CRASH COURSE ON NANOPORE SEQUENCING FOR MICROBIAL ECOLOGY
24- 29 September 2023, CNR-IRSA, Verbania, Italy
The ICME12 is a practical course addressed to 20 PhD students and early career researchers from all over the world, interested in Nanopore sequencing data for microbial ecology. The course focuses on:
- Practical experience in sequencing using Nanopore technology (MinIon)
- Bioinformatic analysis of Nanopore sequencing data
During the course, students will generate and analyze metagenomic data from DNA samples previously extracted and tested for the training activities. The course is hand-on training with a clear practical setting, preceded by theoretical activities. It will cover different analysis approaches including linux-based command line tools and online bioinformatic portal. The participants will be divided into groups of 5 members to work on specific assignments and they will have to present the working group results for comparison and discussion. On the first days participants will have to introduce themselved with a 3 minutes presentation, including the main research topic.
Daily Report – Available
Application and registration fee
Participants are selected based on their CV and motivation letter. No prior knowledge with bioinformatics is needed but familiarity with terminology and concepts is preferred. Application can be done by e-mail or by filling up the ICME12 registration form_CLOSED.
The registration fee is 380 euro/person and it includes the full participation to all the activities, and lunches, coffee breaks and the social evening. Accommodation and travel costs are excluded; however, a few travel grants will be provided upon request by the sponsorship. Travel grants will be announced on this web page.
NEW: practical info for accommodation in Verbania
Hereby a list of suggested places where to stay in Verbania. These are potential hotels that to our opinion could be suitable for the course. There is also a list of potential appartments, but consider that there are many other ones that you might find on AirB&B or other pages. In the document there is also a map where we circled the area that we find the most suitable to book places.
Important dates
15 July: Application deadline
By this date, applicants should send their CV Applications should send max 1 page CV and 1/2 page motivation letter or apply directly using the ICME12 registration form_CLOSED. In the motivation letter the candidate should explain: a) the reason to attend the crash course in Nanopore sequencing for microbial ecology; b) any experience in bioinformatics; c) the need of a travel grant, if not supported by its institution. CV and motivation letter are the basis for selection. You should convince the committee you need the course and you can contribute to its successful realization.
30 July Notification of acceptance
Candidates will be notified of being selected and will have to accept and confirm their participation. The waiting list scrolls down until 14 August.
9 September, deadline payment for the registration fees
The 380 euro registration fee includes all didactical material, with access to a shared folder, the CINECA cluster for the bioinformatics analysis, lunches, coffee breaks and social evening. Dinners, accommodation and travel expenses are excluded. The possibility of travel grant will be posted on this webpage. Please indicate in your application whether you are supported or not by your institutions.
24 September – 14:00 Beginning of the course. The course will start on Sunday 24/09 at 14.00. Participants should prepare 2-3 minute presentation about his/her research activities. The use of a personal computer with adapter socket and possibly extension cable is required.
Invited speakers
Dr. Mina Bizic is an environmental aquatic microbiologist of Serbian and Israeli origin. She completed her BSc in General Biology and MSc in Hydroecology and Inland Water Protection Belgrade, Serbia after which she worked at the Israeli Limnological and Oceanographic Research. She then pursued her PhD studies at the Max Planck Institute for Marine Microbiology (MPI-MM) in Bremen, Germany, where she completed her PhD in Environmental Aquatic Microbiology in the framework of the International Max Planck Research School for Marine Microbiology (IMPRS MarMic).
Presently, she is leading her own research at the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany. Her present work focuses on microbiomes of organic matter aggregates in aquatic environments, with a great focus on heterogeneity between individual particles, and non-classical methanogenesis with emphasis on photosynthesis-associated (oxic) methane production by phytoplankton.
Dr. Danny Ionescu is a molecular microbial ecologist of Romanian and Israeli origin. He completed a BSc in marine sciences and an MSc and PhD in environmental sciences, in Israel after which he conducted several postdoctoral studies at the Max Planck for Marine Microbiology in Bremen. Currently he is a researcher at the Leibniz Institute of Freshwater Ecology and Inland Fisheries. His main research interests include extreme environments, with a special affection to the Dead Sea, and the genomics and evolution of giant bacteria, such as Achromatium.
Andrea Franzetti received the Msc and Ph.D. in Environmental Sciences from the University of Milano – Bicocca, Italy in 2000 and 2007, respectively. He was “FEMS fellow” at the Ulster University (UK) in 2005/2006 and Visiting Research in 2012/2013 at Soderton University (Sweden). He joined the University of Milano Bicocca in 2008 as a research fellow and is currently associate professor of microbiology at the department of Earth and Environmental Sciences. His main scientific interests are the mechanisms and application of pollutants biodegradation in natural environments, and the ecological processes assembling the microbial community in extreme environments. He has published more that 60 papers on these topics in peer review journals.
