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 and SySMO-DB2 project. I was responsible for metadata design (SEEK), conceptual and logical modelling of experimental data (JERM), now our team continue this work as FAIRDOM project (http://fair-dom.org/).
SEEK ID: https://fairdomhub.org/people/136
Locations: Germany , Norway , Austria
ORCID: https://orcid.org/0000-0003-3540-0402
Joined: 12th Feb 2009
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
Roles
Admin
Project administrator
- ZucAt
- FAIRDOM user meeting
- ErasysApp Funders
- EraCoBiotech 2 nd call proposal preparation
- FAIRDOM
- Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW)
- Kinetics on the move - Workshop 2016
- MESI-STRAT
- INCOME
- Multiscale modelling of state transitions in the host-microbiome-brain network
- TRALAMINOL
- Sustainable co-production
- INDIE - Biotechnological production of sustainable indole
- PoLiMeR - Polymers in the Liver: Metabolism and Regulation
- OLCIR: Optimization of Lung Cancer Therapy with Ionizing Radiation
- NAD COMPARTMENTATION
- Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population
- AquaHealth (ERA-BlueBio)
- Modelling COVID-19 epidemics
- SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
- FAIRDOM Community Workers
- SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke
- CC-TOP
- BioCreative VII
- MESI-STRAT Review
- SDBV/HITS
- MESI-Review 2024
Asset housekeeper
Asset gatekeeper
Programme administrator
Related items
- Programmes (15)
- Projects (48)
- Institutions (5)
- Investigations (7+26)
- Studies (8+65)
- Assays (7+125)
- Strains (0+7)
- Data files (22+113)
- Models (1+11)
- SOPs (7+22)
- Publications (54)
- Presentations (39+70)
- Events (19+44)
- Documents (1+62)
- Sample types (0+14)
- Samples (3+38)
- Collections (1+3)
The Deutsche Forschungsgemeinschaft (DFG) is the self-governing organisation for science and research in Germany. It serves all branches of science and the humanities. In organisational terms, the DFG is an association under private law. Its membership consists of German research universities, non-university research institutions, scientific associations and the Academies of Science and the Humanities.
Web page: https://www.dfg.de/en/index.jsp
BlueBio ERA-NET COFUND on the Blue Bioeconomy
Projects: AquaHealth (ERA-BlueBio)
Web page: https://bluebioeconomy.eu/
The Disease Maps Project is designed as a large-scale community effort. It is a network of groups that work together in order to better understand disease mechanisms. The project exchanges best practices, share information, develop tools to make it easier for all the involved groups to achieve their goals.
Projects: COVID-19 Disease Map
Web page: https://disease-maps.org
ERA CoBioTech is an ERA-Net Cofund Action under H2020, which aims to strengthen the European Research Area (ERA) in the field of Biotechnology through enhanced cooperation and coordination of different national and regional research programs, promoting systems biology and synthetic biology as technology driversto speed up research and innovation in industrial biotechnology.
› By maximizing synergies between current mechanisms of biotechnology research funding in Europe; › By fostering the exchange ...
Projects: Sustainable co-production, BESTER, Rhodolive, HOTSOLUTE, TRALAMINOL, C1Pro, Cell4Chem
Web page: https://www.cobiotech.eu/
The main objective of the ERANET proposal Systems Biology Applications - ERASysAPP (app = application = translational systems biology) is to promote multidimensional and complementary European systems biology projects, programmes and research initiatives on a number of selected research topics. Inter alia, ERASysAPP will initiate, execute and monitor a number of joint transnational calls on systems biology research projects with a particular focus on applications - or in other words so called ...
Projects: SysVirDrug, SysMilk, SysMetEx, MetApp, IMOMESIC, WineSys, CropClock, SYSTERACT, XyloCut, RootBook, ROBUSTYEAST, LEANPROT, ErasysApp Funders
Web page: https://www.cobiotech.eu/about-cobiotech/erasysapp
The GMDS (Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie) is the German Association for Medical Informatics, Biometry and Epidemiology and is the only scientific organization in this field in Germany. It is the official national member society within the EFMI and IMIA and closely cooperates with related scientific societies.
