Detailed information about the course

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Organic Programming: Functional Programming Beyond Scripting (an Effective and Practical Approach)


Summer 2019, 5 days

Lang EN Workshop language is English

In collaboration with the CUSO Doctoral Program Ecology and Evolution

Rachel Korn, University of Fribourg
Dr Jose Manuel Nunes, University of Geneva


Dr Jose Manuel Nunes, University of Geneva


Most researchers have already been confronted with the need to extend the possibilities of some existing script or computer program. This need may be due to new techniques that produce more rich or detailed data, to the gathering of much larger data sets or to the wish of adapting existing methods to new contexts.In the simplest situations it is possible just to recode the data and use already existing software, but often this is impossible or inadequate.

This course presents a possible solution to such cases and shall open connections to the multifaceted potentials of computer science for biologists. It aims to counterbalance the participants’ competences in bioinformatics by addressing the following topics:

  • Basic concepts of programming/per se/(functional and imperative paradigms, time allowing also objects and functors)
  • Abstracting data types and drafting in pseudocode/prototyping and their use in
  1. Data manipulation and processing (manipulate file structure, extract target components, etc.)
  2. Handling of large datasets
  3. Analysis of various kinds of data (text, numeric, image, video...)
  • Reproducible and analysis and coding: a primer to elegant documentation and transparency
  • Data storage and access taking into consideration data life time and access

University of Geneva


Full attendance, active participation and possible examination


Reimbursements for CUSO StarOmics students

Train ticket, 2°class, half-fare from your institution to the place of the activity.
NO reimbursement for your meal expenses

Reimbursement form attached with original tickets has to be sent to the StarOmics coordinator Corinne Dentan at University of Lausanne, Centre Intégratif de Génomique, Le Génopode, 1015 Lausanne.

For any question concerning reimbursement please contact the CUSO StarOmics coordinator Corinne Dentan.


CUSO PhD students: through your MyCUSO account.

External participants (non-CUSO PhD students, post-docs, etc...): use the icon "registration" at top of page and the last gray box "non-CUSO student" ("personne hors myCUSO").

Priority is given to PhD students from the CUSO Doctoral Programs StarOmics (3 places) & in Ecology & Evolution (5 places).



Deadline for registration 01.06.2019
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