Effectiveness of vaccination can be estimated from post-vaccination data

Many countries have introduced HPV vaccination programs without establishing the baseline for HPV prevalence. Using prevalence of vaccine versus non-vaccine HPV types from a county where we had actual baseline data we made a reconstructed baseline. Methods were validated by computing the Bhattacharyya coefficient of divergence. Protective effectiveness where baseline data was missing could then be estimated using non-vaccine HPV type data to reconstruct the baseline.

 

Vaccine 1 May 2018  https://doi.org/10.1016/j.vaccine.2018.04.073

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Hands-on workshop in Hadoop/Spark/Flink

NIASC and SICS organised  hands-on workshop in Hadoop/Spark/Flink. Bellow is information about agenda, time, location and paricipants:
Date/time
September 29, 2016,  09:00
Location:
Karolinska Institutet
Alfred Nobels Allé 8, room: Takterassen – 4N (https://internwebben.ki.se/sv/takterassen-4n).
(From Arlanda Airport  take Arlanda express or airport bus or pendeltåg to Stockhom Central Station and then pendeltåg to Flemigsberg station. )
Huddinge
Sweden
AGENDA
– Welcome
– Create Accounts on SICS ICE Hadoop Platform
– Create Projects, Import Datasets, Share Datasets
– Introduction to Apache Hadoop
– Introduction to Apache Spark
– Introduction to Scala programming language
– Develop and Deploy Spark/Flink Programs on Apache Zeppelin
– End of Workshop
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Workshop on Nordic Big Biomedical Data for Action

Day 1 – (11:00 – 17:00) NORDIC big biomedical data

11:00 – 11:30    Arrival

11:30 – 12:30    Lunch

12:30 – 12:45    Davit Bzhalava – Welcome, introduction to the workshop and goals of the day 1

12:45 – 13:00    Joakim Dillner – NIASC and Nordic Big Biomedical Data for Action

Session 1:

Data privacy regulation, ethics and legal issues

13:00 – 13:40 Evert-Ben van Veen. The GDPR, balanced national legislation and exchange of data for research while still respecting national legislation.

13:40 – 14:00 Discussions

Session 2: Nordic Colorectal Cancer consortium – a use case for Synergy of NORDIC Big Biomedical Data Sources

14:00-14:25        Joakim Dillner– Overview of the Nordic CRC Project

14:25-15:50        Karin Sundström – Sweden Available resources and scientific interests of CRC Project

15:50-15:15        Frederik Trier Møller – Acquisition of consumer data, storage, content and possibilities for CRC studies.

15:15 – 15:30      Coffee Break

15:30 – 15:50      Miriam Elfström – NKCx, storage, content and possibilities for CRC studies.

15:50 – 16:15      Anu Jalanko – Finnish Biobanks – Available resources for CRC studies

16:15 – 16:40      Tõnu Esko – Estonian Genome Center, Large scale population genomics and possibilities for CRC studies.

16:40 – 17:05      Laufey Tryggvadóttir – Infrastructure and Potential Participation in Nordic CRC Poject.

17:05 – 17:30      E. Christina M. Wennerström – LABMED registry, storage, content and possibilities for CRC studies.

 

Day 2 (09:00 – 17:00) Infrastructures and emerging technologies for processing big biomedical data

09:00 – 09:15 Davit Bzhalava Welcome, summary of day 1 and goals of the day 2

Session 1: Data centers that could handle sensitive biomedical data in NIASC consortium

09:15 – 09:45     Antti Pursula – Tryggve: Nordic services for sensitive data.

09:45 – 10:15     Davit Bzhalava – Biomedical Computing Center at KI.

10:15 – 10:45     Jaakko Leinonen – ePouta infrastructure

10:45 – 11:15     Joel Hedlund – Tryggve2 planning: scopes and roadmap.

11:15 – 11:45     Discussions

 

12:00 – 13:00      Lunch

 

Session 2: Emerging technologies for storing and processing big biomedical data

13:00 – 13:30 Jim Dowling – HopsWorks

13:30 – 14:00 Maarala Ilari – Big Data processing for genomics.

14:00 – 14:30 Petri Klemelä – Delivering bioinformatics software as virtual machine image

14:30 – 15:00 Discussions

 

15:00   – 15:15   Coffee Break

Session 3: Session algorithms for processing big biomedical data:

15:15 – 15:35 Piotr Bala – PCJ BLAST.

15:35 – 15:55 Raul Vicente – Deep learning for computational biology.

15:55 – 16:15 Davit Bzhalava – Bioinformatics for viral metagenomics.

16:15 – 16:35 Bartlomiej Wilkowski – The Biobank Register: A search system for big biomedical and biobank data.

16:35 – 17:00 Discussions

18:00 Dinner

 

Day 3 (09:00 – 12:00)

09:00 – 09:30 Eero Pukkala – The Nordic Occupational Cancer Study (NOCCA), storage, content and possibilities for CRC studies.

Session 1: Software sustainability

09:30 – 10:00 Mike Croucher – Is your research software correct?

10:00 – 10:30 Radovan Bast – CodeRefinery

10:30 – 11:00 Discussions

Session 2: Plans for the future

11:00 – 11:30 Joakim Dillner – Future work and upcoming big data calls

11:30 – 12:00 Discussions and planning for the future.

12:00 – 13:00 Lunch and Departure

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Save the date for Workshop on Nordic Big Biomedical Data for Action Nov 28-30

NIASC will organise a workshop on “Nordic Big Biomedical Data for Action”. Please save the date: November 28 (starting at 12:00) – November 30th (ending at 12:00), 2016, Stockholm, Sweden.

The workshop will be 2 days lunch-to-lunch and will cover topics from computing infrastructures and bioinformatics algorithms to legislation and ethics.

For more information please write to Davit Bzhalava, davit.bzhalava@ki.se.

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Davit Bzhalava

davit

I have a PhD degree in bioinformatics. Currently, I am a NIASC-employed bioinformatician at the Swedish node and the coordinator of NIASC bioinformatics team. I mainly work on developing parallel bioinformatics pipelines and algorithms for analysing metagenomic datasets generated from Next Generation Sequencing technologies.

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