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FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.
Programme: FAIRDOM
SEEK ID: https://fairdomhub.org/projects/19
Public web page: http://fair-dom.org/
Organisms: No Organisms specified
FAIRDOM PALs: No PALs for this Project
Project start date: 1st Nov 2014
Related items
- People (25)
- Institutions (6)
- Investigations (2+1)
- Studies (3+1)
- Assays (9+3)
- Data files (12+12)
- Models (1+4)
- SOPs (0+3)
- Publications (18)
- Presentations (30+29)
- Events (17+5)
- Documents (1+2)
- Samples (0+8)
Projects: FAIRDOM Community Workers, FAIRDOM
Institutions: University of Manchester - Department of Computer Science
Projects: FAIRDOM
Institutions: University of Manchester - Department of Computer Science
Projects: SysMO DB, FAIRDOM, FAIRDOM Templates
Institutions: University of Manchester - Department of Computer Science

Expertise: Programming
Tools: Ruby on Rails, Javascript, HTML
Projects: FAIRDOM
Institutions: ETH Zurich & Basel / The Scientific IT Services (SIS) division
Projects: SysMO DB, FAIRDOM, FAIRDOM user meeting, COVID-19 Disease Map
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

Roles: Project Coordinator
Expertise: Software Engineering, semantics, VREs, standards, Distributed Systems
Tools: Data Management, Workflows, semantic web, Web services, Ontologies, web development
Professor of Computer Science University of Manchester
Co-Director of the FAIRDOM Initiative and co-leader of the SEEK4Science Platform Development
Deputy Head of Node ELIXIR-UK
Co-lead ELIXIR Interoperability Backbone Platform
Lead ISBE WP Data and Model Management
Data lead SynBioChem Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals
Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, MS_DILI, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, ModeleXchange initiative
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team.
Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and
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Projects: FAIRDOM, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, LiSyM Core Infrastructure and Management (LiSyM-PD), ModeleXchange initiative
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology

Expertise: Genetics, Molecular Biology, Bioinformatics, Data Management, Transcriptomics, semantics, Curation, Ontology, Data Modelling
Tools: Cell and tissue culture, Databases, Chip-chip, BioMart, Protege, RightField, SEEK
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project
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Projects: FAIRDOM
Institutions: University of Zürich
Projects: FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, FAIRDOM user meeting
Institutions: University of Zürich, ETH Zurich, Manchester Centre for Integrative Systems Biology, University of Manchester
Expertise: Bioinformatics, Proteomics, Genomics
Tools: Matlab, Microarray analysis, Data Management, Computational Systems Biology, Perl, Python
I hold a Medical Doctor Diploma (Lviv, Ukraine) with the specialization in General Medicine. After the graduation from the Post Graduate Program in Bioinformatics at the Seneca College/York University (Toronto, Canada), I successfully participated in the number of scientific projects conducted at the University of Toronto (Canada) and the Toronto East General Hospital (Canada).
I obtained the PhD in Bioinformatics at the Swiss Institute of Bioinformatics (Geneva, Switzerland). As a PhD student,
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Projects: FAIRDOM
Institutions: University of Manchester - Department of Computer Science

Expertise: Molecular Biology, Bioinformatics, Genomics, metagenomics, standards, Ontology
Tools: Bioinformatics, Data Management
FAIRDOM Project Wrangler
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

I am group leader of the SDBV (Scientific Databases and Visualisation) group at the HITS gGmbH, the Heidelberg Institute for Theoretical Studies.
I am interested in finding data. Starting with my master's thesis I have always worked on how to store data in a way that you can find it, and how to make sense out of data that has been stored.
Within FAIRDOM I find interesting to help people to store their data in a way that they make sense even after years.
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, Kinetics on the move - Workshop 2016
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: Software Engineering, Data Management, Databases
Tools: Ruby on Rails, MySQL, HTML, Ruby, Java, Javascript
Software developer for FAIRDOM
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting, FAIRDOM Templates, FAIRDOM Community Workers
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

Expertise: Software Engineering, Data Management, Software Architecture, REST, Cloud computing, Agile development
Tools: Databases, Java, Workflows, Web services, Taverna, Ruby, Ruby on Rails, linux, J2EE, semantic web, AWS, Research Objects, Docker
Software Engineer and Architect working within the FAIRDOM team.
