The Unit of Computational Medicine is involved in diverse educational efforts on bioinformatics, data integration, immunology and systems biology.
Those efforts span through national and international activities and events described in the following sections.
1] Graduate studies at Karolinska Institutet.
CompMed is involved in the PhD programs of Karolinska Institutet (KI) through two courses organised by David Gomez-Cabrero and Francesco Marabita and the active involvement of Gordon Ball. In the future we expect to generate new courses that reflect the Systems Medicine and Computational Medicine approaches developed within the unit.
Course 2570: Introduction to R statistical analysis for biologists. Since november 2012 CompMed has organised this course twice per year (6 course occasions by June 2015). This course was initiated due to the high demand for R programming learning stated by students of other PhD courses we have been participating. The idea of the course is that students will learn the basics of R through statistical applications and with the main idea of students becoming independently enough to expanding their R abilities by themselves. The course has been very positively evaluated in all occasions.
Link to course description: http://kiwas.ki.se/katalog/katalog/kurs/2031
Link to previous evaluations: http://doctoralstudies.org/twiki/bin/view/CMBEducation/CellbiologyGenetics/PastCourses
Course 2667: Practical course in microarray data analysis: mRNA, DNA-methylation and DNA arrays. Since May 2013 CompMed has organised this course once per year (3 course occasions by June 2015). During the first occasions were we organised the course 2570 on R students were suggesting the idea of having a second course on microarray analysis where they could further develop their applied programming skills. Similarly to 2570 the course has been very positively evaluated in all occasions.
Link to course description: http://kiwas.ki.se/katalog/katalog/kurs/1643
Link to previous evaluations: http://www.doctoralstudies.org/twiki/bin/view/CMBEducation/CellbiologyGenetics/PastCourses
Additionally, CompMed members has participated regularly in the following PhD courses as lecturers:
Epigenetics in Clinical Medicine (2601)
Link to the course: http://kiwas.ki.se/katalog/katalog/kurs/1934
Omics data analysis: From raw data to biological information (2523)
Link to the course: http://kiwas.ki.se/katalog/kursplan/show/1076)
2] Undergraduate studies at Karolinska Institutet.
CompMed will participate in the organisation of the Master’s Programme in Molecular techniques in Life Science and will be in charge of the organisation of the ”Elucidating human immune response using systems biology” module. Prof. Jesper Tegner and unit members Angelika Schmidt, David Gomez-Cabrero, Narsis Kiani, Francesco Marabita and Gordon Ball will be involved in the lecturing and hands-on.
3] International courses.
CompMed members are participating as lecturers in international graduate and undergraduate programs. A brief list is provided here:
3.1) Regular collaborations:
3.1.1) BioHealth Computing, Erasmus Mundus Program.
David Gomez-Cabrero has participated continuously since 2012.
Link: http://biohealth-computing.org
3.1.2) Master in Clinical Investigation, MSc, Universitat de Barcelona
David Gomez-Cabrero has participated continuously since 2012.
Link: http://www.ub.edu/web/ub/en/estudis/oferta_formativa/master_universitari/fitxa/C/M280D/index.html
3.2) Singular events:
3.2.1) Dynamic networks in system medicine session, at the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, Spain.
Narsis Kiani organised a session in the Summer School associated to the event.
Link: http://iwbbio.ugr.es/sessions_proposals.php
3.2.2) Biomedical Data Integration and Modeling in Translational Research Workshop.
David Gomez-Cabrero participated as a lecturer and also organised a hands-on on data-integration.
Link: http://mon.uvic.cat/bms/2015/05/20/339/
3.3) MOOC: Hector Zenil and Narsis Kiani are organising the following course: Information Theory and Network Biology. It is expected to be ready by the end of next year and will be distributed by the Sta. Fe Institute ComplexityExplorer (http://www.complexityexplorer.org).
Link: http://www.itbit.org/courses/information-theory-computational-biology/
4] Educational events.
Additionally to the regular courses CompMed is involved and/or organising events oriented towards students and raising awareness of bioinformatics challenges. Among them:
4.1 Casym Summer School. CASyM is a joint initiative of the European Commission, several European funding bodies, companies, researchers and clinicians aiming to develop a strategic roadmap for implementing Systems Medicine across Europe.
Link: http://febscasymsummerschool.com
Video Lectures from the Event
Introduction to the Summer School
-Topics available
Systems Biology of the Mammalian Circadian Clock: https://youtu.be/2EY_iL9fD10
Computational Tissue Engineering: https://youtu.be/LZlJ8NGPaXM
4.2 STATegra Summer School. STATegra is a EU funded project for the development of statistical methods and software for the integration of NGS and omics data. The STATegra has now generated several integration methodologies and a benchmarking dataset where up to seven omics data-types were obtained under a controlled experimental setting. During the STATegra Summer School we provided training to experimentalists and bioinformaticians in the analysis of multi-omics experiments.
Link: http://stategrasummerschool.com
Video Lectures from the Event
Introduction to the summer school:
– Topics available:
NGS introduction: https://www.youtube.com/watch?v=R3eCTh1VYto
RNA-seq introduction: https://www.youtube.com/watch?v=VqYLG2tp_YI
DNA Methylation introduction: https://www.youtube.com/watch?v=wUFnYIXEOpI
Single-Cell Through Time: https://www.youtube.com/watch?v=j8T3nbFD_Q4
Metabolomics: https://www.youtube.com/watch?v=cQJWKUsL5fg
Proteomics: https://www.youtube.com/watch?v=J2vlEtKeD6I
5] Conference and Workshop Organisation.
The Unit is also active in the organisation of topic-oriented research events as the following ones:
5.1 High-Throughput Omics and Data Integration Workshop. Barcelona, Spain, 13-15 February, 2013
5.2 Illumina 450K – DNA Methylation analysis in humans. Stockholm, Sweden, 27th August 2013
5.3 Smodia2014, Statistical Methods for Omics Data Integration and Analysis Crete, Greece, 10-12 November, 2014. http://smodia2014.com
5.4 Smodia2015, Statistical Methods for Omics Data Integration and Analysis Valencia, Spain, 14-16 September 2015. http://smodia2015.cipf.es
Finally, as active participation of future educational development at KI, David Gomez-Cabrero is part of the following commissions:
a. Member of the Steering Group for Cell biology and genetics PhD Program.
b. Ledamöter i Kurs- och programkommittén, Karolinska Institutet (from Sept. 2015)