Detailed information about the course

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Going Beyond Scripting Using Functional Programming


11-14 June + 15 July 2019


In collaboration with the CUSO Doctoral Program StarOmics

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, the gathering of much larger data sets or the wish of adapting existing methods to new contexts. In the simplest situations it is possible to just 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 programming for biologists. It aims to raise the participants’ competences 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:
      - Data manipulation and processing (manipulate file structure, extract target components, etc.)
      - Handling of large datasets
      - Analysis of various kinds of data through the use of well defined data structures
    * Reproducible research in analyses and coding: a primer to elegant documentation and transparency
    * Data storage and access with respect to data life time and accessibility

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


2.5 ECTS


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


Marta Bellone
Phone: +41 (0)26 300 88 91

Registration Fees: 

Free for participants enrolled in the CUSO Ecology & Evolution and StarOmics doctoral programs.

Other participants: please contact the program coordinator at ecologie-evolution(at)


PhD students of the DPEE are eligible for reimbursement of incurred travel expenses by train (half-fare card, and 2nd class). Please send the original tickets along with the reimbursement form to:

 Marta Bellone 
Doctoral Program in Ecology and Evolution

 PER04 building
 University of Fribourg
 Rue Albert-Gockel, 3
 CH-1700 Fribourg

NO reimbursement of your meal expenses.

Regarding reimbursement of accomodation, please contact the coordinator of the doctoral program (ecologie-evolution(at) BEFORE the beginning of the course. NO reimbursement of accomodation without the agreement in advance of the course of the coordinator fo the doctoral program.


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 in Ecology & Evolution (5 places) & StarOmics (3 places).


Registration deadline is 12 May. Register via the website of StarOmics



Deadline for registration
Joint activity joint
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