Projects: GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"
Web page: https://gmds.de
Projects: WG Infrastructure for Translational Research, INCOME, Translational Bioinformatics, Medical Biometry, Epidemiology, Medical Informatics
Web page: Not specified
ISBE-Light provides M4 service (Make Me My Mode) where non modelers can request (assistance with) the making of a computational model of their biological system. These models are deposited here.
Projects: Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population
Web page: http://www.isbe.nl
LiSyM (Liver Systems Medicine) represents a research network of German centers and institutions, brought together by a 20 Million Euro funding program of the German Government, in which mathematicians, modelers, pharmacologists, molecular biologists and clinical scientists work together to develop a Systems Medicine approach to study early and advanced liver disease. The aim of this unique research program is to acquire and use new experimental data and data from existing data bases to build ...
Projects: 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), FAIRDOM & LiSyM & de.NBI Data Structuring Training, New LiSyM project
Web page: http://www.lisym.org
FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).
Projects: FAIRDOM, FAIRDOM user meeting, FAIRDOM Community Workers
Web page: http://fair-dom.org
The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, SABIO-VIS
Web page: http://www.denbi.de
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, Function, control and engineering of microbial methylotrophy, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species, Screening of Secondary Plant Metabolites on Antihelmintic Activity in Ascaris scum, Munich Cluster for Systems Neurology, Test project May 2024, Biospecimen Collection Protocol, Winter Wheat (Triticum aestivum L.) Grain Yield, Quality, and Net Photosynthesis When Grown Under Semi-Transparent Cadmium Telluride Photovoltaic Modules Near Maturity, Benefit for All FAIR Data, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, DPL, Glycogen Metabolism in bacteria, ILS Ceramide Ring Trial, Project Test, DeepCurate, Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae, tets, Cancer Systems Biology Consortium (CSBC), Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells, Drug Discovery and Biotechnology Standard Operating Procedures, EDITH (Ecosystem Digital Twins in Health) test project
Web page: Not specified
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
Ionizing radiation (IR) leads to DNA double-strand breaks and can therefore be used as cancer treatment. However, some tumors are less responsive to radiation treatment because of their underlying molecular profile. Our ultimate goal is to understand the reaction of lung cancer cells with different phenotypes to IR on a molecular level to then provide the best therapy options for lung cancer patients with IR therapy.
OLCIR is funded by the Federal Ministry for Education and Research (BMBF, ...
Programme: This Project is not associated with a Programme
Public web page: https://www.sbi.uni-rostock.de/research/projects/detail/74
Start date: 1st Aug 2023
End date: 31st Dec 2027
Organisms: Homo sapiens
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.
Organisms: Not specified
Collection of training material for SEEK/FAIRDOMHub
Programme: FAIRDOM
Public web page: Not specified
Organisms: Not specified
Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!
At our users meeting you can:
- Learn why data and model management is ...
Programme: FAIRDOM
Public web page: Not specified
Organisms: Homo sapiens
SDBV group using Hub
Programme: Independent Projects
Public web page: Not specified
Organisms: Not specified
Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Theyhad and have tremendous influence on the biogeochemical cycles on Earth. Recently,cyanobacteria are increasingly investigated as cell factories for a sustainableeconomy. Despite their global, environmental and rising economic importance, ourknowledge on the regulation of their primary metabolism is fragmented.Cyanobacteria switch between photoautotrophic and heterotrophic modes ofmetabolism during day/night cycles or ...
Programme: DFG founded projects
Public web page: https://gepris.dfg.de/gepris/projekt/397695561
Start date: 1st Sep 2018
Organisms: Synechocystis sp. PCC 6803
MESI-Review 2024
Programme: Independent Projects
Public web page: Not specified
Organisms: Not specified
MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification. Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast ...
Programme: This Project is not associated with a Programme
Public web page: http://www.mesi-strat.eu
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
MESI-STRAT Review
Programme: Independent Projects
Public web page: Not specified
Organisms: Not specified
PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.
Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease ...
Programme: This Project is not associated with a Programme
Public web page: http://polimer-itn.eu/
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Microalgae Microbiomes: A natural source for the prevention and treatment of diseases in aquaculture
Aquaculture is one of the fastest growing food sectors in the world. In order to guarantee continuous, efficient and sustainable production and to safeguard the growth of this important sector, its protection from biological threats is crucial. Within the AquaHealth project, an international consortium of highly experienced partners will assemble and apply an advanced meta’omics toolbox on the ...
Programme: BlueBio ERA-NET COFUND
Public web page: https://aquahealth-project.com/
Start date: 1st May 2020
End date: 30th Apr 2023
Organisms: Microalgae
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.
Programme: e:med
Public web page: Not specified
Organisms: Homo sapiens
Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that ...
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Start date: 1st Mar 2020
End date: 24th Mar 2023
Organisms: Homo sapiens
Amino alcohol moieties are found in highly diverse classes of natural products that are of great importance due to their bioactivity, and they function as chiral building blocks for the synthesis of pharmaceuticals and agrochemicals. The chemical synthesis of stereoisomerically pure amino alcohols is difficult and typically requires uneconomical steps for protective group manipulations. Conventional syntheses in the chemical industry often use hazardous substances, consume large amounts of energy ...
Programme: Era CoBioTech
Public web page: https://www.cobiotech.eu/call-information
Start date: 1st Apr 2018
End date: 31st Mar 2021
Organisms: Escherichia coli K-12
to complete
Programme: Independent Projects
Public web page: Not specified
Organisms: Homo sapiens
The GMDS project group bundles activities for health-related FAIR data infrastructures in the fields of biomedical research, clinical data management and medical informatics in Germany. It aims at providing a platform for information exchange about best practice for and implementation of FAIR data management in these fields and constructing a network of FAIR data managements providers in these fields. Through bridging between providers and potential users of such data management platforms within ...
Programme: German Association for Medical Informatics, Biometry and Epidemiology (GMDS)
Public web page: https://gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/
Start date: 28th Feb 2019
End date: 27th Feb 2022
Organisms: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus
Here we collect curated data to be integrated into public repositories
Submitter: Olga Krebs
Studies: Metabolomics data a for Metabolight DB, Proteomics data for PRIDE, UniProt and others, Sequence data for European Nucleotide Archive (ENA )
Assays: Instructions for ENA submission
Snapshots: No snapshots
Current chemical concept recognition tools have demonstrated significantly lower performance for in full-text articles than in abstracts. Improving automated full-text chemical concept recognition can substantially accelerate manual indexing and curation and advance downstream NLP tasks such as relevant article retrieval. Participating in BioCreative Track NLM-Chem we focus identifying chemicals in full-text articles (i.e. named entity recognition and normalization).
Submitter: Olga Krebs
Studies: Chemical named entity recognition and annotation
Assays: Usage of fine-tuned BioBERT for identification of chemical entities, Using semantic search in MesH and PubChem databases for entity linking
Snapshots: No snapshots
Submitter: Christoff Odendaal
Studies: Model analysis, Model construction, Model validation
Assays: ACAD activity partitioning, Comparing acyl-CoA dehydrogenase deficiencies, HepG2 oxygen consumption, Kinetics Minireviews, MCADD patient personalised modelling, MCADD rescue titration, Metabolic control analysis, Models, Predicting urinary acylcarnitines under metabolic decompensation., Whole-body ketogenic flux
Snapshots: Snapshot 1
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 ...
Submitter: Olga Krebs
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
Snapshots: Snapshot 1, Snapshot 2
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 ...
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 ...
Snapshots: No snapshots
Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped ...
Sequence data for European Nucleotide Archive (ENA ) https://www.ebi.ac.uk/ena/
Submitter: Olga Krebs
Investigation: MESI-STRAT data for submission into public re...
Assays: Instructions for ENA submission
Snapshots: No snapshots
Metabolomics data a for Metabolight DB
Submitter: Olga Krebs
Investigation: MESI-STRAT data for submission into public re...
