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EMBL-SciLifeLab Data Science workshop
We would like to cordially invite members of the SciLifeLab and EMBL Communities to this workshop! This event will bring together researchers, scientific and technical staff at the EMBL and SciLifeLab, to make new acquaintances and collaborations and to learn and be inspired by each other.
The workshop program starts at 09:00 on May 15 and ends after lunch on May 16.
The workshop will be a hybrid event enabling participation to the wider community at all EMBL and SciLifeLab sites.
Looking forward to meeting you in Uppsala in May!
- Internal and external training and support
- Provision of public data services – computational tools
- Artificial intelligence
- Integrated data management and Scientific workflow sharing
- Technical infrastructure – computational solutions
- Biological theme – Imaging
- Biological theme – Human data
Participation by invitation only. Target audience: SciLifeLab and EMBL staff.
- Johan Rung, SciLifeLab
- Carolina Wählby, SciLifeLab
- Jan Korbel, EMBL
- Rupert Lueck, EMBL
- Rolf Apweiler, EMBL
Monday May 15
|Time slot||Monday, May 15|
|09:00||Welcome and introduction|
Olli Kallioniemi, SciLifeLab and DDLS Director, and Jan Korbel, Head of Data Science, EMBL
|09:15||Session 1: Internal and external training and support|
Themes: what is training at EMBL, Data Science training work stream -SciLifeLab training hub -Areas for synergies
Moderator: Cath Brooksbank, Head of Training, EMBL-EBI
|EMBL Data Science Training: the story so far|
Lisanna Paladin, Bioinformatics Community Project Manager, EMBL
|SciLifeLab Training Hub: the story starts now – what are the goals?|
Nina Norgren, Training manager, SciLifeLab
|Panel discussion and questions on stimulating exchange and collaboration|
Mounting of posters
|10:50||Session 2: Provision of public data services – computational tools|
Moderator: Johanna McEntyre, Associate Director for Service, EMBL-EBI
|Successfully managing a portfolio of data services|
Johanna McEntyre, Associate Director for Service, EMBL-EBI
Mihail Anton, NBIS expert, SciLifeLab
Sameer Velankar (PDB Europe), Team Leader, EMBL-EBI
|Panel discussion: the future challenges and opportunities for public data services|
Mihail Anton (Metabolic Atlas)
Matthew Hartley (BioImage Archive)
Cecilia Lindskog (Human Protein Atlas)
Fergal Martin (Ensembl)
Sameer Velankar (PDB Europe)
|13:15||Session 3: Artificial Intelligence|
Moderator: Carolina Wählby, Scientific Director of BioImage Informatics and Group Leader, SciLifeLab
|AI in Image Analysis|
Anna Kreshuk, Group Leader, EMBL
|AI in Cancer genomics, prediction of treatment|
Isidro Cortes-Ciriano, Group Leader, EMBL-EBI
|AI in spatial omics|
Carolina Wählby, Scientific Director of BioImage Informatics and Group Leader, SciLifeLab
|Serving AI models|
Ola Spjuth, Group Leader and AI coordinator, SciLifeLab
|Discussion on how to foster AI further|
|14:50||Session 4: Integrated data management and scientific workflow sharing|
Moderator: Henning Hermjakob, Head of Molecular Systems, EMBL-EBI
Irene Papatheodorou, Team Leader – Gene Expression, EMBL-EBI
Mats Nilsson, Platform Director Spatial Biology and Group Leader, SciLifeLab
|16:00||Session 5: Technical infrastructure – computational solutions|
Moderator: Johan Rung, Head of Data Centre, SciLifeLab
|Cloud – Beyond the hype|
Andy Cafferkey, Head of Technical Services, EMBL-EBI
|The IT role in empowering advanced research data management|
Rupert Lück, Head of IT Services, EMBL
|The great datawanderung – how sensitive data is reshaping research infrastructures. Data transfer, Compute moving to data|
Johan Viklund, NBIS Chief Technical Officer, SciLifeLab
|Needs and requirements to provide next generation of compute services (notebooks, containerization, GPUs, etc) – energy, carbon issues|
Ola Spjuth, Group Leader and AI coordinator, SciLifeLab
|17:10||Poster session with refreshments|
Tuesday May 16
|Time slot||Tuesday, May 16|
|09:00||Session 6: Biological theme – imaging|
Moderator: Anna Klemm, Head of the BioImage Informatics Facility, SciLifeLab
|Image Data and Image analysis|
Hjalmar Brismar, Platform Scientific Director Advanced Light Microscopy unit and Group Leader, SciLifeLab
Christian Tischer, Centre for Bioimage Analysis, Scientist/IT Engineer, EMBL
|Panel discussion: Workflows from image data generation to data analysis and finally image data publication. How are projects and data managed?|
Hjalmar Brismar, SciLifeLab
Matthew Hartley, BioImage Archive Team Leader, EMBL-EBI
Anna Klemm, SciLifeLab
Erik Lindahl, Group Leader, SciLifeLab
Christian Tischer, EMBL
|10:35||Session 7: Biological theme – human data|
Moderator: Helen Parkinson, Team Leader SPOT, EMBL-EBI