Leads the development of SEEK and RightField.
Projects: SysMO-LAB, de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", MIX-UP, CEPLAS – Cluster of Excellence on Plant Sciences, COVID-19 Disease Map, ERNEST Mapping Group Pilot Study
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: Biochemistry, Molecular Biology, Microbiology, Phytopathology, Data curation
Within the de.NBI project my functions in the de.NBI-SysBio node comprise content curation, requirements elicitation, and community engagement for the users of biochemical reaction kinetics database SABIO-RK as well as of the data management platform SEEK.
Projects: FAIRDOM
Institutions: ETH Zurich & Basel / The Scientific IT Services (SIS) division
Expertise: Software Engineering, Scientific Computing, Databases, Distributed Systems
Tools: High Performance Computing, Statistics, SQL, Java, Python
Head of Scientific IT Services and member of the ITS executive board at ETH Zurich.
Project manager of SyBIT.
Project partner of the FAIRDOM Initiative.
Projects: FAIRDOM
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, University of Manchester - Department of Computer Science, Stellenbosch University
Data integration is an essential part of Systems Biology. Scientists need to combine different sources of information in order to model biological systems, and relate those models to available experimental data for validation. Currently, only a small fraction of the data and models produced during Systems Biology investigations are deposited for reuse by the community, and only a smaller fraction of that data is standards compliant, semantic content.
By embedding semantic technologies into familiar
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Snapshots: Snapshot 1, Snapshot 2
Studies: Creating Templates for Proteomics, Creating Templates for Transcriptomics, Creating template for metabolomics data
Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, Metabolomics Master Template, NimbleGen Transcriptomics Templates, Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry), RT-PCR Excel Template, Standard-based Excel template for metabolomics data
Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and
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Snapshots: No snapshots
Studies: No Studies
Assays: No Assays
Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
These templates can be used for a selection of metabolomics data types. There is a MASTER template for general use and adaptation as well as several more specific templates for particular types of experiment (e.g. HPLC), or specific assay types (e.g glucose pulse)
Person responsible: Olga Krebs
Snapshots: No snapshots
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Submitter: Katy Wolstencroft
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating template for metabolomics data
Organisms: No organisms
SOPs: No SOPs
Data files: Metabolomics Master Excel Template and 1 hidden item
Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat
Submitter: Olga Krebs
Assay type: Metabolite Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating template for metabolomics data
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: Excel sheet template : concentrations of intrac..., The FAIR Guiding Principles for scientific data...
Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Transcriptomics
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: 3' or Whole Gene Expression Array Template (Aff..., Chip-chip Array Template (Affymetrix)
A example of an RT-PCR Excel template. RT-PCR is Reverse Transcriptase PCR (NOT to be confused with Real Time PCR, which is normally referred to as qPCR)
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using templates will mean easier submission to public databases on publication and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Transcriptomics
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: RT-PCR Excel Template
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model).
Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: ChIP-on-chip
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Transcriptomics
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: Chip-chip Excel template example
Some examples of transcriptomics templates for NimbleGen data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using templates will mean easier submission to GEO/ArrayExpress upon publication and greater consistency of data in SEEK for easier searching and comparing.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Transcriptomics
Organisms: No organisms
SOPs: No SOPs
Data files: Genomic Data Submission Excel Template (NimbleGen), Transcriptomics Gene Expression Excel Template ...
Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Electrophoresis
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Proteomics
Organisms: No organisms
SOPs: No SOPs
Data files: Proteomics Gel Electrophoresis Excel Template, Template for proteomics (2D gel)
Some generic examples of transcriptomics templates that conform to the MAGE-TAB specification. These templates were created and modified from templates produced by ArrayExpress and GEO.