Assays: No Assays
Snapshots: No snapshots
Proteomics data for PRIDE, UniProt and others
Submitter: Olga Krebs
Investigation: MESI-STRAT data for submission into public re...
Assays: No Assays
Snapshots: No snapshots
Chemical named entity recognition (NER) is a significant pre-processing task in natural language processing. Identification and extraction of chemical entities from biomedical literature and entities linking to the knowledge base are essential steps for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we ...
Submitter: Olga Krebs
Investigation: Chemical Identification and Indexing in PubMed ...
Assays: Usage of fine-tuned BioBERT for identification of chemical entities, Using semantic search in MesH and PubChem databases for entity linking
Snapshots: No snapshots
Experimental study for hands on session
Submitter: Olga Krebs
Investigation: Using SEEK and I-S-A structure to integrate ex...
Assays: How to use templates for FAIR experimental data representation, How to use templates to structure experimental data 222
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.
Submitter: Katy Wolstencroft
Investigation: Creating data sheet template for 'omics data
Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, NimbleGen Transcriptomics Templates, RT-PCR Excel Template
Snapshots: No snapshots
we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll ...
Submitter: Maksim Zakhartsev
Investigation: Metabolic analysis of effects of sucrose transl...
Assays: Flux Balance Analysis of multi-compartment metabolic model of growing Ar...
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)
Submitter: Olga Krebs
Investigation: Creating data sheet template for 'omics data
Assays: Metabolomics Master Template, Standard-based Excel template for metabolomics data
Snapshots: No snapshots
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
Investigation: Creating data sheet template for 'omics data
Organisms: Saccharomyces cerevisiae, Homo sapiens : MCF-7 (wild-type / wild-type)
SOPs: No SOPs
Data files: Excel sheet template : concentrations of intrac..., The FAIR Guiding Principles for scientific data...
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
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: No SOPs
Data files: Metabolomics Master Excel Template and 1 hidden item
Snapshots: No snapshots
Here we will use JERM templates with embedded ontologies to describe and annotate example data
Submitter: Olga Krebs
Assay type: Interactomics
Technology type: Technology Type
Investigation: Using SEEK and I-S-A structure to integrate ex...
Organisms: No organisms
SOPs: Extraction and quantitative analysis of protein...
Data files: Master template, Transcriptomics Template (ArrayExpress Format)
Snapshots: No snapshots
Here we will use JERM templates with embedded ontologies to describe and annotate example data 222
Submitter: Olga Krebs
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Using SEEK and I-S-A structure to integrate ex...
Organisms: Bacillus subtilis : test 1 (insertion xyl / wild-type)
SOPs: Extraction and quantitative analysis of protein...
Data files: 0804_shake-flask-sigB-starvation
Snapshots: No snapshots
Usage of fine-tuned BioBERT for identification of chemical entities
Submitter: Olga Krebs
Biological problem addressed: Annotation
Investigation: Chemical Identification and Indexing in PubMed ...
Organisms: No organisms
Models: WELT code
SOPs: No SOPs
Data files: BioCreative VII Track 2 - NLM-CHEM
Snapshots: No snapshots
Using semantic search in MesH and PubChem databases for entity linking
Submitter: Olga Krebs
Biological problem addressed: Annotation
Investigation: Chemical Identification and Indexing in PubMed ...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: BioCreative VII Track 2 - NLM-CHEM
Snapshots: No snapshots
Here we present ENA-requirements compliant template and SOP for submission steps
Submitter: Olga Krebs
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: MESI-STRAT data for submission into public re...
Organisms: No organisms
SOPs: Standard Operating Procedure (SOP) for integra...
Data files: Excel template for metadata required by ENA t...
Snapshots: No snapshots
Excel template for metadata required by ENA to submit sequence data
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: MESI-STRAT data for submission into public re...
Studies: Sequence data for European Nucleotide Archive (...