|Integrated FEGA/FDA-components/Federated Analysis|
Oliver Stegle, Associate Group Leader, EMBL
|Developments from Human Data Services|
Bengt Persson, Platform Director NBIS, SciLifeLab
Carolina Wählby, Scientific Director of BioImage Informatics, SciLifeLab and Rolf Apweiler, Joint Director of EMBL-EBI
|Afternoon:||Self-organized break-out tech workshops, Site visits, etc|
EMBL and SciLifeLab recently launched data science training initiatives. In this session we will share our approaches to developing data science training – our plans, our successes and our greatest challenges. An open discussion will explore areas for future collaboration and how we might work together to recognise those who dedicate their time, usually on a volunteer basis, to advanced scientific training.
Explore how to manage a portfolio of public computational tools and data services, with real-world examples from both emerging and established resources, and a panel discussion on the future challenges and opportunities for public data services
In this workshop:
- A keynote talk introduces key points of successfully managing a portfolio of data services
- One emerging and one established data service summarize their management approach
- A panel discussion including other data service leads from EMBL-EBI and SciLifeLab discuss the future challenges and opportunities for public data services
In this session we will focus on how to foster AI further (within EMBL-EBI and SciLifeLab) – What are the lessons learned during the last decade of incorporating learning-based methods using neural networks in biomedical research? Where lies the power, and what are the limitations? How do we handle bottle-necks such as lack of reliably annotated training data, and how do we avoid biases introduced by factors such as sample preparation and data collection? How can we include ‘the human in the loop’, and how can we share models?
Modern, data-intensive science requires complex and ideally reproducible workflows. Based on two opening presentations, one from a complex “research” workflow background, one from a repeatable “service” background, and a subsequent panel discussion, we want to explore
- What are the scientific demands and requirements for computational workflows?
- How to strike the right balance between reproducibility and flexibility?
- What is the current status and future aspirations for technical support of computational workflows?
- What are the opportunities for coordination / integration of internal /external workflows between SciLifeLab and EMBL?
The technical infrastructures and computational solutions provided by teams across EMBL and SciLifeLab are at the heart and the critical foundation of data science activities in both institutions. In this session, we aim to initiate a cross-organizational dialogue and to set the stage for further networking among interested stakeholders to explore key IT and technical challenges and learn more about potential solutions being explored on both sides.
The session will start with four short presentations to stimulate the open discussion that will follow. Our input from the presentations will cover a wide range of technical topics and challenges:
i) key aspects of using cloud services,
ii) opportunities to improve scientific data management via dedicated IT solutions,
iii) the challenges associated with shared analysis and transfer of (sensitive) data across centres, and
iv) exploring the needs for next-gen computational, data analytics, and management services for data science in the life sciences.
In the imaging session we will discuss workflows from image data generation to data analysis and finally publication. Which paths does microscopy data take at EMBL and SciLifeLab? How can data analysis and data management be integrated early on in the project discussions? The session will also give an insight to which kind of imaging projects are handled at both EMBL and SciLifeLab, since imaging data can have a broad range of characteristics and comes with different analysis and data management needs.
The Human Data session will focus on challenges working with federated and multidimensional human data, interfacing with national data , e.g. Genomics Data Infrastructure (GDI; Persson) enabling realisation of the European 1+ Million Genome project, and the experience of working at the interface of clinical research with industrial partners, including the Mannheim alliance (Stegle) and precompetitive industrial collaborations, e.g.OpenTargets (https://www.opentargets.org/). The session will have two presentations (Stegle, Persson) followed by a panel discussion. It aims to define the skills set, mindset, technical solutions to address shared problems of human research data.