These templates are generic and non-specific for any particular array platform.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Transcriptomics
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: Transcriptomics Template (ArrayExpress Format)
Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Creating data sheet template for 'omics data
Study: Creating Templates for Proteomics
Organisms: No organisms
SOPs: Guidelines for Proteomics Templates
Data files: Proteomics Mass Spec Template (SysMO JERM), Proteomics Template (empty) from PRIDE, Proteomics Template from PRIDE
Excel sheet template : concentrations of intracellular metabolites
Creators: Olga Krebs, Katy Wolstencroft
Submitter: Olga Krebs
Investigations: Creating data sheet template for 'omics data
Report of the Data Management Foundry Workshop,
19th-20th of March, 2012, Vienna, Austria
Creators: Natalie Stanford, Katy Wolstencroft, Olga Krebs, Stuart Owen, Carole Goble, Wolfgang Müller
Submitter: Natalie Stanford
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Tutorial given at the Reproducible and Citable Data and Models Workshop, Warnemunde September 14th-16th 2015.
Creators: Natalie Stanford, Stuart Owen
Submitter: Natalie Stanford
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
a test file
Creator: Wolfgang Müller
Submitter: Wolfgang Müller
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Agenda for the satellite data management tutorial of Synthetic Biology 2017.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Martin Golebiewski
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
3rd ERASysAPP – EXCHANGE Day: Networking and Info Day for research projects of the first and second ERASysAPP calls
Creators: Olga Krebs, Katalin Zsuzsanna Nagy, Heide Marie Hess
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
List of participants/1st EraSysApp PALs meeting
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Participants of 2nd FAIRDOM PALs meeting in Munich
Creators: Olga Krebs, Wolfgang Müller, Rostyslav Kuzyakiv
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The tutorial provided for EraSysAPP PALs. Covers new features associated with generating snapshots, research objects, and assigning DOIs to investigation snapshots in order to make them citable structures.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model).
Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Transcriptomics
Assays: Chip-chip Excel Template
This is not my model
Creator: Alan Williams
Submitter: Alan Williams
Model type: Not specified
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Abstract (Expand)
Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers
Date Published: 29th Jun 2020
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 0(0)
Abstract (Expand)
Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
Date Published: 29th Jun 2020
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 0(0)
Abstract (Expand)
Authors: N. J. Stanford, M. Scharm, P. D. Dobson, M. Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep
Date Published: 12th Oct 2019
Publication Type: Journal
PubMed ID: 31602618
Citation: Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17.
Abstract (Expand)
Authors: Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
Date Published: 13th Jul 2019
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 16(2)
Abstract (Expand)
Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Date Published: 1st Mar 2019
Publication Type: Journal
DOI: 10.1093/bib/bby087
Citation: Briefings in Bioinformatics 20(2):540-550
Abstract (Expand)
Author: Martin Golebiewski
Date Published: 2019
Publication Type: InBook
DOI: 10.1016/B978-0-12-809633-8.20471-8
Citation: Encyclopedia of Bioinformatics and Computational Biology,pp.884-893,Elsevier
Abstract
Author: Timon Oefelein
Date Published: 20th Nov 2018
Publication Type: InProceedings
DOI: 10.7557/5.4510
Citation: SCS(1)
Abstract
Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
Date Published: 29th Mar 2018
Publication Type: Journal
Citation: Journal of Integrative Bioinformatics 15(1)
Abstract (Expand)
Authors: Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novere, David P. Nickerson, Falk Schreiber, Dagmar Waltemath
Date Published: 1st Dec 2017
Publication Type: InProceedings
Citation: 2017 Winter Simulation Conference (WSC),pp.884-895,IEEE
Abstract
Authors: Wolfgang Müller, Meik Bittkowski, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig
Date Published: 1st Mar 2017
Publication Type: Journal
DOI: 10.1007/s13222-016-0243-4
Citation: Datenbank Spektrum 17(1):21-28
Abstract (Expand)
Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath
Date Published: 12th Feb 2017
Publication Type: Not specified
PubMed ID: 28187405
Citation: J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Abstract (Expand)
Authors: vikash bhardwaj, Vikash bhardwaj, Kulbhushan Sharma
Date Published: 5th May 2016
Publication Type: Journal
Citation: Protocol Exchange
Abstract (Expand)
Authors: D. Nickerson, K. Atalag, B. de Bono, J. Geiger, C. Goble, S. Hollmann, J. Lonien, W. Muller, B. Regierer, N. J. Stanford, M. Golebiewski, P. Hunter
Date Published: 7th Apr 2016
Publication Type: Not specified
PubMed ID: 27051515
Citation: Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103.
