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BIOINFORMATICS
COMPETITION

 

The Department of Bioinformatics at Semmelweis University is announcing an academic competition to solve a bioinformatics problem.

The goal of the task is to identify the gene expression pattern involved with the chemo-resistance of cancer cell lines. The dataset dedicated for the task contains the gene expression data of cancer cell lines from a published data portal, treatment data for the cell lines and their outcomes (therapy resistant / therapy sensitive). During the analysis the competitor is expected to identify the genes, gene clusters involved with the resistance against (a) therapeutic agent(s) of their choices with supervised / unsupervised learning methods.

Applied solutions and tools may include:

  • any statistical method or artificial intelligence algorithm
  • MS Excel /SPSS
  • Galaxy platform
  • R statistical software packages
  • Python

Notes for the task:

  • The normalized gene expression dataset to be used for the task will be provided to the competitor after entry.
  • The dataset contains data of nearly 1000 therapeutic agents. Therefore, the analysis should be performed on one specific agent or on a narrowed subset of agents (e.g. MEK inhibitors, taxanes, etc.).

Application:

Competitors can enter the competition by sending their names and NEPTUN codes to  bioinformatika@med.semmelweis-univ.hu. Applicants will receive the input data via email.

Deadline for entry: 28 February 2022

Evaluation:
The solutions will be tested on an independent dataset and the work that proves to be the most accurate through validation will be the winner.

The submitted work must include:

  • the source code or algorithm of the solution
  • documentation (up to three A4 pages)

Deadline for submitting the work: 30th April 2022

Contact: Dr. János Tibor Fekete

e-mail: fekete.janos@med.semmelweis-univ.hu

tel.: +36 20 770 0513

Announcement of the results: 15 May 2022

Prizes:

1st placeparticipation at an international bioinformatics course or conference

2nd place: participation at a national bioinformatics course or conference

  • The first place winner is entitled to select an international conference (within the European Union), while the second place winner can choose a national (Hungarian) bioinformatics course listed on the website of Elixir Europe and Elixir Hungary, respectively:
  • The duration of the course should be no longer than 6 days.
  • The prize includes the registration fee for the course as well as the travel and accommodation costs in case of personal participation. (The accommodation should be no higher than a three-star hotel.) Online courses can be chosen too.
  1. We offer an excellent grade for the practical exam for students of the Clinical Bioinformatics course for the 1st, 2nd and 3rd place winners.

We wish all competitors successful work!

Prof. Dr. Balázs Győrffy and Dr. János Tibor Fekete