Summary
The PhD School on Evolution in Computational Pangenomics took place at Villa Grumello in Como (Italy) from September 8, 2024 to September 12. The school has been supervised by Paola Bonizzoni (Univ. Milano-Bicocca), Gianluca Della Vedova (Univ. Milano-Bicocca), and Alexander Schönhuth (Univ. Bielefeld) and it has been a joint ALPACA-PANGAIA school.
The 2nd Summer School was originally scheduled for July 2024, organized by Pasteur Institute in France, but time and location have changed due to the summer Olympics in Paris.
Organization
The school has been organized by the University of Milano-Bicocca (Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, and Luca Denti) and by Fondazione Alessandro Volta.
Participants
A total of 23 participants attended the school, joining us from France, Italy, Germany, Denmark, Finland, Slovakia, and the United Kingdom. Regarding gender balance, it is noteworthy that two out of the five speakers and one out of the three school directors are female. However, only four out of the 23 participants are female.
Programme
According to the Grant Agreement, the plan has been organizing a 5-day event with 4 ETC with a provisional programme as follows:
Preliminary course topics: (i) Building and comparing recombination networks (P.Bonizzoni UNIMIB, 1 ECTS); (ii) Advanced Linear Programming (L.Stougie NWO-I, 1 ECTS); (iii) Cancer evolution (G.Della Vedova UNIMIB, 0.5 ECTS); (iv) Probabilistic and machine learning methods (T.Vinař UKBA, 0.5 ECTS); (v) Reproducible research (J.Kö ster, 0.5 ECTS); (vi) Innovation, entrepreneurship, and commercial exploitation (F.Perraudeau PENDULUM, 0.5 ECTS).
The school will include a multi-session hackathon where groups of participants will analyze pan-genomic data sets provided by non-academic partners (analysis leaders Z.Iqbal EMBL, F.Perraudeau PENDULUM, P.Bonizzoni UNIMIB).
Following the plan, the school started with a half-day hackathon, while the following days have been dedicated to lectures. Wednesday afternoon, after 15:30 we had an excursion and a social dinner. The lectures have focused on several topics in Computational Pangenomics. The lecturers have been:
- Manuela Sironi (Associate Professor of Genetics at the School of Medicine and Surgery at University of Milano-Bicocca)
- Evan Eichler (Professor of Genome Sciences and Howard Hughes Medical Institute Investigator)
- Dan Gusfield (Distinguished Professor Emeritus at University of California at Davis)
- Iman Hajirasouliha (Associate Professor of Computational Genomics at the Institute for Computational Biomedicine, Dept. of Physiology and Biophysics at Weill Cornell Medicine of Cornell University)
- Layla Oesper (Associate Professor in the Computer Science Department at Carleton College)
The speakers have been available to interact with the students, especially during lunches, coffee breaks, and the social events. Moreover the students have cooperated during the hackathon.
