Events

Agenda:

14:00 - Welcome

14:10 - Korbinian Bösl (University of Bergen, Norway): “Integrating FAIRDOM-SEEK with storage and data management planning tools”

14:30 - Martin Golebiewski, Xiaoming Hu (HITS, Germany), **Frank Meineke **(University of Leipzig, Germany): “Extended metadata feature of SEEK in the Local Data Hub of NFDI4Health”

14:50 - Nick Juty (University of Manchester, UK): “SOPs in WorkflowHub”

15:10 - Charles Demurjian (Massachusetts Institute of Technology, US): ...

Agenda:

14:00 - Welcome & Agenda

14:05 - Update about Samples related features in FAIRDOM-SEEK

Flora D’Anna, VIB

14:30 - Overview of the latest FAIRDOM-SEEK release

Stuart Owen, University of Manchester

14:40 - Presentation of the new roadmap

Stuart Owen, University of Manchester

15:00 - Discussion about the roadmap

15:15 - Q&A: ask me anything

The workshop “Novel leads and drugs and their mechanism of action in the field of vector borne parasitic disease” is jointly organized by WG1 “Compound libraries coordination and integration of compound design” and WG2 “Integration of early phase studies and low environmental impact actions” of the COST Action CA21111 OneHealthDrugs. The focus of the workshop is to bring together experts to report and discuss common definitions of novel leads and drugs and their mechanisms of action in view also ...

Agenda:

• 14:00 - Welcome
• 14:10 - Ulrich Sax (University Medical Center Göttingen, Germany) "A translational use case for SEEK in current cancer research"
• 14:30 - Dagmar Waltemath (University Medicine Greifswald, Germany) "Managing computational models in biology and medicine: Experiences from running FAIRDOMHubs in the COMBINE and Medical Informatics communities"
• 14:50 - Jacky Snoep (Stellenbosch University, South Africa) _"Running reproducible modelling projects on the ...

Agenda:

• 14:00 - Welcome
• 14:10 - Marek Ostaszewski (Luxembourg Centre for Systems Biomedicine, LU): “FAIRDOMHub - a platform for the research community building the COVID-19 Disease Map”
• 14:30 - Sara El-Gebali (SciLifeLab Data Centre, SE): “Samples Metadata at the SciLifeLab”
• 14:50 - Huiming Ding (Massachusetts Institute of Technology, US): “Creating mutable samples using NExtSEEK”
• 15:10 - Rafael Andrade Buono (VIB, BE): “DataHub: focusing on sample metadata”
• 15:30 - Discussion

The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2022 will be a workshop-style event with oral presentations, breakout sessions and tutorials. The three meeting days will include talks about the COMBINE standards and associated or related standardization efforts, presentations of tools using these standards, breakout sessions for detailed discussions ...

The purpose of a new series of user meetings is to establish an active FAIRDOM user community to allow networking between various FAIRDOM-SEEK users and learn from each other’s experiences. Within the two-hours event the FAIRDOM team will give an introduction on current developments and the invited users will showcase the use of FAIRDOMHub and other FAIRDOM-SEEK instances for their research projects.

Invited speakers: Cyril Pommier, Frank Meineke, Jasper Koehorst, Andrej Blejec

Date recorded: September 14 2021

Enzymes are the catalysts of life, accelerating chemical reactions in living organisms. Enzyme reactions are widely applied in industry, for example as ingredients in laundry detergents, in the production of cheese, or to synthesize pharmaceutical drugs.

To apply enzymes in industrial processes, a detailed understanding of the molecular mechanisms is needed, requiring in depth studies on their reaction mechanisms. Such mechanistic studies can be performed with ...

Day 4 of Best practices in research data management and stewardship 17 June 2021. Introduction to and Hands-on training on FAIRDOMHub to manage your research assets

The workshop gave an in-depth introduction to data management with SEEK and openBIS, two leading open-source data management solutions. Plenary talks including use cases by "power users" of SEEK and openBIS were complemented by hands-on sessions led by professional data management trainers.