Assays: Instructions for ENA submission and 1 hidden item
An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment). This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)
Creators: Katy Wolstencroft, Olga Krebs
Submitter: Katy Wolstencroft
Global microRNA expression profiling of high-risk ER+ breast cancers from patients receiving adjuvant Tamoxifen mono-therapy: a DBCG study
Creator: Lyng MB, Lænkholm A, Søkilde R, Gravgaard KH, LItman T, Ditzel HJ
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
GEO Data set GSE9893 : A gene expression signature predicting the recurrence of tamoxifen-treated primary breast cancer.
Creator: Chanrion M, Vincent N, Fontaine H, Salvetat N, Bibeau F, MacGrogan G, Mauriac L, Katsaros D, Molina F, Theillet C, Darbon JM
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
Shared version of Publication "Welcome to the Family: Identification of the NAD+ Transporter of Animal Mitochondria as Member of the Solute Carrier Family SLC25"
Creators: Mathias Ziegler, Ines Heiland, Magnus Monné, Andrey Nikiforov, Gennaro Agrimi, Ferdinando Palmieri
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Deatiled agenda forBest practices in research data management and stewardship (2021-06-14)
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Master template for hands on session
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: Using SEEK and I-S-A structure to integrate ex...
Excel sheet template : concentrations of intracellular metabolites
Creators: Olga Krebs, Katy Wolstencroft
Submitter: Olga Krebs
Investigations: Creating data sheet template for 'omics data and 1 hidden item
Studies: Creating template for metabolomics data and 1 hidden item
Assays: Standard-based Excel template for metabolomics ... and 2 hidden items
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.
Creators: Katy Wolstencroft, Olga Krebs
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating template for metabolomics data
Assays: Metabolomics Master Template
Here published artikel about The FAIR Guiding Principles for scientific data management and stewardship
Creators: None
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
test file
Creators: Olga Krebs, Vânia Pobre
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
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
MIAPE based Gel Electrophoresis Data Entry Worksheet
Creators: Olga Krebs, Holger Janssen
Submitter: Olga Krebs
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Proteomics
Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.
Creators: None
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Please fill in thistravel expense reimbursement report and send it together with original receipts to HITS
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Meeting location map
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
How to get to the hotel from rail station
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl... and 1 hidden item
Studies: Analysis of central carbon and energy metabolis... and 1 hidden item
Assays: Flux Balance Analysis of multi-compartment meta... and 1 hidden item
Standard Operating Procedure (SOP) for integration of MESI-STRAT sequence data stored in MESI-SEEK into ENA
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: MESI-STRAT data for submission into public re...
Studies: Sequence data for European Nucleotide Archive (...
Assays: Instructions for ENA submission and 1 hidden item
A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.
Creator: Olga Krebs
Submitter: Deleted submitter
Standard Operating Procedure for human genomic DNA extraction ( copied from GEO DataSets GSM1375121)
Creators: Olga Krebs, Christiane Opitz
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
Standard Operating Procedure describes the labeling of eukaryotic RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules (published by The Institute For Genomic Research
Creators: Olga Krebs, Jeremy Hasseman , Emily Chen, Ivana Yang
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This guidlines has been developed by Rita Volkers from Wageningen University for IBISBA project, as example to use
Creators: Olga Krebs, Rita Volkers
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Written Standard Operating Procedures provide workers with the operational information necessary to perform a job properly and ensure consistency in the operations. Standard Operating Procedures provide a historical record of steps in the how, why and when and serve as a training tool for teaching users.