Donato Giovannelli is a Microbial Ecologist, working on the microbiology of extreme environments and Entrepreneur. Since November 2021, he is Professor of Microbiology at the University of Naples “Federico II” and affiliated Scientist at the Earth-Life Science Institute, Tokyo, a Visiting Associate Research Professor at Rutgers University, USA and an adjunct scientist at the Institute for Marine Biological and Biotechnological Resources of the National Research Council of Italy (CNR-IRBIM) in Ancona, Italy, and a guest investigator at the Woods Hole Oceanographic Institution (WHOI), USA. He is also part of a new no-profit institute dedicated to exploring the origins and nature of consciousness, YHouse, located in Manhattan, New York, USA.
A member of Cineca will present the computing facilities hosting the bioinformatics analysis to be performed during the ICME12.
Tomasa Sbaffi is a post-doc at the Microbial Ecology Group at the CNR-IRSA- Institute of Water Research in Verbania. Her research activities regards microbial ecology/evolution of prokaryotes and microbial eukaryotes in natural/controlled environment, statistical methods to analyse community structure, synthetic communities, ecological functions, public good dynamics, theoretical ecology.
Organizing Committee
Several researchers and communicators contributed to the organization of the course: Ester Eckert, Alejandro Martinez, Emanuele Ferrari, Gianluca Corno, Laura Garzoli, Andrea Di Cesare – Molecular Ecology Group (MEG) of CNR-IRSA-Verbania | Grazia Quero, Manuela Coci – CNR-IRBIM- Ancona | M.Antonietta Buccheri – CNR IMM | Elena Panariello – Unina | Luigi Gallucci – Max Planck Institute for Marine Microbiology | Stefano Amalfitano – CNR-IRSA Roma.
Program and travel grant information
The detailed program will be posted on this page. With respect to the travel grants: we are working to obtain a few travel grants by sponsoring companies and institutions.
Location and practical information
The course will be held at the CNR-Institute of Water Research, in Verbania- Pallanza, Italy at the historical Villa De Marchi, on the shore of Lake Maggiore. The Course will start around 14:00 at the IRSA- Institute. Complete address is: LARGO TONOLLI 50, Verbania-Pallanza. Below some information how to reach Verbania Pallanza. If you take the Local Bus (trasporti VCO) from the train station, the final bus stop is located on the back of the institute and it is called PALLANZA.
Verbania by plane
Verbania’s closest airport is the Malpensa International Airport of Milan (MPX). It is located about 55 km South. Once you landed in Malpensa the best way to reach Verbania is to take a ALIBUS coach. They run every 2-3 hours, and the journey to Verbania Pallanza takes 1 hour. A different company organizing coach services from Malpensa is Comazzi. Both requires online reservation of the seats. Other closed airports are: Linate (110 km, LIN) and Orio al Serio– Bergamo (145 km, BGX). From these airports, the best way to Verbania is to take local transportation (city bus, coach) to Milano Centrale (train station) and from there catch a train (Trenitalia) from Milano Centrale to Verbania-Pallanza. The whole journey can take between 2 and 3 hours.
Verbania by train
Verbania station is on the Simplon Line, connecting Milan to Geneva, Basel and Zurich. Direct fast trains from many German, French, Belgian, and Dutch cities reach Milan through the Simplon and usually they stop in Verbania-Pallanza or Stresa. Trains from Milan Centrale and Milan Porta Garibaldi to Verbania or Stresa are scheduled every hour during daytime.Timetables and tickets availabe either on www.trenitalia.it (Italian Railways), on www.sbb.ch (Swiss Railways), or on the webpages of French and German Railways. From Milan Malpensa there is no direct train to Verbania: if you arrive there and you want to come to Verbania by train then you have either to go by train to Milan (40 minutes) or by bus to Gallarate (15 Minutes) where you can then catch a train to Verbania or Stresa.
If you stop in Stresa you can reach Verbania Pallanza by a coach service of SAF company or by boat of Navigazione Lago Maggiore. If you stop in Verbania-Pallanza the best way to reach Pallanza is a bus of VCO TRASPORTI (route Omegna Verbania ).
Verbania by Car
Verbania is served by the A26 Highway, as well as by the SS33 (Simplon National Road). We suggest you the highway. If you come from south follow direction Gravellona Toce and take the exit called “Baveno-Stresa”, then follow the indications Verbania (you will first have to cross the town of Feriolo). If you come from North (Motorway from the Simplon-Domodossola SS33 , or National Road SS34 from Bellinzona-Locarno ) follow indications for Milan. From Simplon suggested highway exit (if you take the highway) is “Gravellona Toce” direction Verbania-Pallanza. Free park are available outside the Institute.
Sponsorship