Abstract (Expand)
Authors: M. D. Wilkinson, M. Dumontier, I. J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. W. Boiten, L. B. da Silva Santos, P. E. Bourne, J. Bouwman, A. J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C. T. Evelo, R. Finkers, A. Gonzalez-Beltran, A. J. Gray, P. Groth, C. Goble, J. S. Grethe, J. Heringa, P. A. 't Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S. J. Lusher, M. E. Martone, A. Mons, A. L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. A. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M. A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, B. Mons
Date Published: 15th Mar 2016
Publication Type: Journal
PubMed ID: 26978244
Citation: Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.
Abstract (Expand)
Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, , Martin Golebiewski, Michael Hucka, Nick Juty, , Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet
Date Published: 15th Mar 2014
Publication Type: Journal
DOI: 10.4056/sigs.5279417
Citation: Stand. Genomic Sci. 9(3):1285-1301
Abstract (Expand)
Authors: K. Smallbone, H. L. Messiha, K. M. Carroll, C. L. Winder, N. Malys, W. B. Dunn, E. Murabito, N. Swainston, J. O. Dada, F. Khan, P. Pir, E. Simeonidis, I. Spasic, J. Wishart, D. Weichart, N. W. Hayes, D. Jameson, D. S. Broomhead, S. G. Oliver, S. J. Gaskell, J. E. McCarthy, N. W. Paton, H. V. Westerhoff, D. B. Kell, P. Mendes
Date Published: 9th Jul 2013
Publication Type: Not specified
PubMed ID: 23831062
Citation: FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4.
Abstract (Expand)
Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Mueller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble
Date Published: 2012
Publication Type: Journal
DOI: 10.1007/978-3-642-33876-2_42
Citation: Knowledge Engineering and Knowledge Management 7603:438-441,Springer Berlin Heidelberg
FAIRDOM introduction by Olga Krebs
Creators: Olga Krebs, Carole Goble, Katy Wolstencroft
Submitter: Olga Krebs
Introductory talk given by Olga Krebs in the Department of Chemical Engineering at the University of Rovira i Virgili on 19th of July 2017
Creator: Olga Krebs
Submitter: Olga Krebs
Introductory talk given by Olga Krebs in the Department of Chemical Engineering at the University of Rovira i Virgili on 19th of July 2017
Creator: Olga Krebs
Submitter: Olga Krebs
SEEK functionalities presented by Olga Krebs
Creators: Olga Krebs, Wolfgang Müller
Submitter: Olga Krebs
Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016
Creators: Olga Krebs, Carole Goble, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford
Submitter: Olga Krebs
FAIRDOMHub training for SYSTERACT project meeting on 10th of November 2016 in Leiden, NL
Creator: Olga Krebs
Submitter: Olga Krebs
Talk given by Olga Krebs at FAIRDOM-LiSyM-de.NBI Data Structuring Course - Nov 22-23 in Hünfeld (D)
Creator: Olga Krebs
Submitter: Olga Krebs
This document helps Horizon 2020 beneficiaries make their research data findable, accessible, interoperable and reusable (FAIR), to ensure it is soundly managed. Good research data management is not a goal in itself, but rather the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse. Note that these guidelines do not apply to their full extent to actions funded by the ERC. For information and guidance concerning Open Access and the
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Creator: Olga Krebs
Submitter: Olga Krebs
Presented by Martin Böhm, German Cancer Research Center, Heidelberg, Germany
Creators: Markus Stepath, Martin Böhm
Submitter: Olga Krebs
The presentation was given during the PALs meeting in Munich on Dec. 10th, 2015
It talks about openBIS, an open, distributed system for managing biological information.
The main goal of openBIS is to support biological research data workflows from the source (i.e. the measurement instruments) to data processing and analyzing facilities.