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: K.A. Krishnamurthy, M.G.S. Rutten, J.A. Hoogerland, T.H. van Dijk, T. Bos, M. Koehorst, M.P. de Vries, N.J. Kloosterhuis, H. Havinga, B.V. Schomakers, M. van Weeghel, J.C. Wolters, B.M. Bakker, M.H. Oosterveer
Date Published: 2024
Publication Type: Journal
DOI: 10.1016/j.molmet.2023.101838
Citation: Molecular Metabolism 79:101838
Abstract (Expand)
Authors: Han Jin, Cheng Zhang, Martin Zwahlen, Kalle von Feilitzen, Max Karlsson, Mengnan Shi, Meng Yuan, Xiya Song, Xiangyu Li, Hong Yang, Hasan Turkez, Linn Fagerberg, Mathias Uhlén, Adil Mardinoglu
Date Published: 1st Dec 2023
Publication Type: Journal
DOI: 10.1038/s41467-023-41132-w
Citation: Nat Commun 14(1),5417
Abstract
Authors: Christiane A. Opitz, Pauline Holfelder, Mirja Tamara Prentzell, Saskia Trump
Date Published: 1st Oct 2023
Publication Type: Journal
DOI: 10.1016/j.bcp.2023.115798
Citation: Biochemical Pharmacology 216:115798
Abstract (Expand)
Authors: S. D. Wolf, C. Ehlting, S. Muller-Dott, G. Poschmann, P. Petzsch, T. Lautwein, S. Wang, B. Helm, M. Schilling, J. Saez-Rodriguez, M. Vucur, K. Stuhler, K. Kohrer, F. Tacke, S. Dooley, U. Klingmuller, T. Luedde, J. G. Bode
Date Published: 1st Aug 2023
Publication Type: Journal
PubMed ID: 37486964
Citation: Hepatol Commun. 2023 Jul 24;7(8):e0208. doi: 10.1097/HC9.0000000000000208. eCollection 2023 Aug 1.
Abstract (Expand)
Authors: Marie Solvay, Pauline Holfelder, Simon Klaessens, Luc Pilotte, Vincent Stroobant, Juliette Lamy, Stefan Naulaerts, Quentin Spillier, Raphaël Frédérick, Etienne De Plaen, Christine Sers, Christiane A Opitz, Benoit J Van den Eynde, Jingjing Zhu
Date Published: 21st Jun 2023
Publication Type: Journal
Citation: J Immunother Cancer 11(6):e006728
Abstract (Expand)
Authors: Wolfgang Müller, Lukrécia Mertová
Date Published: 23rd Mar 2023
Publication Type: Journal
DOI: 10.18420/BTW2023-57
Citation:
Abstract (Expand)
Authors: Alienke van Pijkeren, Anna-Sophia Egger, Madlen Hotze, Elisabeth Zimmermann, Tobias Kipura, Julia Grander, André Gollowitzer, Andreas Koeberle, Rainer Bischoff, Kathrin Thedieck, Marcel Kwiatkowski
Date Published: 3rd Mar 2023
Publication Type: Journal
DOI: 10.1021/acs.jproteome.2c00758
Citation: J. Proteome Res. 22(3):951-966
Abstract (Expand)
Authors: Pauline Pfänder, Lucas Hensen, Patricia Razquin Navas, Marie Solvay, Mirja Tamara Prentzell, Ahmed Sadik, Alexander M. Heberle, Sophie Seifert, Leon Regin, Tobias Bausbacher, Anna-Sophia Egger, Madlen Hotze, Tobias Kipura, Bianca Berdel, Ivana Karabogdan, Luis F. Somarribas Patterson, Michele Reil, Deepak Sayeeram, Vera Peters, Jose Ramos Pittol, Ineke van ’t Land-Kuper, Teresa Börding, Saskia Trump, Alienke van Pijkeren, Yang Zhang, Fabricio Loayza-Puch, Alexander Kowar, Sönke Harder, Lorenz Waltl, André Gollowitzer, Tetsushi Kataura, Viktor I. Korolchuk, Shad A. Mohammed, Phillipp Sievers, Felix Sahm, Hartmut Schlüter, Andreas Koeberle, Carsten Hopf, Marcel Kwiatkowski, Christine Sers, Benoit J. Van den Eynde, Christiane A. Opitz, Kathrin Thedieck
Date Published: 17th Jan 2023
Publication Type: Journal
DOI: 10.1101/2023.01.16.523931
Citation: biorxiv;2023.01.16.523931v1,[Preprint]
Abstract
Authors: Ghadeer Mobasher, Wolfgang Müller, Olga Krebs, Michael Gertz
Date Published: 2023
Publication Type: InProceedings
DOI: 10.18653/v1/2023.bionlp-1.40
Citation: The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks,pp.427-438,Association for Computational Linguistics
Abstract (Expand)
Authors: M. Abdellatif, T. Eisenberg, A. M. Heberle, K. Thedieck, G. Kroemer, S. Sedej
Date Published: 30th Nov 2022
Publication Type: Journal
PubMed ID: 36447531
Citation: Cell Stress. 2022 Aug 8;6(8):72-75. doi: 10.15698/cst2022.08.270. eCollection 2022 Aug.
