Developers’ Meeting?
The EuBIC Developers’ Meeting is organized each second year by the European Bioinformatics Community (EuBIC), an initiative of the European Proteomics Association (EuPA) for user-oriented bioinformatics.
This meeting is aimed at bringing together computer scientists and developers in the field of proteomics bioinformatics to discuss and work together in an open and constructive spirit. The program is split between keynote lectures and multiple hackathon sessions where the participants develop bioinformatics tools and resources addressing outstanding needs in the proteomics bioinformatics and user community. The 2020 EuBIC Developers’ Meeting was held from January 13th – 17th 2020 in Nyborg, Denmark. All bioinformaticians were invited to join this second EuBIC Developers’ Meeting.
Keynote recordings
All keynotes, including the introduction to computational mass spectrometry, were recorded and are freely available on YouTube:
Why attend the Developers’ Meeting?
By joining the Developers’ Meeting, you will gain experience in developing bioinformatics tools, build long-lasting international collaborations and participate in a dynamic peer-network. In turn, your contribution will help the community at large, making a concrete impact for users.
Keynote speakers
- Eric Deutsch (Institute for Systems Biology, Seattle, WA, USA)
- Ole N. Jensen (University of Southern Denmark, Odense, DK)
- Andy Jones (Institute of Integrative Biology, University of Liverpool, Liverpool, UK)
- Lydie Lane (Swiss Institute of Bioinformatics, CMU, Geneva, CH)
- Alexander Peltzer (Quantitative Biology Center, University of Tübingen, Tübingen, GE)
- Olga Vitek (Northeastern University, Boston, MA, USA)
Hackathons
During the meeting, participants will engage in the active development of novel achievements for mass spectrometry-based proteomics. This will encompass the creation of new tools, scripts, resources or any other collaborative project important for the field. A preliminary list of all hackathons can be found below.
Social event
No EuBIC event, without a social event! This year, we are visiting the Nyborg Destilleri. Registration for the social event costs €50 and includes a tour of the distillery and dinner (drinks not included).
Registration
Early Bird registration is open until November 28, 2019. General registration closes on December 23, 2019. The capacity of the meeting is limited to 50 participants.
Sponsors
The EuBic 2020 Developers’ Meeting is proudly supported by the European Proteomics Association (EuPA) and Novo Nordisk Fonden.
Become a sponsor?
Sponsoring the EuBIC 2020 Developers’ Meeting improves the visibility of your company. The EuBIC 2020 Developers’ Meeting will bring together leading international scientists conducting bioinformatics and computational proteomics research. As such, this forms a unique occasion in the field of proteomics bioinformatics to communicate the impact of your institution or your products to the meeting attendees.
Multiple sponsorship options are available. For sponsorship inquires or for more information, please contact us.
Contact information
Marie Locard-Paulet / Veit Schwämmle
eubic2020@rub.de
Social media
Follow EuBIC on twitter at @EuBIC_ms and tweet about the Dev Meeting with #EuBIC2020!
More info
Program
| Monday, January 13th, 2020 | |
| 13.00 14.00 | Registration |
| 14.00 14.15 | Welcome and meeting opening |
| 14.15 15.45 | Introduction to Computational Proteomics Brief overview on the field of computational proteomics targeting students starting their PhD in computational mass spectrometry or proteome bioinformatics. In the final part of the tutorial, we will briefly introduce OpenMS and pyOpenMS. |
| 15.45 16.00 | Coffee break |
| 16.00 16.45 | Keynote: Eric W. Deutsch Application of the Universal Spectrum Identifier |
| 16.45 17.30 | Keynote: Andy Jones Statistical considerations for determining PTM site localisation confidence, including discovery of rare or unusual modification types |
| 17.30 18.15 | Keynote: Olga Vitek Components of reproducible quantitative mass spectrometry-based research: a statistician’s perspective |
| 18.15 20.00 | Poster session with snacks |
| Tuesday, January 14th, 2020 | |
| 09.00 09.45 | Keynote: Alexander Peltzer Scalable, reproducible bioinformatics workflows using Nextflow & nf-core |
| 09.45 10.30 | Keynote: Ole N. Jensen Top-down and middle-down proteomics: experimental methods and computational challenges |
| 10.30 11.00 | Coffee break |
| 11.00 11.45 | Keynote: Lydie Lane Mining the dark human proteome using neXtProt’s SPARQLing tools |
| 11.45 12.30 | Short presentations of hackathon topics |