Creator: Rostyslav Kuzyakiv
Submitter: Rostyslav Kuzyakiv
Slides that were presented alongside a SEEK demonstration at the EraSysApp PALS meeting in Munich - December 2015
Creator: Stuart Owen
Submitter: Stuart Owen
Written and presented by Carole Goble (University of Manchester) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
Creators: Natalie Stanford, Carole Goble, Stuart Owen
Submitter: Natalie Stanford
Documentation for using FAIRDOMHUB / SEEK for a workshop in Warnemunde, September 2015.
Creators: Natalie Stanford, Stuart Owen, Norman Morrison, Olga Krebs
Submitter: Natalie Stanford
Written and presented by Carole Goble (University of Manchester) at Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015.
Creators: Natalie Stanford, Carole Goble
Submitter: Natalie Stanford
Written and presented by Carole Goble (University of Manchester) at Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015.
Creators: Natalie Stanford, Carole Goble
Submitter: Natalie Stanford
Written and presented by Wolfgang Müller (HITS) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
Creators: Natalie Stanford, Wolfgang Müller
Submitter: Natalie Stanford
Written by Martin Scharm (University of Rostock), Ron Henkel (University of Rostock), Dagmar Waltemath (University of Rostock), Olaf Wolkenhauer (University of Rostock, Stellenbosch University), and presented by Martin Scharm (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.
Creators: Natalie Stanford, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel, Martin Scharm (University of Rostock)
Submitter: Natalie Stanford
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
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Start Date: 6th Nov 2019
End Date: 7th Nov 2019
Event Website: https://digitallifenorway.org/arrangementer/workshop-getting-your-hands-on-data-management
Country: Norway
City: Trondheim
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
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Start Date: 18th Jul 2019
End Date: 19th Jul 2019
Event Website: https://fair-dom.org/events/fairdom-pals-users-meeting-2019/
Country: Germany
City: Heidelberg
FAIRDOM training for HOTSOLUTE /EraCoBioTech
Start Date: 30th Apr 2019
End Date: 30th Apr 2019
Event Website: Not specified
Country: Germany
City: Essen
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
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Start Date: 18th Mar 2019
End Date: 20th Mar 2019
Event Website: http://copasi.org/denbi-modsim/workshop_2019/
Country: Germany
City: 69120 Heidelberg
Start Date: 28th Oct 2018
End Date: 1st Nov 2018
Event Website: http://www.biosyl.org/news/icsb-2018
Country: France
City: Lyon
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
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Start Date: 27th Aug 2018
End Date: 31st Aug 2018
Event Website: http://conf.bionet.nsc.ru/sbb2018/en/
Country: Russian Federation
City: Novosibirsk
The overarching integrating power of computational modelling, from systems biology to systems medicine
Country: Germany
City: Bremen
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
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Country: Germany
City: Bremen
We are excited to announce our 2017 SynBio Data Management Training Day. The event is co-located with Synthetic Biology UK, in Manchester. The venue will be the Manchester Institute for Biotechnology (http://www.mib.ac.uk/contact/).
Topics that will be covered include
- Model management in FAIRDOMHub
- Publishing using FAIRDOMHub
- Samples in FAIRODMHub
On top of this we will have talks about general data management using FAIRDOM, and also smart publications.
Participation is free. We have limited
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Start Date: 29th Nov 2017
End Date: 29th Nov 2017
Event Website: https://fair-dom.org/synbiotraining
Country: United Kingdom
City: Manchester
Target audience: Wet-lab scientists and people dealing with experimental and/or clinical data for research
Topics include:
- Best practice data structuring (spreadsheets) for experimental and (clinical) samples data
- Comprehensive and unambiguous data description and annotation
- Standard formats and terminologies for data and metadata
- Guidelines for reporting data (Minimum information standards)
- Annotation tools (e.g. RightField: http://www.rightfield.org.uk)
- Using SEEK & FAIRDOMhub
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Start Date: 22nd Nov 2017
End Date: 23rd Nov 2017
Event Website: Not specified
Country: Germany
City: Hünfeld
This event is a jointly organized Data Management PALs Meeting that involves PALs from the German LiSyM (Liver Systems Medicine) network and from the ERASysAPP (ERA-Net for Systems Biology Applications) initiative. PALs (Project Area Liaisons) are the front line experts of the data management teams of these projects. They act as data management advocates and help gathering user requirements and testing potential data management solutions. An important part of the meeting will be to gather the
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Start Date: 2nd May 2017
End Date: 3rd May 2017
Event Website: Not specified
Country: Germany
City: 36088 Hünfeld bei Fulda
FAIRDOM team is inviting all PALs to participate in the second FAIRDOM PALs meeting. The event will take place on Dec. 9-10th , 2015 in Munich, immediately after the ERAsysAPP exchange meeting scheduled for Dec 8-9th.