Program Day 1 of the workshop is devoted to the data sharing and dissemination platform SEEK. Day 2 will cover the integrated data management solution openBIS, featuring an Electronic Lab Notebook, Laboratory ...

Crash course of Mathematical modelling, for any learners who want to use models to better understand and assess COVID-19 policies around the world! This course aims at anyone who seeks to understand and assess the utility of mathematical models to make a prediction which could play a key role in government policymaking, as well as a research strategy for pandemic diseases such as COVID-19. The strategies of ‘learning by example’ and ‘learning by doing’ will be here instantiated as learning how ...

Protein Engineering Congress EU

This workshop will be organized by the GMDS project group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", established in early 2019. The aim of this project group is to present the activities in various projects and at different German research locations with regard to infrastructures for FAIRes (Finadable, Accessible, Interoperable, Reusable) data management. To this end, a joint exchange of experience will take place in order to plan joint concepts (e.g. dissemination of FAIR, ...

Managing your data and metadata well is an important research skill. Good data management enables the preparation, handling, storing, sharing, and reuse of data. These attributes of good data management equates to efficient research and saving of time and resources. Data management tools, utilizing data standards and best practices can help to make your research data and models FAIR (Findable, Accessible, Interoperable and Reusable).

SEEK, is a web-based (or locally installed) resource platform ...

Aim Multicellular spatial models have become an essential tool in quantitative biology and multiple model formalisms and simulation frameworks coexist. Progress towards software interoperability and reproducibility requires a novel model description language and conversion library, complementing SBML. Building on the community‘s practical experiences with multiple formalisms and simulators, we aim at (1) defining the concept for a multicellular language while simultaneously (2) exploring automated ...

FAIRDOM PALS and users meeting 2019 is happening in Heidelberg, as a satellite meeting of the COMBINE (COmputational Modeling in BIology Network) meeting. FAIRDOM is a research infrastructure offering data management support. The SEEK software is designed as registry and storage place for data, models, biological samples, processes, publications and presentations, and at the same time as yellow pages for projects, people and events. SEEK is implemented as central data management platform FAIRDOMhub ...

The first Digital Salmon industry workshop raised awareness of the Digital Salmon vision and engaged major industry players in discussions on data sharing and reuse, guidelines and best practices for private-public collaboration. The workshop was a success, and a Digital Salmon working group was formed, comprising industry, academia and funding bodies. Its first task is to develop a white paper to be presented to the industry in summer of 2020.

FAIRDOM training for HOTSOLUTE /EraCoBioTech

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is ...

The 16th conference on Computational Methods in Systems Biology (CMSB 2018) will take place on the 12th to 14th September 2018 in Brno, Czech Republic. Its aim is to bring together researchers from across biological, mathematical, computational, and physical sciences who are interested in the study, modelling, simulation, advanced analysis, and design of biological systems.

CMSB 2018 will be hosted at Faculty of Informatics, Masaryk University, Brno. Brno is the city where the modern genetics has ...

The 10th Young Scientists School “Systems biology and Bioinformatics” SBB-2018 will be held on 27–31th of August 2018 in Novosibirsk, Russia Bioinformatics is a rapidly developing field of knowledge. Each of the past Young Scientists Schools concerned topics urgent at those times. To preserve this tradition, the SBB-2016 will be dedicated to bioinformatics and systems biology in such areas as: Genomics and evolutionary bioinformatics Structural biology and molecular dynamics Molecular-genetic ...

The overarching integrating power of computational modelling, from systems biology to systems medicine

Participants will learn how to structure and share complex data in a Findable, Accessible, Interoperable and Reusable (FAIR) manner. Hands-on sessions, lectures and software demonstrations will provide attendees with the necessary skills to apply components of the FAIRDOM infrastructure in their daily work for interrelating and exchanging data, models and corresponding information.

FAIRDOM is a research infrastructure offering data management support. The SEEK software is designed as registry and ...