Croissants and coffee
Conference agenda
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Monday 13 June
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Council of Group Leaders
14:00 - 17:30
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Tuesday 14 June
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Arrival & registration
09:00 - 09:45 -
Welcome speech
09:45 - 10:00Room: Kongresssaal / Salle des congrès
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Keynote lecture #1: Antonella Santuccione Chadha
10:00 - 10:40Sex and gender differences as a biological variant: the work of the Women's Brain Project.
Antonella Santuccione Chadha
Session Chairs: Franziska Singer & Santiago Carmona
Room: Kongresssaal / Salle des congrès -
Parallel session 1
10:50 - 11:50-
Genes & genomes
Navigating the rapidly expanding space of Genes and Genomes
Session chairs: Evgenia Kriventseva & Damian Szklarczyk
Room: Kongresssaal / Salle des congrèsOral presentations
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10:50 - 11:05
Reference genome-independent taxonomic profiling of microbiomes with mOTUs
Alessio Milanese (Group: Shinichi Sunagawa)
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11:05 - 11:20
Evol-Feat, a bioinformatics tool to map and explore evolutionary-functional correspondences of non-model arthropod genes
Livio Ruzzante (Group: Robert Waterhouse)
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11:20 - 11:35
Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression
Arianna Vallerga (Group: Luciano Cascione)
Poster pitches
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11:38 - 11:41
Evolution of gene expression in the chemosensory tissues of ecologically diverse fly species
Bastien Saint-Leandre (Group: Roman Arguello)
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11:42- 11:45
Integration and homologous comparison of bulk and single-cell RNA-seq in Bgee
Frederic Bastian (Group: Marc Robinson-Rechavi & Frédéric Bastian)
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11:46 - 11:49
OpenGenomeBrowser: A reusable database independent and scalable web platform for genome database management and comparative genomics
Thomas Roder (Group: Rémy Bruggmann)
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10:50 - 11:05
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Structural biology
Structural bioinformatics: innovative tools to address bio-macromolecular structure and dynamics
Session chairs: Andrea Cavalli & Maria Marcaida Lopez
Room: Vereinssaal / Salle des sociétésOral presentations
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10:50 - 11:05
Covalent Ligand Docking with Attracting Cavities
Mathilde Goullieux (Group: Olivier Michielin and Vincent Zoete)
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11:05 - 11:20
Structure and Plasticity of Indoleamine 2,3-Dioxygenase 1 (IDO1)
Ute Roehrig (Group: Olivier Michielin and Vincent Zoete)
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11:20 - 11:35
Investigating the critical amino acids differentiating POU5F1B from its parent OCT4
Anastasia Theodoropoulou (Group: Matteo dal Peraro)
Poster pitches-
11:38- 11:41
TBvar3D: Mycobacterium tuberculosis resistance variants mapped on protein structures
Erblin Asllanaj (Group: Torsten Schwede)
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11:42 - 11:45
SwissSimilarity 2021
Maïa Bragina (Group: Vincent Zoete)
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11:46 - 11:49
Benchmarking ligand structure prediction methods
Xavier Robin (Group: Torsten Schwede)
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10:50 - 11:05
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Systems biology
Standards, analyses and trends in systems biology
Session chairs: Enkelejda Miho & Daniele Tavernari
Room: Workshop 1&2Session description
Oral presentations-
10:50 - 11:05
MNXtools – a software tool to diagnose chemistry of metabolites and reactions in genome-scale metabolic networks
Marco Pagni (Group Vital-IT)
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11:05 - 11:20
OMA Annotation Pipeline
Sade Bates
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11:20 - 11:35
The super-enhancer landscape reflects molecular subgroups of adrenocortical carcinoma
Samuel Gunz
Poster pitches
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11:38 - 11:41
Interpretation of T cell states from single-cell transcriptomics data using reference atlases
Massimo Andreatta (Group: Santiago Carmona)
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11:42 - 11:45
CanIsoNet: A Database to Study the Functional Impact of Isoform Switching Events in Diseases
Tülay Karalulak (Group: Christian von Mering)
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11:46 - 11:49
CREMA: Automated modelling of genome-wide chromatin state in terms of local constellations of regulatory sites
Mikhail Pachkov (Group: Erik van Nimwegen)
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10:50 - 11:05
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_Ad hoc session: How to present SIB and its missions
Room: Workshop 5
Objective:
In this ad hoc session, you will learn how to present the SIB Swiss Institute of Bioinformatics and explain its missions, with practical examples.