Beginning at 14:00 on Dec 9h, it will continue till 13:00 on Dec. 10th. Please, consider this when booking your plane/train tickets as well as hotel rooms.
The FAIRDOM team considers the meeting as an opportunity to update the PALs on available data/model management solutions, recent
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Start Date: 9th Dec 2015
End Date: 10th Dec 2015
Event Website: Not specified
Country: Germany
City: Munich
This workshop is for computational biologists and experimentalists who wish to learn about standards, citeable data, about how to make scientific results sustainable, available through open repositories, and about how to find and reuse other people’s works. It comprises of a mixture of lectures and hands-on sessions. We will teach you the major standards and tools that support these standards, as well as steps towards encoding and publishing reproducible modeling results. Topics include data
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Start Date: 14th Sep 2015
End Date: 15th Sep 2015
Event Website: https://sems.uni-rostock.de/reproducible-and-citable-data-and-models/
Country: Germany
City: Rostock-Warnemünde
The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 22 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. Joining forces with the European Conference on Computational Biology (14th Annual Conference) ISMB/ECCB 2015 will be the year's most important computational biology event globally.
The conferences
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Country: Ireland
City: Dublin
The BBSRC has recently funded the UK Multiscale Biology network, motivated by BBSRC strategic discussions which identified ‘Multi-Scale Biology’ (MSB) as a key area of research and capability that will be at the forefront of bioscience research over the next 5-10 years. The network will aim to:
• facilitate the exploitation of areas of synergy between researchers across the UK in the broad area of multi-scale biology (MSB);
• raise awareness of the benefits of MSB;
• identify areas that are most
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Start Date: 1st Jun 2015
End Date: 1st Jun 2015
Event Website: http://www.multiscalebiology.org.uk/events/event/springboard/
Country: United Kingdom
City: Nottingham
1st FAIRDOM + EraSysApp PALs meeting will be co-located with ERASysAPP – EXCHANGE: Networking and Info Day in Berlin, on 16 -17 April 2015
April 16th
ABION Spreebogen Hotel, Salon Charlottenburg
18:00 -22:00 Social gathering and informal presentations with FAIRDOM team + old PALs +new PALs (with food and drinks served)
April 17th
ABION Spreebogen Hotel, Salon Bellevue
9:00 -9:15 Short introduction from funders (Christian Rückert, PtJ)
9:15 -10.00 Warming up FAIRDOM, FAIRDOMHub and openSEEK
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Start Date: 16th Apr 2015
End Date: 17th Apr 2015
Event Website: Not specified
Country: Germany
City: Berlin
Semantic web applications and tools for life science.
Since 2008, the SWAT4LS Workshop has provided a platform for the presentation and discussion of the benefits and limits of applying web-based information systems and semantic technologies in the domains of health care and life sciences.
SWAT4LS will provide the same open and stimulating environment that has previously brought together researchers, developers, and users, from various fields including eHealth, biomedical and clinical informatics,
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Start Date: 9th Dec 2014
End Date: 11th Dec 2014
Event Website: http://www.swat4ls.org/workshops/berlin2014/
Country: Germany
City: Berlin
This is the fifth and final draft of the Recommendations and Guidelines from the RDA COVID-19 working group, and is open for public comment until 8th of June 2020. Following the open period, feedback will be considered and then the WG will seek endorsement of the document from the RDA governance bodies prior to final publication.
Creators: Martin Golebiewski, see full list of members of the RDA COVID-19 working group: https://www.rd-alliance.org/node/68704/members
Submitter: Martin Golebiewski
Investigations: No Investigations
Studies: No Studies
Assays: No Assays