Projects: FAIRDOM user meeting
Institutions: University of Edinburghorcid.org/0000-0003-1756-3654
Roles: Project Coordinator
Projects: COMBINE Multicellular Modelling
Institutions: Indiana University Bloomingtonorcid.org/0000-0002-7440-2905
Research Associate in the Macklin Lab, School of Informatics, Computing, and Engineering. Indiana University, Bloomington, IN USA.
Institutions: Wageningen University & Researchorcid.org/0000-0001-8172-8981
Institutions: Norwegian University of Life Sciencesorcid.org/0000-0002-4699-0308
I am the Data and Model Manager for the Digital Salmon and the GenoSysFat projects. We are building a knowledge base of salmon physiology in the form of mathematical models interlinked with omics data, for applications in aquaculture, ecology and management. My duties entail managing and standardizing the data formats, protocols, and annotations generated related to these data; serving as our point of contact with the FAIRDOM initiative for findable, accessible, interoperable and reusable data,
Institutions: National Institute of Biologyorcid.org/0000-0003-0913-2715
Projects: Not specified
Institutions: Not specifiedorcid.org/0000-0003-3947-488X
Institutions: University Medical Center Göttingenorcid.org/0000-0002-1505-594X
Institutions: National Institute of Biologyorcid.org/0000-0001-7484-6031
Roles: Project Coordinator
Projects: Not specified
Institutions: Not specifiedorcid.org/0000-0002-3671-895X
Researcher at the European Institute for Systems Biology and Medicine, working on network-based data analytics within the EU eTRIKS Project.
Projects: HUMET Startup
Institutions: Centro de Investigación Príncipe Felipeorcid.org/0000-0003-3318-120X
Roles: Not specified
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data Management, Databases, Dynamic modelling, Genetics, Genomics, R, Systems Biology, Transcriptomics, Java
My scientific interests revolve around functional genomics, systems biology and the development of algorithms and software for the analysis of high-throughput data (mainly, but not restricted to, Next Generation Sequencing) and its application to the relationship between genotype and phenotype, mainly oriented to personalized and precision medicine. I am especially interested in the study of disease mechanisms and drug action mechanisms, drug repositioning and the definition of mechanism-based
Projects: FAIRDOM user meeting
Institutions: SYSBIO - Centre of Systems Biologyorcid.org/0000-0002-6566-2844
Scientific Project Manager at Luxembourg Centre for Systems Biomedicine, University of Luxembourg
Projects: Kinetics on the move - Workshop 2016
Research associate at HITS, software developer
Institutions: Norwegian University of Life Sciencesorcid.org/0000-0002-7778-4515
Systems biology for salmon farming is what I do. I lead the DigiSal project (http://tinyurl.com/digisal), whose full title is "Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture". DigiSal is part of Digital Life, the first call dedicated to systems biology by the Research Council of Norway. I'm also one of the lead modellers in GenoSysFat (http://tinyurl.com/genosysfat), working to improve the omega-3 content of salmon farmed on sustainable feeds by
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 Trainingorcid.org/0000-0002-8683-7084
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
I'm a biologist working in the field of scientific datases as a biocurator.
Institutions: University of Rostockorcid.org/0000-0002-5886-5563
Reproducibility of results is fundamental to all sciences. In computational biology, standard formats like Systems Biology Markup Language (SBML), CellML, or NeuroML enable the exchange of simulation models, and foster interoperability between software tools importing and exporting these formats.
My main research interest is in developing methods and tools that (1) improve the reuse of computational models in biology, (2) ensure reproducibility of modeling results and (3) that lead to easier
Institutions: School of Computer Science, University of Manchesterorcid.org/0000-0003-1604-1512
FAIRDOM Project Wrangler
Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meetingorcid.org/0000-0003-4958-0184
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Institutions: Institute of Cytology and Genetics
I am a biomodeler, PhD student. Actually, I've graduated from Novosibirsk State University on two specialities: my bachelor diploma is done in computer science and the master thesis is defended in information biology. So, I'm kind of drifting towards biology. I am a part of the Haploid Evolutionary Constructor project. Our research group studies are dedicated to the simulation of prokaryotic communities. Personally, I am involved into the simulation of spatially distributed bacterial communities
Roles: Not specified
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,
Software developer for FAIRDOM
I am a research technician at the Institute of Medical Science in Aberdeen, working for Prof. Ian Booth. The topic of our workpackage deals with K+ homostasis in Escherichia coli. I am working with the protein KefF, a regulatory subunit of the potassium channel KefC.
Roles: Not specified
Expertise: Nonlinear Dynamics, Data integration, Dynamic optimization., Optimal experimental design, bioreactor models, dynamics of biological networks, parameter estimation, coupling metabolome and environome, rapid sampling experiments, Data Management, Mathematical modelling
Process engineer, modeling biological systems since 1985.
Research fellow in Bioinformatics at the Warwick Systems Biology Centre, University of Warwick.
Working on high throughput data analysis (microarray data, next generation sequencing) and data integration (database management, text-mining, gene annotation via public databases)...
PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMO-DB pals for SUMO.
Software Engineer and Architect working within the FAIRDOM team.
Leading the development of SEEK and RightField.
I created this for all SysMo Modellers
http://www.semanticsbml.org/aym Annotate Your Model
There you can annotate your non SBML models with biological terms (MIRIAM annotations). As a cool extra you can view you model source code with inserted biological infomation.
Together with this http://www.semanticsbml.org/semanticSBML
you can serach for similar BioModels. The similarity search is based on MIRIAM annotations that are attached to you model. AYM also allows you to create annotations without
I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems.
I am a PAL and I am looking forward to communication with other SYSMO members.
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, Glycon 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 Trainingorcid.org/0000-0003-3540-0402
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
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 Trainingorcid.org/0000-0002-4980-3512
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.
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
Institutions: University of Leidenorcid.org/0000-0002-1279-5133
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
Metabolic networks with gene expression are researched under very different banners with different techniques. For example, there are the dynamic enzyme-cost Flux Balance Analysis (deFBA) , conditional Flux Balance Analysis , Metabolism and Expression models (ME models) , Resource Balance Analysis , etc. At their core, these methods can all understood as Resource Allocation Models (RAM) and while investigating their potential and their results, we encountered the problem of sharing
Contributor: Henning Lindhorst
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Date Published: 24th Oct 2017
Journal: Not specified
Citation: Knopp C. Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung [Bachelorarbeit]. Göttingen: Georg-August-Universität; 2017.
Date Published: 7th Apr 2016
Journal: Interface Focus
PubMed ID: 27051515
Citation: Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103.
Authors: Katy Wolstencroft, Olga Krebs, Jacky Snoep, Natalie Stanford, Finn Bacall, Martin Golebiewski, Rostyslav Kuzyakiv, Quyen Nguyen, Stuart Owen, Jakub Straszewski, Alan Williams, Bernd Rinn, Wolfgang Müller, Carole Goble, Soiland-Reyes S.,van Niekerk D. D.,Malmstrom L.
Date Published: 3rd Dec 2016
Journal: Nucleic Acids Res
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2016 Nov 28. pii: gkw1032.