Speakers:
- Maïa Berman, Team Lead, Communications
- Marie Dangles, Director, Public Relations, Communications, People & Culture & Resource Usability
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Lunch break
12:00 - 13:00 -
Parallel session 2
13:00 - 14:00-
Ecology, environment & agriculture
Ecosystems bioinformatics in ecology and agriculture
Session chairs: Natasha Glover & Guillem Salazar
Room: Workshop 1&2Session description
Oral presentations-
13:00 - 13:15
Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity
Anne-Florence Bitbol (Group: Anne-Florence Bitbol)
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13:15 - 13:30
A global survey of the contribution of ecological factors to rates of horizontal gene transfer
Marija Dmitrijeva (Group: Christian von Mering)
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13:30 -13:45
Towards taxon-specific growth prediction in microbial communities by metatranscriptomics
Melanie Stäubli (Group: Shinichi Sunagawa)
Poster pitches
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13:45 - 13:48
The good the bad and the ugly: the three sequencing approaches to compare microbial communities in aquaculture farms
Adamandia Kapopoulou (Group: Claudia Bank)
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13:48 - 13:51
Microbe Atlas Project: a global analysis and web resource of microbiome data enabling the characterisation of species habitats and comparative community analysis
Joao Rodrigues (Group: Christian von Mering)
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13:51 - 13:54
Using microbiome data to assemble a plant-inspired biocontrol community against the potato late blight
Vivien Pichon
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13:00 - 13:15
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Evolution and phylogeny
Evolutionary modelling with trees and beyond
Session chairs: Richard Neher & Ana Morales-Arce
Room: Vereinssaal / Salle des sociétés
Oral presentations
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13:00 -13:15
Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes
Diana Ivette Cruz Dávalos (Group: Anna-Sapfo Malaspinas)
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13:15 -13:30
TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses
Pierre Barrat-Charlaix (Group: Richard Neher)
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13:30 - 13:45
Joint Alignment and Tree Inference
Jūlija Pečerska (Group: Maria Anisimova)
Poster pitches
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13:45 - 13:48
Benchmarking methods using time-series data to infer selection
Lucas Anchieri (Group: Anna-Sapfo Malaspinas)
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13:48 - 13:51
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
Gholamhossein Jowkar (Group: Maria Anisimova)
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13:51 - 13:54
Epistasis defines the transmission fitness of multidrug-resistant Mycobacterium tuberculosis
Etthel Windels (Group: Tanja Stadler)
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13:00 -13:15
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Medicine and health
Immunology, health and disease
Session chairs: Valérie Barbié & Giancarlo Croce
Room: Kongresssaal / Salle des congrèsOral presentations
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13:00 - 13:15
FollicleFinder: an open source software for automated ovarian follicle detection and measurement
Kevin Akira Yamauchi
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13:15 - 13:30
SARS-CoV-2 – Two years on: How curation meets the challenge of variants
Philippe Le Mercier (Group: Swiss-Prot)
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13:30 - 13:45
Responsible sharing of health-related data in multi-center research projects
Julia Maurer (Group: Personalized Health Informatics)
Poster pitches
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13:45 - 13:48
TCRpcDist: Estimating the physico-chemical similarity of TCR. Application to TCR repertoire analysis and TCR specificity prediction
Marta Andreia Da Silva Perez (Group: Vincent Zoete)
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13:48 -13:51
Clinical tools for interpreting genetic variants, SwissGenVar on BioMedIT, Switzerland's secure infrastructure for biomedical research
Shubham Kapoor (Group: Personalized Health Informatics)
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13:51 - 13:54
Uncovering the Diverse Roles of Short Tandem Repeat Variation in Colorectal Cancer
Max Verbiest (Group: Maria Anisimova)
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13:00 - 13:15
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Panel discussion - Who is afraid of data sharing?
14:10 - 15:00Session chairs: Katrin Crameri, Franziska Singer, Patricia Palagi
Room: Kongresssaal / Salle des congrès
Together with representatives from biomedical research and legal, ethical, and technical experts, we will jointly explore why data-sharing is so essential, what challenges and risks it poses, and what this means for researchers as well as for data-donating citizens and patients. We want to discuss solutions that help ensure data protection and data security and enter into dialogue with the audience about their opinions, concerns, and expectations regarding the reuse of (health) data and the sharing of data in the life-science field in general.Our panel speakers are:
- Aitana Neves, Team Lead Data Science, Clinical Bioinformatics
- Antonella Santuccione Chadha , CEO of Women's Brain Project
- Frederic Erard, Head of Legal & Technology Transfer, SIB Management
- Johannes Rainer, Head of Computational Metabolomics at Eurac Research
- Julia Maurer, Senior Scientific Coordinator (ELSI), Personalized Health Informatics
- Mark Ibberson, Director, Vital-IT
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Poster session 1 - with coffee
15:00 - 16:15 -
SIB days summer party at Römerhof farm
17:30 - 01:00We will spend the evening at Römerhof, a traditional Bernese farm with mother cow herd, crops and homemade delights. Get close to real-life nature as you embark on a mother cow safari - or test your skills with other entertaining games such as archery and bow shooting - and, last but not least, show us your moves on the dance floor!
