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Python Machine Learning in Biology
July 20-24, 2020 (Greece)
Genetics and Genomics
IMPORTANT INFORMATION
We realise that, due to the COVID-19 virus outbreak, making travel arrangements during this time is difficult. Therefore, registration for this course is open, but it does not require payment at this moment. We will only receive payments once the outbreak has calmed down and travel restrictions have been lifted.
Course Overview
Genome-wide association studies have become increasingly popular to identify associations between genetic risk factors and phenotypic traits.
This introductory course is addressed to medical students, social scientists and biologists without formal training in the field. The aim of the course is to provide a guideline for conducting genetic analyses. In addition to the illustration of the standard GWAS process, we will also demonstrate how to perform functional enrichment and apply polygenic risk score (PRS) analysis in order to provide individual‐level scores of genetic risk.
A mix of theoretical background and hands‐on experience will walk students through a series of increasingly complex data manipulation and visualization tasks. These exercises will be based on PLINK, PRSice, and R, among others, which are commonly used, freely available software tools that are accessible for novice users.
LOCATION
Alexander Hotel
Gerakári, Municipality of Amari, 74 061
Rethymno
Crete, Greece
DATE
July 6th-10th, 2020
LANGUAGE
English
COURSE LENGTH & ECTS
35 hours on-site.
This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School and ForBio.
The recognition of ECTS by other institutions depends on each university or school.
PLACES
Places are limited to 20 participants and will be occupied by strict registration order.
Participants who have completed the course will receive a certificate at the end of it.
Instructors
Dr. Gerard Muntané
Universitat Rovira i Virgili / Universitat Pompeu Fabra
Spain
Dr. Juan Rodríguez
CNAG · CRG
Requirements
Graduate or postgraduate degree in any Biosciences discipline. All participants must bring their own personal laptop (Windows, Macintosh, Linux). Basic knowledge of programming (basic level) is required, you do not need any previous experience with genomics analyses.
All participants must bring their own personal laptop (Windows, Macintosh, Linux).
Program
Monday.
- Morning:
- Introduction to Unix and R (theoretical)
- The process of GWAS (Introduction, Study designs, genomic controls, LD, sample size, power)
- GWAS Catalog
- Afternoon:
- Getting the data and starting (SNP array genotyping)
Tuesday.
- Morning:
- Quality Control (QC) for GWAS
- Variant identification
- Population stratification
- HWE
- MAF
- Afternoon:
- Imputation (Michigan Imputation Server)
Wednesday.
- Morning:
- Basic association analyses
- Statistical tests (PLINK, multiple testing, binary or continuous phenotype, covariates, etc)
- Discovery and replication studies
- Gene-based analysis. Bioinformatic follow-up of results to explore functional mechanism (Pascal, Magnum, FUMA GWAS)
- Afternoon:
- Practical
Thursday.
- Morning:
- Annotation of Genomic Variants (LocusZoom, CADD)
- Use of summary statistics
- Afternoon:
- Genetic risk scores (LDSC, Heritability explained, PRS)
Friday.
- Morning:
- Wrap-up
- Hands-on training. Perform an association test from scratch
Fees
- Course Fee
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- Early bird (until April 30th, 2020):
- 530 € *
(424 € for Ambassador Institutions)
- Regular (after April 30th, 2020):
- 640 € *
(512 € for Ambassador Institutions)
- This includes course material, coffee breaks and lunches (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
- Course Fee + Accommodation Package
- {{content-1}}
- Early bird (until April 30th, 2020):
- 530 € * + 350 € = 880 €
(774 € for Ambassador Institutions)
- Regular (after April 30th, 2020):
- 640 € * + 350 € = 990 €
(862 € for Ambassador Institutions)
- This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
You can check the list of Ambassador Institutions HERE. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.org.
Discounts (see Funding below) are not cumulative and apply only on the fee.
We offer the possibility of paying in two instalments (contact the course coordinators).
Accommodation
If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village (take a look at the venue), in shared en-suite twin rooms, although you will only share rooms with other course participants. There is a possibility that the rooms will be mixed. If this is an inconvenience for you, and you would prefer to stay in an all-female or all-male room, please indicate so in the “Comments” field of the Registration form (below).
If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.
The Accommodation Package includes transportation from the centre of Heraklion to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. If you require transportation from or to Chania (the other city of Crete with an airport), please contact the course coordinator who can arrange it at an additional cost.
If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.
Alexander Hotel, Gerakári
Alexander Hotel twin room
Alexander Hotel, Gerakári
Alexander Hotel, Gerakári
Schedule
Course Schedule
Monday to Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
- 15:00 to 18:00 Lessons.
The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.
Accommodation Package Schedule
Sunday:
- 18:30 Meeting at Heraklion Archaeological Museum to take the bus to Gerakári.
- 20:15 Check-in at Alexander Hotel.
- 20:45 Dinner.
Monday to Thursday:
- 8:30 to 9:00 Breakfast.
- 20:30 Dinner.
Friday:
- 8:30 to 9:00 Breakfast.
- 18:30 Meeting at Alexander Hotel to take the bus to Heraklion.
- 20:15 Arrival at Heraklion Archaeological Museum.
Funding
Discounts
Former participants will have a 5 % discount on the Course Fee.
Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).
Unemployed scientists living in Greece, as well as PhD students based in Greece without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.
Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.
Organizers
Collaborators
Registration
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Transmitting Science started in 2012 to manage specialized courses and workshops we were already organizing within our own Partnerships. Up to date, we have already run more than 120 advanced courses in different topics related to Life Sciences.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.