A community proposal to integrate proteomics activities in ELIXIR

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on ‘The Future of Proteomics in ELIXIR’ that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes.   These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR’s existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper

Beyond 1 Million Genomes (B1MG) D1.4 Report of Stakeholders Forum 2022 including recommendations to the 1+MG Working Groups

<p>The Beyond 1 Million Genomes (B1MG) project aims to facilitate the 1+MG initiative to provide access to genomics data and associated health data across borders and drive the development of personalised health strategies within Europe. The 1+MG/B1MG Stakeholder Forum 2022 held in October 2022, assembled for the third time a broad range of stakeholder experts, active in scientific and technical communities, international initiatives, projects, national healthcare systems, as well as industry to capture their input in the design of the infrastructure, the legal guidance and the best practices to realise the 1+MG infrastructure. </p><p>Being the last Stakeholder Forum (SF) organised by the B1MG project, this meeting centred on identifying how <strong>stakeholders</strong> could <strong>contribute to the scale up and sustainability of the 1+MG/B1MG efforts</strong>. The day included key updates on the progress of 1+MG/B1MG, specifically on the 1+MG Trust Framework (focussed on the ELSI and technical recommendations and guidelines for privacy-preserving access to genomics data), and including the B1MG Maturity Level Model as a tool for countries to assess progress towards implementation of genomics-based personalised health strategies into healthcare. This was then followed by a session on the next steps towards scale-up and implementation of the genomics data-sharing landscape by speakers from the recently established (1+MG-associated and EC-funded) Genomic Data Infrastructure (GDI) project, TEHDAS/EHDS and GAIA-X. </p><p>Acknowledging the role of industries in the scale-up and sustainability of these efforts, the day specifically included several ways to explore the role of companies as key stakeholders in realising cross-border genomic data sharing efforts and in developing a practice of genomics-based personalised health in 1+MG associated countries. A dedicated panel discussion included representatives from 1+MG WG7 (industry engagement), an umbrella industry organisation (EFPIA), an SME (Hyve - EHDEN project), as well as Australian Genomics, an initiative outside of Europe that has considered industry as part of their genomics activities. Clear recommendations were made to build a continuous exchange with industry to build mutual trust between public and private stakeholders. Further to this there was a proposal to explore the opportunity to establish a set of projects, such as under the framework of IHI. This clear output from the SF meeting should be explored further by the 1+MG initiative.</p><p>The second half of the day led into parallel workshops to consider scale up and sustainability in the context of rare diseases, cancer, common complex disease and infectious disease. The Trust Framework was regarded and the user communities addressed the question how stakeholders, including industry, could help realise these key components of the 1+MG infrastructure. It is clear that there are requirements specific to each disease community that are important to continuously review, discuss and understand in order to develop and sustain the 1+MG Trust Framework. The balance between how much research and care are entangled differs across use cases (rare diseases and cancer breakouts are already intertwined) and discussions stressed how the 1+MG infrastructure must be able to support primary and secondary use equally well.  </p><p>The annual Stakeholder Forum meetings run by the B1MG project have all been very successful. They have strengthened the alignment of the stakeholders with the 1+MG initiative, enabling the leads of various activities to take on board suggestions and ensuring the outcomes of the project fit with stakeholder needs, encouraging innovation and alignment across a broader landscape. To continue stakeholder engagement and ensure further impact, these events will be continued as part of the GDI project.</p&gt

Bioinformatics in the Netherlands: The value of a nationwide community

This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly

Bioinformatics in the Netherlands: The value of a nationwide community

This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly.Pattern Recognition and Bioinformatic

A community proposal to integrate proteomics activities in ELIXIR

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper

Gaps and Plugs: TNO, and the Problems of Getting Knowledge out of Laboratories

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The future of metabolomics in ELIXIR [version 1; referees: 2 approved, 1 approved with reservations]

Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

BACKGROUND: Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. FINDINGS: PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. CONCLUSIONS: PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains