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NordBioMedNet Summer School 2019 in Computational Biomedicine - Imaging, machine learning and precision medicine
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README.md

NordBioMedNet Summer School 2019 in Computational Biomedicine - Imaging, machine learning and precision medicine

Seili-2019 image

Seili-2019 is part of the "Open Educational Resources in Computational Biomedicine"* (OERCompBiomed) project conducted by the NordBioMed.org and funded by Erasmus+.

NordBioMed is a collaborative network in the field of Biomedicine(*) between the Universities of Turku, Eastern Finland (Kuopio), Bergen, Odense and Karolinska Institutet. The network was originally formed in 2013 to strengthen the individual biomedical teaching programs within the component universities and make them internationally more competitive by providing complementary activities from the partner universities. The network supports both student and teacher mobility, organises intensive courses and develops virtual online teaching and an information platform on the Open edX platform, supported by a GitHub repository. Links that redirects to the study programme pages of each NordBioMed partner universities can be found here.

Summer School Programme (preliminary)

Sunday, August 11

Arrival to Turku by plane, bus or train. NB! If you are planning to fly to Helsinki, reserve at least 3 hours to get to Turku by bus from the airport.

  • At 17.45 Get together in Turku riverside (Östra Strandgatan 66), and boat transportation to Seili island
  • Dinner at Seili
  • Welcome and presentation of the Summer School activities and projects (Lars-Arne Haldosen, KI Stockholm and Junior Mentors - names)
  • Check in and free time

Monday, August 12

07:45-08:30 Breakfast
08:30-09:15 Why are computational skills needed in biomedicine - relevance to uncovering disease mechanisms and for diagnostics (Arvid Lundervold, UIB, Bergen)
09:15-10:40 Bioimage informatics and machine learning (Pekka Ruusuvuori, Tampere University)
10:45-12:10 Prostate cancer - clinical aspects TITLE (Pekka Taimen, UTU, Turku)
12:15-13:15 Lunch
13:15-14:40 Review of pre-assignments - Jupyter notebooks on tools and data repositories (Arvid and yy)
14:45-18:00 Student work with group project (coffee break 16:30-17:00)
19:00 - Evening snack and Sauna

Tuesday, August 13

07:45-08:30 Breakfast
08:30-12:00 Workshop - image data analysis, e.g. using xx to analyse zz (Arvid and yy)
12:00-13:00 Lunch
13:00-14:25 Prostate cancer – molecular mechanisms TITLE (Leena Latonen, UEF Kuopio)
14:30-15:25 Ethics and genetic screening (with a focus on cancer) (Niklas Juth, KI Stockholm)
15:30-17:30 Workshop - ethics and genetics screening (16:00-16:30 Coffee break)
17:30-20:00 Student work with own project
20:00-20:30 Evening snack

Wednesday, August 14

07:45-08:30 Breakfast
08:30-12:00 Follow up discussions on ethics workshop (Niklas Juth)
12:00-13:00 Lunch
13:00-14:00 Guided tour Seili
14:00-18:00 Student work with group project (Break 16:30-17:00 with snacks) Network meeting
19:00 - Evening snack and sauna

Thursday, August 15

07:45-08:30 Breakfast
08:30-10:25 Deep learning models to recognize tissue types (Bjarne Thorsted, SDU, Odense)
10:30-12:00 EuroBioimaging (Pasi Kankaanpää, UTU Turku)
12:00-13:00 Lunch
13:00-14:25 Career opportunities outside academia - companies in bioimage informatics – Aiforia, Helsinki (SPEAKER)
14:30-15:30 Career opportunities outside academia - companies in bioimage informatics – Misvik, Turku (SPEAKER)
15:30-18:00 Student work with group project (Coffee break 16:30-17:00) Network meeting
19:00- Summer school dinner

Friday, August 16

07:45-08:30 Breakfast
08:30-10:30 Student presentations with feedback
10:30-10:45 Coffee break
10:45-12:00 Student presentations with feedback
12:00-12:30 Check out and transport to boat
Around 13.00 Departure to Turku and light lunch on board
Around 15:00 Arrival to Turku city centre and Goodbye!

Setting up your system

Follow the instructions at Setting up your system (setup.md) to get ready

Note: To access the course notebooks interactively without downloading any software we are planning to use Binder, see also BinderHub and try Jupyter without installing anything

Notebooks

The course is based on the Jupyter Notebook, a web-based framework for developing and presenting code-based projects (take a look at https://youtu.be/HW29067qVWk og https://youtu.be/2eCHD6f_phE for introductions to Jupyter Notebooks).

Throughout the course you will work with notebooks that contain various material and programming tasks. We recommend that you make a copy of our notebooks before you are editing them. In this respect you might adopt the naming convention my_[name_of_notebook].ipynb.

Test your environment and Get started

BEFORE the Summer School:

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SPONSORS

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