Abstract (Expand)
Authors: M. Abdellatif, V. Trummer-Herbst, A. M. Heberle, A. Humnig, T. Pendl, S. Durand, G. Cerrato, S. J. Hofer, M. Islam, J. Voglhuber, J. M. Ramos Pittol, O. Kepp, G. Hoefler, A. Schmidt, P. P. Rainer, D. Scherr, D. von Lewinski, E. Bisping, J. R. McMullen, A. Diwan, T. Eisenberg, F. Madeo, K. Thedieck, G. Kroemer, S. Sedej
Date Published: 21st Jun 2022
Publication Type: Journal
PubMed ID: 35616058
Citation: Circulation. 2022 Jun 21;145(25):1853-1866. doi: 10.1161/CIRCULATIONAHA.122.059863. Epub 2022 May 26.
Abstract (Expand)
Authors: B. Feng, J. Gao
Date Published: 2nd Jun 2022
Publication Type: Journal
PubMed ID: 35653350
Citation: Database (Oxford). 2022 Jun 2;2022:baac037. doi: 10.1093/database/baac037.
Abstract (Expand)
Authors: Jörn Dietze, Alienke van Pijkeren, Anna-Sophia Egger, Mathias Ziegler, Marcel Kwiatkowski, Ines Heiland
Date Published: 1st Dec 2021
Publication Type: Journal
DOI: 10.1007/s00216-021-03732-7
Citation: Anal Bioanal Chem 413(30):7333-7340
Abstract (Expand)
Authors: Ghadeer Mobasher, Lukrécia Mertová, Sucheta Ghosh, Olga Krebs, Bettina Heinlein, Wolfgang Müller
Date Published: 11th Nov 2021
Publication Type: Proceedings
DOI: 10.1101/2021.11.09.467905
Citation: biorxiv;2021.11.09.467905v1,[Preprint]
Abstract (Expand)
Authors: Cecilia Cattelani, Dominik Lesiak, Gudrun Liebscher, Isabel I. Singer, Taras Stasyk, Moritz H. Wallnöfer, Alexander M. Heberle, Corrado Corti, Michael W. Hess, Kristian Pfaller, Marcel Kwiatkowski, Peter P. Pramstaller, Andrew A. Hicks, Kathrin Thedieck, Thomas Müller, Lukas A. Huber, Mariana Eca Guimaraes de Araujo
Date Published: 1st Oct 2021
Publication Type: Journal
Citation: Cells 10(10):2711
Abstract (Expand)
Authors: S. R. Mohapatra, A. Sadik, S. Sharma, G. Poschet, H. M. Gegner, T. V. Lanz, P. Lucarelli, U. Klingmuller, M. Platten, I. Heiland, C. A. Opitz
Date Published: 8th Mar 2021
Publication Type: Journal
PubMed ID: 33679737
Citation: Front Immunol. 2021 Feb 19;12:590532. doi: 10.3389/fimmu.2021.590532. eCollection 2021.
Abstract (Expand)
Authors: A. M. Heberle, U. Rehbein, M. Rodriguez Peiris, K. Thedieck
Date Published: 26th Feb 2021
Publication Type: Journal
PubMed ID: 33544134
Citation: Biochem Soc Trans. 2021 Feb 26;49(1):41-54. doi: 10.1042/BST20190730.
