Cracow Training Event „Agile Bioinformatics for Agile Science” 03 - 08.02.2019

About the Workshop

During the course CONTRA ESRs will become familiar with Agile and project management and software development practices and tools useful in bioinformatics. First two days will be composed of half-day of lectures followed by half-day of practical exercises. Next two days will be dedicated for group projects strongly connected with previously acquired knowledge and skills. Last day will begin with summary of the course prepared by students who will present their achievements after 2 initial days of working in groups. At the end, necessary information and invitation to the next event will be announced. The work on projects will be continued after the event in a distributed fashion, peer reviewed, committee reviewed and presented on webinars.

Registration deadline: December 15th, 2018

Apply now!

Speakers & Tutors

Dr. John Quackenbush
Department of Biostatistics at the Harvard TH Chan School of Public, Biostatistics and Computational Biology at the Dana-Farber Cancer Institute

John Quackenbush is Professor of Computational Biology and Bioinformatics and Chair of the Department of Biostatistics at the Harvard TH Chan School of Public Health and Professor of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute. John’s PhD was in Theoretical Physics, in 1992 he received a fellowship from the National Institutes of Health to work on the Human Genome Project, which led him from the Salk Institute to Stanford University to The Institute for Genomic Research (TIGR) before moving to Harvard in 2005. John’s research uses massive data from DNA sequencing and other assays to model functional networks in human cells. By comparing networks between groups of individuals, he has found new drug targets, explored chemotherapy resistance, and investigated differences between the sexes. He has made pioneering discoveries about how the genetic variants work together to determine our traits. John has published more than 280 papers; his work has been cited more than 65,000 times. He has received numerous awards for his work, including recognition in 2013 as a White House Open Science Champion of Change. He is also the co-founder of Genospace, a precision medicine software company that was purchased by the Hospital Corporation of America in 2017.

Dr. Barbara Kalinowska

Barbara Kalinowska is an experienced bioinformatician with a strong background in biophysics. She obtained her Ph.D. from the Jagiellonian Univerisity in the field of computational biology, specifically in the protein structure prediction. The research she performed during her doctoral studies resulted in several publications and was presented on international events. While the master studies, she gained also experience in the laboratory work and the research on the photodynamic therapy of cancer.
Barbara joined Ardigen at the beginning of 2017 and since then she has broadened her practical knowledge in the field of the modern genomics. She participated in several projects focused on topics like CNV detection, CRISPR/Cas9 screening or single-cell RNA-seq data analysis.

Piotr Radkowski

A scientist and an experienced software engineer. With over a decade of experience working in IT industry as well as academia.
He developed passion for Life Sciences while working in Center for Medical Genomics – OMICRON, where he was responsible for entire computing infrastructure of genomics core, including: NGS data analysis, automatic liquid handling systems and creation of new bioinformatic pipelines.His recent endeavours focus on developing robust solutions for Life Science research and integrating cutting-edge computer technologies. Piotr is very passionate about information technology, constantly looking for new and exciting tools for creating elegant solutions.

Piotr Stępniak

Mr. Piotr Stępniak joined Ardigen in 2015 as Bioinformatics & Data Science Consulting Director. His collective 10 years of experience in academic and commercial bioinformatics projects include working with partners from universities, medical research institutions, cancer clinics and biotech companies. Piotr conducted bioinformatics research dedicated to biomarker discovery, enzyme redesign, drug discovery, as well as prediction of clinical events such as surgery complications and early brain metastasis. His role in shaping the scientific grounds of projects with partners and within the company as well as expertise spreading across Life Sciences, Data Science and IT was instrumental in creating a successful collaboration relationship with over a dozen partners ranging from academia, through emerging biotech companies, up to big pharma located in San Francisco Bay Area, Greater Boston Area and European Union.

Venue & Accommodation

The Cracow Training Event „Agile Bioinformatics for Agile Science” will take place in the Jagiellonian Center of Innovation, Life Science Park. It is located in the south-west of Kraków near the campus of the Jagiellonian University with convenient connection to the city center and ring road and the John Paul II Kraków–Balice International Airport.

Jagiellońskie Centrum Innowacji Sp. z o.o.
ul. Michała Bobrzyńskiego 14
30-348 Kraków

All Participants will be accommodated in the Vanila ApartHotel ( located close to venue.
The Vanila ApartHotel offers special rates to Cracow Training Event „Agile Bioinformatics for Agile Science” participants:

(1) the price of a single room + breakfast is 170 PLN per day,
(2) the price for two people in a double room + breakfast (x2) is 240 PLN per day.

Accommodation may be booked on the conference registration form. Additional nights before or after the CONTRA workshop can be booked through the online registration form.

Please note that the payment of the Guest House accommodation fee will be handled by the hotel directly.



    Package 1 – lectures and tutorial, 6 days (3-8.02), fee: 250 EUR
    Package 2 – lectures, 3 days (3-5.02), fee: 110 EUR

    All packages cover lunches, dinners, special dinner, coffee breaks and writing materials. Payment must be made to this bank account:
    Bank Account Name: ARDIGEN S.A.
    Bank Name: Bank PEKAO S.A.
    Bank Country: Poland
    Account Number:
    IBAN: PL25 1240 2294 1978 0010 7451 0909
    Title: CONTRA Name & Surname

    If your arrival/departure dates are different please inform before starting registration procedure.

    Travel information

    By plane: Krakow Airport – Balice (KRK) offers direct flights from main European cities.
    By train: The city also offers convenient direct railway connections with most of the larger towns in Poland, and Europe.
    By car: Many national roads and motorways intersect in Krakow, among others the A4 running directly from the German border.

    Tram and bus tickets
    Tickets can be bought at newsagents or ticket machines at bus and tram stops. Ticket machines can also be found in a number of buses and trams. Drivers can sell tickets as well, but please note: they only have multiple trip tickets valid for 60 min and concessionary tickets. In all these places you can only pay in cash.

    Ticket prices for all day lines and night lines:
    one journey for one person: 3,80 PLN (normal), 1,90 PLN (half-rate)
    24 h ticket: 15,00 PLN (normal), 7,50 PLN (half-rate)
    48 h ticket: 24,00 PLN (normal), 12,00 PLN (half-rate)
    72 h ticket: 36,00 PLN (normal), 18,00 PLN (half-rate)
    7 days ticket: 48,00 PLN (normal), 24,00 PLN (half-rate)

    For planning trips by public transport refer to:


    Local Organizers
    Barbara Kalinowska
    Bożena Milanović
    Piotr Radkowski
    Piotr Stępniak

    CONTRA Organizers
    Jens Lagergren
    Ewa Szczurek
    Iwona Zielińska


    If you have any questions, please contact


    H2020 MSCA-ITN-2017-766030

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