Summer School in Bioinformatics & NGS Data Analysis (#NGSchool2018) will be held 16-23 September 2018 in Lublin, Poland. In 2018, we'll focus on single molecule real-time sequencing & personalised medicine. The registration is open now (see below)! We'll publish detailed programme soon, so stay tuned!
For the first time, we'll organise:
- MinION hackatons: from sample to results
- #OpenScience projects in collaboration with Open Science Foundation
- and satellite meetings
#NGSchool is a summer school in bioinformatics, aimed at researchers in the early stage of their careers, while being open to strongly motivated applications with any background. Our goal is to close the gap in the field of genomics between Western and Central & Eastern Europe, and boost research & development (R&D) in developing countries. The upcoming edition - #NGSchool2018: Nanopore sequencing and personalised medicine will be focused on single molecule, long reads sequencing using Nanopore technology and precision medicine.
How many people will attend?
#NGSchool2018 will be attended by 60 participants (40 students and 20 lecturers). In the previous editions of the summer school (2016, 2017) we have received 290 applications in total from 42 countries. We expect even more applications this year.
- Rosa Fernández, CRG, Barcelona, ES
- Andre Kahles, ETH, Zurich, CH
- Nikolay Kulemin, Zenome, Moscow, RU
- Paweł Łabaj, MCB, Cracow, PL
- Stephan Ossowski, IMGAG, Tübingen, DE
- Fritz Sedlazeck, Baylor College of Medicine, Houston, TX, USA
- Fran Supek, IRB, Barcelona, ES
- Robert Vaser, University of Zagreb, HR
This year in addition to hands-on workshops and lectures, #NGSchool will host MinION hackathons. Portable, single-molecule sequencing is the technology of today and tomorrow. Its countless applications, especially in precision medicine, stimulate the imagination - sequencing can now reach beyond the sophisticated labs. We plan to undertake four parallel projects at #NGSchool2018:
- sequencing and de novo assembling the genomes of previously unsequenced organisms
- metagenomics of oral microbiomes including volunteers from the course, so you can sequence and analyse your own oral microbiome
- direct RNA-seq & de novo transcriptome assembly of non-model fish species
- and human genomics (depending on external funding)
Participants will be divided into small groups (~10 people) and each project will be assigned a mentor, an expert from the field. Students will conduct the whole experiment, starting from sample preparation, through sequencing and data analysis to report writing. We plan to meet daily for updates of every project progress, data analysis and troubleshooting. Importantly, sequenced genomes will be deposed in the public database and the reports and results will be published.
We will do sample prep in the afternoon, sequencing overnight and data analysis the next morning (in total 26 hours reserved). Our initial schedule divided by days:
- Theoretical introduction to Nanopore sequencing [3h] & Sample preparation and sequencing run overnight [3h]
- First batch of sequencing data ready, basecalling, QC, preliminary analysis [3h]
- Second batch of sequencing data ready, basecalling, QC, de novo genome assembly [3h]
- De novo genome assembly [4h]
- Gene prediction and functional annotation [4h]
- Report writing and data deposition to public databases [3h]
- Summary, team presentations [3h]
Mentors & organisers
Data analysis experts:
German Demidov, Center for Genomic Regulation, Barcelona, Spain
Alina Frolova, Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
Katarzyna Kędzierska, University of Virginia, Charlottesville, USA
Bogumił Konopka, Wroclaw University of Technology, Wroclaw, Poland
Maja Kuzman, University of Zagreb, Croatia
Maciej Migdał, International Institute of Molecular and Cell Biology, Warsaw, Poland
Adrian Odrzywolski, Medical University of Lublin, Poland
Registration will be opened from 3rd May to 30th June 2018.
You can register here. Please, secure enough time to fill out the form as some questions require considerable amount of thinking. Every year we receive several applicants per place, therefore we strongly recommend preparing your application well. You can read more about selection criteria here.
We are happy to announce that we received Visegrad+ grant from International Visegrad Fund, which means we can keep registration fee at minimum! Registration fee (€100) covers participation in all course-related activities, as well as, accommodation, meals and coffee breaks during the course. The registration fee can be waived depending on the personal circumstances of the applicant. In addition, a number of travel grants are available (the exact information will be announced shortly).
#NGSchool2018 will take place in Lublin - the largest city in southeastern Poland, with breathtaking Old Town baring amazing historic architecture and thriving cultural scene. The workshops, lectures and hackathon will be held at the Medical University of Lublin. We will have access to four fully equipped laboratories which will allow us to carry out the experiments in parallel. For computational analysis we will secure a dedicated cluster and provide access to high speed internet connection.
If you are interested in supporting #NGSchool or would like to learn more, please contact us directly. We are looking forward to initiating rewarding and lasting professional relationships.