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Wednesday 15 June
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Prize draw to win a mini beamer
08:00 - 09:15 -
Workshops & tutorials
09:15 - 12:00Coffee break: 10:15 -10:30
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T1: Good practice in design of high-throughput experiments
Room: restaurant
This workshop offers an overview of good practice in experimental design for high-throughput experiments. Particularly we focus on pitfalls in the design of projects (e.g. too low sample size or sequencing coverage, or sample batches overlap with biological groups), how to successfully plan an experiment and how to deal with challenges, e.g. batch effects or confounding factors. More
Organizers:
- Michael Prummer
- Eva Riegler
- Franziska Singer
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T2: Inferring gene regulatory networks from high-throughput epigenomic data
Room: workshop 3
In this tutorial users will learn about the CREMA theory behind the analysis, and explore in detail how it can be used in practice. CREMA has a large number of interactive possibilities to explore predictions and to generate new analyses of the data which will be demonstrated in the tutorial. More
Organizers:
Erik van Nimwegen
Mikhail Pachkov -
T3: Introduction to Snakemake for reproducible analyses
Room: foyer
The workshop is for beginners and will focus on explaining all the basic concepts required to implement simple workflows. We will briefly introduce a few advanced topics that are particularly useful for common use cases. More
Organizers:
- Romain Feron
- Antonin Thiebaut
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T4: Latest methods and tools for protein structure prediction
Room: workshop 1
In this tutorial, you will learn about the most recent advances in protein structure prediction, starting with a short presentation introducing the current state of the art. A hands-on tutorial will then focus on web based tools that can go from one or more input protein sequences to an accurate 3D model of a single protein chain or a protein complex. Topics covered will include homology modelling with SWISS-MODEL and deep learning powered modelling with AlphaFold. More
Organizers:
- Gabriel Studer
- Joana Pereira
- Gerardo Tauriello
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T5: Simplifying large and complex single-cell RNA-Seq data with metacells
Room: vereinssaal
In this tutorial, you will learn different approaches to simplify single-cell RNA-Seq data by merging highly similar, and possibly biologically redundant cells into metacells. These will include the SuperCell method developed in the Computational Cancer Biology Group's lab. More
Organizers:
- David Gfeller
- Mariia Bilous
- Aurélie Gabriel
- Léonard Hérault
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T6: Your science made easy and fun
Room: Kongresssaal
This workshop will teach the participants how to describe the work they do and its impact on society; plan an activity that introduces the general public to their work and prepare a brief communication around the activity.
Organizers:
- Marie-Claude Blatter
- Natasha Glover
- Monique Zahn
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W1: 'In all fairness': sex and gender biases in data science and AI, and how to address them
Room: workshop 5
In this workshop, you will investigate the hidden biases that might exist in our bioinformatics daily practices, be it in the use of particular data repositories, the curation process, the way we design experiments and implement models, or the analysis approaches we undertake and the interpretation of their results. More
Organizers:
SIB Diversity working group:
- Aitana Lebrand (Chair)
- Maïa Berman
- Ute Roehrig
- Julien Roux
- Gerardo Tauriello
- Robert Waterhouse
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W2: Making Epigenomics Data FAIR Workshop
Room: workshop 2
The aims of this workshop are:
• Learning from participants about common practices and challenges in re-using published epigenomics data
• Discussing FAIRness issues in epigenomics with colleagues
• Raising awareness of FAIR principles among younger scientists
• Initiating a SIB focus group to continue the discussions initiated at the workshop
• Information on related initiatives: SwissBioData ecosystem, FAIRtracks
MoreOrganizers:
- Philipp Bucher
- Michael Stadler
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W3: Rapid genomic surveillance of new outbreaks
Room: foyer
In this workshop, you will discuss the challenges of implementing a rapid genomic surveillance strategy that can be activated in case of emergencies. The discussions will focus on three target areas: rapid data generation, practical analyses and effective communication. More
Organizers:
- Louis du Plessis
- Chaoran Chen
- Cecilia Valenzuela Agüi
- Adrian Lison
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Lunch break
12:00 - 13:00 -
Keynote lecture #2: Johannes Rainer
13:00 - 13:40The Power of Open Software Development in Metabolomics Research
A personal view on advantages of reproducible research and open software development in mass spectrometry data analysis.