| 12.30 13.30 | Lunch break |
| 13.30 17.30 | Hackathon parallel sessions |
| Wednesday, January 15th, 2020 | |
| 09.00 12.30 | Hackathon parallel sessions |
| 12.30 13.30 | Lunch break |
| 13.30 17.30 | Hackathon parallel sessions |
| 18.00 … | Social event |
| Thursday, January 16th, 2020 | |
| 09.00 12.30 | Hackathon parallel sessions |
| 12.30 13.30 | Lunch break |
| 13.30 14.00 | Open EuBIC meeting |
| 14.00 17.30 | Hackathon parallel sessions |
| Friday, January 17th, 2020 | |
| 09.00 09.15 | Announcements |
| 09.15 10.15 | Hackathon reporting |
| 10.15 10.45 | Coffee break |
| 10.45 11.45 | Hackathon reporting |
| 11.45 12.00 | Meeting closing + poster prize |
| 12.00 14.00 | Closing lunch |
Important dates and deadlines
- Deadline for Project Proposal Submission: September 25th, 2019
- Announcement of Selected Projects: October 10th, 2019
- Registration Opens: October 10th, 2019
- End of Early Bird: November 28th, 2019
- End of Registration: December 23rd, 2019
- Dev. Meeting: January 13-17th, 2020
Registration fees
| Early bird | Early Bird EuPA member | Regular | Regular EuPA member | |
| Student | €100 | €75 | €150 | €112.50 |
| Academic | €150 | €112.50 | €200 | €150 |
| Industry | €250 | €187.50 | €300 | €225 |
The registration fee includes:
– Access to all main Developers’ Meeting sessions (projects, poster session, social event)
– Receipt of all main conference materials
– Coffee breaks and lunches on all conference days
– WiFi
The registration fee does NOT include:
– Any travel costs
– Hotel accommodation
– Breakfast, dinner
– Social activities
Keynote speakers
PhD Eric Deutsch (Institute for Systems Biology, Seattle, WA, USA) is co-chair of the HUPO Proteomics Standards Initiative, defining standard formats for various types of proteomics datasets. These universal formats have greatly advanced the integration of different software tools into larger workflows.
Prof. Ole N. Jensen (University of Southern Denmark, Odense, DK) focuses on chromatin biology, epigenetics, and top-down/middle-down proteomics approaches to study co-existing post-translational modifications and their cross-talk in proteins. He will give an overview of the emerging computational challenges in the fast-evolving field of top-down and middle-down proteomics.
Prof. Andy Jones (Institute of Integrative Biology, University of Liverpool, Liverpool, UK) is professor in bioinformatics and director of the Computational Biology Facility at the University of Liverpool. Furthermore, he is chair of the HUPO Proteomics Standards Initiative. His scientific interests expand to the fields of proteogenomics and metabolomics and their integrated analyses.
PhD Lydie Lane (Swiss Institute of Bioinformatics, CMU, Geneva, CH) is co-director of Computer and Laboratory Investigation of Proteins of Human Origin (CALIPHO) and one of the driving forces behind the neXtProt reference knowledge base, an invaluable freely accessible resource for proteomics, transcriptomics, and genomics data. She has a vast experience in collecting, categorizing and interpreting different omics data.
Dr. Alexander Peltzer (Quantitative Biology Center, University of Tübingen, Tübingen, GE) is one of the founders of the nf-core project: A community initiative for creating reproducible, standardized best-practice omics workflows. The project has gained significant attraction both amongst various institutions in the life sciences and in commercial settings, where research and development teams aim to shift complex analysis workflows between various types of infrastructure.
Assoc. Prof. Olga Vitek (Northeastern University, Boston, MA, USA) is the major player in defining and applying statistical methods in quantitative proteomics. With her team, she works towards keeping high standards with respect to statistics and its application in the computational MS community.
Hackathons
- Batch XIC and spectra extraction in ThermoRawFileParser (by Vladimir Gorshkov, Niels Hulstaert, Yasset Perez-Riverol)
- How can we best use Cytoscape for proteomics data analysis? (by Nadezhda T. Doncheva, Marc Legeay)
- Mapping proteins to functions: method and benchmark development (by Bart Mesuere, Pieter Verschaffelt, Henning Schiebenhoefer)
- Online spectrum identification validation by comparison to predicted/experimental spectra (by Mathias Wilhelm, Tobias Schmidt, Patroklos Samaras)
- Simulating a quantified phosphoproteome for software benchmarking and algorithm development (by Marie Locard-Paulet, Veit Schwämmle, Vasileios Tsiamis)
- Formation of spectral libraries by representative spectra (by Lukas Käll)
Full abstracts at github.com/EuBIC/EuBIC2020/issues.
