CBB Information Meeting
KI Campus Flemingsberg 2021-04-29
12.15-12.55
This Zoom meeting will be recorded!
Agenda for today
• Welcome and Background from KI Perspective
• Maria Eriksdotter, KI Dekan Syd
• Welcome and Background from CIMED Perspective
• Annika Bergquist, CIMED Director
• Expressed needs
• Hannes Hagström, CBB Co-director
• Current plan for CBB
• Carsten Daub, CBB Director
• Activities Medical Image Informatics
• Birgitta Janerot, KI CLINTEC
• Discussion and questions
Welcome and
Background from a KI Perspective
• Maria Eriksdotter
• Dekan KI Syd
CIMED -
centrum för innovativ
medicin
• Organized under KI/Region Stockholm
• Financed by Region Stockholm with 80 MSEK/year
• Overall aim: To support clinical and translational research at Campus Flemingsberg
• Specific aims for 2021:
• To develop support structures for clinical research
• Actively participate in the build-up of CLINICUM and develop the local hub (CBB at Campus Flemingsberg)
• To develop processes in dialogue with KI and the hospital to support the use of
Project grant 74%
Strategic recruitments
4%
Clinical research months 9%
Infrastructure 10%
Operational costs
3%
2021
Distribution of CIMED funds 2021
Timeline
Questionnaire
• September 2020
• >90 group leaders of all the KI departments located at Campus Flemingsberg
• BioNut, CLINTEC, MedH, Dentmed, Labmed, NVS
• More than 60% of groups expressed additional need for bioinformatics or biostatistics
• More than 60% of groups declared having financial resources for such
support
Expressed needs for support
• More than 60% of groups expressed their need for bioinformatics or biostatistics while this need is covered for around 40% of
these groups.
• Around 10% and 20% of the groups have bioinformaticians or biostatisticians employed, respectively.
• Most of all groups currently have need of less than one full
time bioinformatics or biostatistics full-time equivalent (FTE) but rather up to 25% of an FTE.
• 70% of the groups express that their need for bioinformatics or
biostatistics is currently not met.
Themes from personal interviews
• Teaching of methods to junior researchers
• Short questions on basic principles, e.g.
• Which statistical test to use
• Power calculations
• Responding to specific reviewer questions
• Long-term connections with a single point of contact
• Increase subject matter knowledge in biostatisticians/bioinformaticians
• Increase method knowledge in clinical researchers
CBB Activities – Underlying principles
• CBB Activities are developed based on
• expressed need by the departments at Campus Flemingsberg
• available resources
• Current CBB activity plan is based on the interviews and questionnaire
• Plan will be adjusted as we learn what works well and what more is needed
• Your input is essential for CBB to design the most relevant activities
CBB Activities (1)
• Information hub for guidance
• Website
• collecting Bioinformatics and Biostatistics resources in Sweden
• answer the most asked questions
• Book consultation meetings with CBB experts
• Support for the early stages of the research process
• Help with grant applications
• How much Bioinformatics and/or Biostatistics do I need for my project proposal?
• What do I write about Bioinformatics and Biostatistics so it might convince the grant reviewers?
• Coordinate with available resources at Campus Flemingsberg
• With whom can I collaborate to address my Bioinformatics and Biostatistics needs?
• Can I employ a Bioinformatician or Biostatistician together with another group?
CBB Activities (2)
• Support recruitments
• Help writing open call texts to recruit Bioinformatics or Biostatistics staff
• Help with candidate selection and interviews
• Mentor program
• I want to employ a Bioinformatics/ Biostatistics but cannot supervise her/him
• CBB offers mentors for Early-Stage Researchers (PhD students/ postdocs)
• CBB might have to ask for financial contribution from the research group leader
CBB Activities (3)
• Office space and social networking
• Bioinformaticians and Biostatisticians can (once a week) sit in the same room to exchange about technical and conceptual questions
• Strictly following covid recommendations
• Education
• Seminars about Bioinformatics and Biostatistics concepts and methods
• Doctoral courses
• Seminar series/ invitation of guest speakers
CBB Activities (4)
• Computational resources
• Provide computer resources for temporary heavy computes
• Relationship to existing KI and national core facilities
• CBB complements existing KI core facility services
• Proximity at Campus Flemingsberg is important
• Relationship to CLINICUM
• CBB is the Campus Flemingsberg hub for the KI CLINICUM efforts
CBB Current status
• Steering group for 2021 in place
• Annika Bergquist
• Peter Stenvinkel
• Carsten Daub, CBB director
• Hannes Hagström, CBB Co-director
• Affiliate for August 2021
• 0.6 FTE (e.g. 3 * 20%) Bioinformatician
• 0.3 FTE Biostatistician
Contact CBB
• Website
• www.ki.se/cbb
• cbb@ki.se
Medical Image Informatics
Campus Flemingsberg
A community network and
collaborative infrastructure built on Campus Flemingsberg´s
multi-disciplinary Medical and Technology skills, Equipment, Training and Education
• NVIDIA DGX Servers
• Specialized state-of-the-art software for AI applied to medical imaging, DL and ML frameworks
• Placed in KI-IT Data Center
• Three-factor authentication(3FA)
• NetApps SSD Storage
•http://Smile.ki.se
Stockholm Medical Image Lab & Education (SMILE KI)
• 3D Theatre
• Mobile gammacamera
• MRI 3T – HIFU
•https://www.kth.se/en/jcmi
Jonasson Centre for Medical Imaging (KTH)
• Photoacoustic Imaging
• Preclinical and clinical Ultrasound systems
• MicroCT – miniPET
• Microscopes (STORM, Electrone…)
• 2-3D bioluminescence imaging
• Flourescence imaging
Preclinical Imaging Facility (PIF) at K Preclinical Laboratory (PKL)
Collaborations
IT at Karolinska Institute and
Karolinska
University Hospital
KI Department of Medical
Epidemiology and Biostatistics (MEB)
Analytic Imaging Diagnostics Arena
(AIDA)
The Swedish National
Infrastructure for Computing (SNIC)
NVIDIA MathWorks MedTechLabs SciLifeLab
Services
Medical Imaging Equipment and Support for Preclinical and Clinical Investigations
Technical Support for Medical Image Processing and Analysis Applications Infrastructure and Support for Artificial Intelligence
Academic courses Expert network Workshops
Seminars
Submitted questions
• Will CBB provide analysis support free of charge?
• No, except for short consultations <1 hour depending on availability
• Does CBB have a physical office?
• Currently no, aim is to provide this during 2022
• If I have money for a 30% bioinformatics position, can CBB be the employer?
• CBB currently does not employ personnel directly.
• CBB might consider direct employment in the future if this model is requested by several groups.