Session chairs: Etthel Windels & Robert Waterhouse
Room: Kongresssaal / Salle des congrès
With ever more comprehensive data sets and complex analysis algorithms, reproducibility is becoming increasingly important to ensure trust in research results. Availability and stability of the employed software algorithms are, along with data availability, crucial aspects of reproducible research. Open and collaborative software development can increase stability and long term support of software as the development is not carried out by a single research group and hence maintenance is less dependent on individual developers or funding of a single research group. Heavily interdisciplinary sciences, such as for example metabolomics, also benefit from open collaborative software development, as researchers with different background will contribute functionality from their specific expert areas resulting thus in a potentially more complete software solution.
In this presentation Johannes Rainer will share his own experiences with reproducible research and open software development in metabolomics research. He will discuss advantages, but also potential pitfalls of open software development and highlight opportunities that openness and collaborative efforts bring to modern data science. -
Parallel session 3
13:50 - 14:50-
New methods in bioinformatics
Mathematical and computational approaches to solve biological problems
Session chairs: Patrick Ruch & Sarah Brüningk
Room: Kongresssaal / Salle des congrèsSession description
Oral presentations-
13:50 - 14:05
Metacells untangle large and complex single-cell transcriptome networks
Mariia Bilous (Group: David Gfeller)
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14:05 - 14:20
Protein language models trained on multiple sequence alignments learn phylogenetic relationships
Umberto Lupo
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14:20 - 14:35
Bayesian phylodynamic inference of multi-type population trajectories using genomic data
Timothy Vaughan (Group: Tanja Stadler)
Poster pitches
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14:38 - 14:41
Classification of oncology treatment responses from radiology reports with supervised machine learning
Luc Mottin (Group: Patrick Ruch)
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14:42 - 14:45
Taxonbridge: an algorithm for the creation and analysis of custom taxonomies
Werner Pieter Veldsman (Group: Marc Robinson-Rechavi & Frédéric Bastian)
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14:46 - 14:48
Somatic Copy Number Alteration Data Calibration
Hangjia Zhao (Group: Michael Baudis)
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13:50 - 14:05
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Proteins and proteomes
Proteins and proteomes, from data to knowledge
Session chairs: Bernd Wollscheid & Fanny Krebs
Room: Vereinssaal / Salle des sociétésSession description
Oral presentations-
13:50 - 14:05
Disentangling phylogeny and optimization contributions in protein sequences
Nicola Dietler
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14:05 - 14:20
Glycan-protein interaction motifs: A semantic based annotation method
Catherine Hayes (Group: Frédérique Lisacek)
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14:20 - 14:35
Proteogenomics identifies conserved and lineage-specific novel small proteins in clinical Mycobacterium tuberculosis reference strains
Benjamin Heiniger (Group: Christian Ahrens)
Poster pitches
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14:38 - 14:41
Swiss-PO and its upcoming updates
Fanny Krebs (Group: Vincent Zoete)
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14:42 - 14:45
Delineation of kinase signaling networks in tumor-associated macrophages
Tiberiu Totu (Group: Marija Buljan)
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14:46 - 14:49
Protein detection sensitivity in 2D electrophoresis experiments strongly depends on imaging parameters
Sonja Voordjik (Group: Valérie Barbié)
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13:50 - 14:05
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_Ad hoc session: Project management basics – Sharing internal best practices
Room: Workshop 1&2
Objective: This informal session will provide the opportunity to exchange knowledge and best practices around the management of small or bigger projects.
- Part 1 - Being agile with the Scrum framework (20 min)
Séverine Duvaud, Team Lead, Resource Usability & Support and Software Developer
Description: In this presentation, we will describe the principles of the Scrum framework and its main components. In particular, we will focus on what the framework does, what it does not do, and what it is and is not for. Breaking down myths, giving a new perspective on project management, and perhaps inspiring some of you, will be the overall goals of this session.
- Part 2 – Demo of the tool Click-up: how to organise your project and collaborate (20 min)
Maïa Berman, Team Lead, Communications
Description: Recurring meetings, releases, reports… Processes, in particular collaborative ones, can get messy, and it is easy to forget a task and get lost across tools. In this session, find out how ClickUp has help us in the Communication and Scientific events team to (somewhat) streamline our workflows, and get ideas on how to structure your own work.
- Q&A (10 min)
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Poster session 2 - with Beers & Bretzels
14:50 - 16:00Posters and software demonstrations served with beer and bretzel.
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Poster prizes and closing remarks
16:00 - 16:15
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