications database where the results of research assisted by SciLifeLab facilities can be found. A second database was set up for publications of researchers and fellows affiliated with SciLifeLab.

DATA MANAGEMENT PLANS

We encourage SciLifeLab facilities to support users with data management plans. We provide templates and a software system to manage such plans, the SciLifeLab instance of the Data Stewardship Wizard.

FACILITY MANAGEMENT SYSTEM

A facility management system (scheduling, invoicing, pricing, operational management etc) has procured by KI and UU, Agilent Technologies iLab Operations Software was awarded the contract. The implementation process is ongoing at KI and UU.

SURVEY TOOLS

The online survey tool Typeform is offered to the facilities and administration. It allows to collect questionnaire responses from users/researchers. Email us for access.

DATA DELIVERY SYSTEM

This service is currently under construction. The primary goal of the delivery system will be to provide cloud based storage for data delivery for facilities and their users.

HOSTING SERVICES

The Data Centre can provide hosting of some services and data for facilities, and in specific cases also for research groups. In most cases, the hosting will require a Docker image of the service, but we may also be able to host e.g. Shiny apps. Please fill in and send the service request form to datacentre@scilifelab.se for inquiries.

Collaboration and communication systems

CONFLUENCE

Confluence is a tool for team collaboration. It can be used to share and edit documents, manage tasks and project plans, and much else. Visit our Confluence guide for a quick overview of the system and how to get started.

NEXTCLOUD

For sharing files we provide you with a Nextcloud solution, all granted projects will be able to use this Dropbox style file sharing option for their files and data. See Nextcloud user guide. Log in using your scilifelab.se email or contact datacentre@scilifelab.se to get an account.

PROJECTPLACE

A cloud based system for project planning and storing documents, made available through agreement with UU, and approved also for storage of non-sensitive personal data.

SLACK

Slack is an online lightweight communication tool. Anyone with an email address that ends in scilifelab.se, scilifelab.uu.se, bils.se or nbis.se can immediately register themselves in the SciLifeLab Slack workspace. Anyone else: request an invite by emailing the Data Centre.

SCILIFELAB FORUM

The SciLifeLab Forum is good for more substantial, permanent reference information that is still easy to update. It is a public Discourse instance. Sign up using the blue Sign Up button at the top. See Guide to getting started.

Facility IT planning meetings

The Data Centre has a mandate from the SciLifeLab board to express the voice of SciLifeLab units towards host universities, SNIC and other parties for issues concerning IT and data management, and to promote better coordination of the data infrastructure of life sciences in Sweden.

As a part of this work, we will host meetings on a regular basis to meet with the facilities, so you can talk to us directly about your current IT, systems or data management needs.

We will follow up on these meetings by meeting SciLifeLab management, as well as SNIC, to present and discuss what you tell us and work to get the decisions and the funding to concretely address your needs, in synergy with the needs of all SciLifeLab units. Your input is invaluable and there will be many other ways for you to interact with us to improve IT and data handling in SciLifeLab.

Service request form

As a way of documenting and tracking your IT/data needs we have a Service Request Form to be used.  It can be brought to us at one of the meetings or sent to us by emailing datacentre@scilifelab.se.

Download
SHARE AND EXPLORE DATA

SciLifeLab Data Repository

The SciLifeLab Data Repository, powered by Figshare and maintained by the Data Centre, is a repository for publishing any kind of research-related data, e.g. documents, figures, or presentations.

Learn more
RESPONDING TO THE COVID-19 PANDEMIC

National COVID-19 Data Portal

The Data Centre maintains the Swedish National COVID-19 Data Portal. The aim of the portal is to provide information, guidelines, tools and services to support researchers in utilising Swedish and European infrastructures for data sharing.

Swedish COVID-19 Data Portal

How can SciLifeLab help you to publish your human data?

If you are a researcher at a Swedish academic institution working in SciLifeLab’s areas of activity, you can get help from the SciLifeLab Data Management support team with publishing your human data and managing access requests or alternatively with setting up an access request system in your own safe environment.

Read more

Workshops and events

The Data Centre regularly organizes workshops and events on IT and data management for SciLifeLab facilities, researchers and fellows.

Past events

  • Reproducibility and Data Reuse in Life Science
  • Data Set Excavation Event
  • Data Management for Human Genomics
  • Open science workshop
  • GDPR webinar
  • Linked Data Workshop

2020/2021: SciLifeLab AI seminar series

SciLifeLab AI Seminar Series, launched by SciLifeLab Data Centre, combines scientific highlights from SciLifeLab-affiliated researchers and invited experts on the general topic of AI applications in Life Science. The SciLifeLab AI Seminar Series will be held virtually on Zoom and videos will be published openly after the seminars at the SciLifeLab YouTube channel.

Read more

Contact SciLifeLab Data Centre

If you have questions regarding data management, systems or data access contact the Data Centre using datacentre@scilifelab.se. For other inquiries, please see the general SciLifeLab contact page.

Johan Rung
Head of Data Centre
Per Kraulis
System development team leader, data engineer
Hanna Kultima
Data manager, coordinator
Senthilkumar Panneerselvam
Systems developer
Ina Odén Österbo
Systems developer
Linus Östberg
Systems developer, system administrator
Ola Spjuth
Uppsala University
Professor, AI coordinator
Anders Larsson
System administrator
Anna Asklöf
Data steward
Arnold Kochari
Webmaster
Katarina Öjefors Stark
Coordinator
Parul Tewatia
Data Steward
Liane Hughes
Data Engineer
Hamza Imran
Data Engineer
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