Venue and travel
Venue
Hotel Storebælt
Østerøvej 121
5800 Nyborg
Denmark
Travel
We recommend using this website when planning your travel between airport and venue:
– Travel information: https://www.rejseplanen.dk/webapp/index.html?language=en_EN
– Getting to Nyborg: detailed description
Tickets
Tickets for the train from Copenhagen Airport can be bought online in advance on www.dsb.dk/en/, but not on the train. Alternatively, you can buy tickets for the bus on global.flixbus.com.
Travel grants
The following travel grants are available for the Developers’ Meeting:
EuPA
- €500 / applicant, maximum 5 applicants
- Requirements:
- Junior scientist: Max 7 years since Master/PhD (student status to be proven)
- Submission of an abstract for the Developers’ Meeting
- Application:
- Applications, including abstract, student status (and status of EuPA membership, if applicable) should be sent to eubic2020@rub.de and the EuPA Secretary (viviana.greco@unicatt.it).
- Deadline for application is December 23rd, 2019.
- Priority will be given to EuPA members and based on the relevance of the abstract, on gender balance, and on the seniority of the applicants. Awardees will be identified by a selection commission composed of the local organizers, combined with representatives from EuPA.
- Travel cost receipts, including the original invoices, and certificates of attendance at the Developers’ Meeting are needed in order to document and justify the final grant payments.
- For any question, please contact the organizers.
APMA (Austria)
- €350 / applicant
- Requirements:
- PhD/Master student, PhD degree ≤ 2 years ago (confirmation of enrolment)
- APMA membership fee paid
- Application:
- Short CV and motivation statement
- Accepted abstract as first author for the conference
- Amount will be bank-transferred according to travel cost receipts after proof of attendance
- Applications should be sent to office@apma.at with the subject line “EuBIC Developer’s Meeting – Travel Grant”.
- Deadline for application is Nov 30, 2019. (Decision on funding will be made by Dec 15, 2019)
SFEAP (France)
- €500 / applicant, maximum 1 applicant
- Requirements:
- SFEAP member
- Application:
- For other requirements see General conditions for awarding of our grants
For general questions, contact us at info@eubic-ms.org.
Organizing committee
Main organizers
Marie Locard-Paulet
Novo Nordisk Foundation Center for Protein Research
Blegdamsvej 3
2200 København N / Denmark
marie.locard-paulet@cpr.ku.dk
Veit Schwämmle
Protein Research Group
Department for Biochemistry and Molecular Biology
University of Southern Denmark
Campusvej 55
5230 Odense M / Denmark
veits@bmb.sdu.dk
Co-organizers
Wout Bittremieux
University of Antwerp
2020 Antwerpen / Belgium
wout.bittremieux@uantwerpen.be
David Bouyssié
Institute of Pharmacology and Structural Biology (CNRS)
205 route de Narbonne
31077 Toulouse / France
bouyssie@ipbs.fr
Viktoria Dorfer
Bioinformatics Research Group
University of Applied Sciences Upper Austria
Softwarepark 11
4232 Hagenberg / Austria
viktoria.dorfer@fh-hagenberg.at
Ralf Gabriels
VIB-UGent Center for Medical Biotechnology
A. Baertsoenkaai 3
9000 Gent / Belgium
ralf.gabriels@vib-ugent.be
Dominik Kopczynski
Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V.
Otto-Hahn-Straße 6b
44227 Dortmund / Germany
dominik.kopczynski@isas.de
Alessio Soggiu
Dipartimento di Medicina Veterinaria
Universita Delgi Studi di Milano
Via Celoria 10
20133 Milano / Italy
alessio.soggiu@unimi.it
Julian Uszkoreit
Medizinisches Proteom-Center – Medical Bioinformatics
Ruhr-Universität Bochum
Centre for Clinical Research
Universitätsstr. 150D
44801 Bochum / Germany
julian.uszkoreit@rub.de
Bart Van Puyvelde
Department of Pharmaceutics
Ghent University
Ottergemsesteenweg 460
9000 Gent / Belgium
bart.vanpuyvelde@ugent.be
Sander Willems
Department of Pharmaceutics
Ghent University
Ottergemsesteenweg 460
9000 Gent / Belgium
sander.willems@ugent.be
Previous Developers’ Meeting
In January 2018 the first-ever EuBIC Developer’s Meeting was held in Ghent, Belgium. More information can be found on the official site. The proceedings of this event, including a description of the different hands-on hackathon sessions, were published in the Journal of Proteomics: