Summary
The event took place on September 5–9, 2022 at Hasso-Plattner-Institut in Potsdam. The workshop was organized by Bielefeld University and held jointly with WABI 2022 and PANGAIA workshop.
The program (with total 2.5 ETC) covered topics foreseen in the ALPACA Grant Agreement which are:
Three half-days will be dedicated to scientific courses, one half-day to the soft-skills course. Other activities will include business meeting (afternoon of day 1), hackathon (afternoon of day 3), and problem sessions (evenings). The preliminary topics of the courses:
(i) Metagenome assembly and analysis (R.Chikhi IP, 1 ECTS); (ii) Latest pan-genome research trends (seminars by advisory board members, 0.5 ECTS); (iii) Soft-skills: Improving research impact with social media presence (P. Peterlongo INRIA, 0.5 ECTS), (iv) Peer Community in bioinformatics: a new approach to reviewing and publishing (C. Scornavacca, CNRS, 0.5).
Program
(Program on WABI website and in PDF)
Pangenome sequencing and analysisAll timings shown are Central Europe Summer Time (CEST) | |
|---|---|
| Monday, September 5 | |
| 10:10 – 11:10 | WABI Session on k-mer Sets |
| 14:00 – 15:00 | WABI Session on Succinct Data Structures |
| Tuesday, September 6 | |
| 8:50 – 9:50 | WABI Session on BWT-like Data Structures |
| Wednesday, September 7 | |
| 8:50 – 9:50 | WABI Session on Indexing Genomes |
| 11:30 – 12:30 | Leena Salmela Efficient solutions to biological problems using de Bruijn graphs |
| 14:00 – 15:00 | Knut Reinert Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries |
| and ALPACA business meeting (Alexander Schönhuth) |
|
| 15:20 – 16:20 | PANGAIA network meeting, part I (Paola Bonizzoni) |
| 16:30 – 21:30 | Social event Boat tour including dinner and drinks (register by email to jens.stoye[at]uni-bielefeld[dot]de) |
| Thursday, September 8 | |
| 8:50 – 9:50 | PANGAIA network meeting, part II (Paola Bonizzoni) |
| 10:10 – 11:10 | Camille Marchet Round table discussion: how to improve communication with your advisors, and a few other items about wellness at work |
| and Mathias Weller Peer Community in bioinformatics: a new approach to reviewing and publishing |
|
| 11:30 – 12:30 | Christina Boucher Computational Problems in Metagenomic Amplification |
| 14:00 – 15:00 | Erin K. Molloy Recent advances and open challenges in estimating evolutionary histories from low-homoplasy markers |
| and Rayan Chikhi Metagenome assembly and analysis |
|
| 15:20 – 16:20 | Paul Medvedev The theoretical analysis of sequencing bioinformatic algorithms |
| 16:40 – 18:00 | Open problems session (Travis Gagie) |
| Friday, September 9 | |
| 8:50 – 9:50 | Hackathon, part I (Rayan Chikhi) |
| 10:10 – 11:10 | Hackathon, part II (Rayan Chikhi) |
| 11:30 – 12:30 | Gene Myers High Fidelity Genome Sequencing: What have we been missing? |
| Closing remarks | |
Venue
Building H, Room 2.57, Hasso-Plattner-Institut (HPI), Potsdam, Germany
