Projects: 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, GMDS Project Group FAIR Data Infrastructuresorcid.org/0000-0002-9077-5664
Institutions: National Institute of Biologyorcid.org/0000-0002-1669-6482
Roles: PhD Student
Expertise: Data analysisMathematical modellingBioinformaticsSystems biology, Data Management, Data analysis, Data integration, Visualization, computational biology, Molecular Biology, Statistics, Bioinformatics, Mathematical and statistical modeling, Programming
Tools: Bioinformatics, Computational and theoretical biology, Computational Systems Biology, Data integration, Data Management, Databases, Dynamic modelling, Molecular Biology, Python, R, Systems Biology
Computational Biologist, Young Researcher at Department of Biotechnology and Systems Biology, National Institute of Biology NIB and PhD candidate in Statistics, Ljubljana, Slovenia
Projects: Not specified
Institutions: Not specifiedorcid.org/0000-0002-8363-0678
Institutions: University Medical Center Göttingenorcid.org/0000-0002-1505-594X
Student (M.Sc. Medical Informatics) @ Georg-August-University Göttingen
Research Assistant @ Department of Medical Informatics, University Medical Center Göttingen
Institutions: National Institute of Biologyorcid.org/0000-0003-4776-7164
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time pathways in Arabidopsis on the summer Solstice., PlaSMo model repository
Institutions: University of Edinburghorcid.org/0000-0003-1756-3654
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: National Institute of Biologyorcid.org/0000-0003-0913-2715
Institutions: National Institute of Biologyorcid.org/0000-0001-7484-6031
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
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
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 Training, New LiSyM project, EnzymeML, GMDS Project Group FAIR Data Infrastructuresorcid.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.
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
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 meeting, FAIRDOM Templatesorcid.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
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.
Institutions: Beuth University of Applied Sciences Berlinorcid.org/0000-0001-6096-1354
Roles: Project Coordinator
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, 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 Regulationorcid.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 Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group FAIR Data Infrastructuresorcid.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.
Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016
Contributor: Olga Krebs