Detailed information about the course

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Going Beyond Scripting Using Functional Programming


11-14 June + 15 July 2019

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

This activity includes creating a program that will be presented in the final session. The participants are asked to submit a project of some program that supports their own research (otherwise a project could also be provided by the tutor). The tutor will provide online help in order to have a complete, or at least a functioning, version of the program for the final session.


University of Geneva




Full attendance, active participation and presentation of the project in the final session.



Participants are expected to have a strong interest and some previous experience with scripting or programming, but knowledge of a specific programming language is not required. Familiarity with a textual interface (command line or terminal or bash shell) is expected. If you have followed Computer Skills for Biological Research you will find this activity as its follow-up extension to more computer intensive tasks.

Side note:

Old title of the course was Organic Programming: Using Functional Programming to Go Beyond Scripting (an Effective and Practical Approach)



11 - 14 June 2019 from 9:00 to 17:00 + 1 final session about 2 or 3 weeks later (the date will be a joint decision during the activity)


University of Geneva, Sciences II
4th floor, UA Computer Lab, room 419


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 12.05.2019
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