Abstract (Expand)
Authors: Hans V. Westerhoff, Alexey N. Kolodkin
Date Published: 1st Dec 2020
Publication Type: Journal
DOI: 10.1038/s41540-020-0138-8
Citation: npj Syst Biol Appl 6(1),18
Abstract (Expand)
Authors: Ahmed Sadik, Luis F. Somarribas Patterson, Selcen Öztürk, Soumya R. Mohapatra, Verena Panitz, Philipp F. Secker, Pauline Pfänder, Stefanie Loth, Heba Salem, Mirja Tamara Prentzell, Bianca Berdel, Murat Iskar, Erik Faessler, Friederike Reuter, Isabelle Kirst, Verena Kalter, Kathrin I. Foerster, Evelyn Jäger, Carina Ramallo Guevara, Mansour Sobeh, Thomas Hielscher, Gernot Poschet, Annekathrin Reinhardt, Jessica C. Hassel, Marc Zapatka, Udo Hahn, Andreas von Deimling, Carsten Hopf, Rita Schlichting, Beate I. Escher, Jürgen Burhenne, Walter E. Haefeli, Naveed Ishaque, Alexander Böhme, Sascha Schäuble, Kathrin Thedieck, Saskia Trump, Martina Seiffert, Christiane A. Opitz
Date Published: 1st Sep 2020
Publication Type: Journal
DOI: 10.1016/j.cell.2020.07.038
Citation: Cell 182(5):1252-1270.e34
Abstract (Expand)
Authors: Lukas Metzler, Ulrike Rehbein, Jan-Niklas Schönberg, Thomas Brandstetter, Kathrin Thedieck, Jürgen Rühe
Date Published: 4th Aug 2020
Publication Type: Journal
DOI: 10.1021/acs.analchem.0c00187
Citation: Anal. Chem. 92(15):10283-10290
Talk given by Olga Krebs and Aleyey Kolodkin at the" Best practices in research data management and stewardship" training on 17 June 2021
Creator: Olga Krebs
Submitter: Olga Krebs
COVID-19 modelling efforts in advice to Luxembourg government , talk given by Atte Aalto
Creators: Olga Krebs, Stefania Astrologo, Atte Aalto, Jorge Goncalves
Submitter: Olga Krebs
FAIRDOMHub: Implementing FAIR Data Principles for scientific data management and stewardship. Talk given by Olga Krebs
Creators: Olga Krebs, FAIRDOM team
Submitter: Olga Krebs
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 ...
Creator: Olga Krebs
Submitter: Olga Krebs
Talk by Jon Olav Vik, Norwegian University of Life Sciences
Creator: Jon Olav Vik
Submitter: Olga Krebs
Talk given by Sergey Lashin from Institute of Cytology and Genetics, Novosibirsk, Russia
Creators: Sergey Lashin, Alexandra Klimenko
Submitter: Olga Krebs
Presented by Martin Böhm, German Cancer Research Center, Heidelberg, Germany
Creators: Markus Stepath, Martin Böhm
Submitter: Olga Krebs
Documentation for using FAIRDOMHUB / SEEK for a workshop in Warnemunde, September 2015.
Creators: Natalie Stanford, Stuart Owen, Norman Morrison, Olga Krebs
Submitter: Natalie Stanford
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): ...
Start Date: 5th Jun 2024 (5th Jun 2024 (Etc/UTC))
End Date: 5th Jun 2024 (5th Jun 2024 (Etc/UTC))
Event Website: https://fair-dom.org/events/2024-06-05-FAIRDOM-user-meeting
Country: Germany
City: Heidelberg
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
Start Date: 17th Jun 2021
End Date: 17th Jun 2021
Event Website: https://elixir-luxembourg.org/events/2021_06_14_research_data_management
Country: Luxembourg
City: Not specified
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 ...
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 ...
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
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 ...
Start Date: 27th Aug 2018
End Date: 31st Aug 2018
Event Website: http://conf.bionet.nsc.ru/sbb2018/en/
Country: Russian Federation
City: Novosibirsk
Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you! At the meeting you can
- Learn why data and model management is important, ...
Start Date: 15th Sep 2016
End Date: 15th Sep 2016
Event Website: http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/
Country: Spain
City: barcelona
Here we collect all the presentations, hands on instructions and documentation for Kinetics on the move Workshop on Data for Computational Modeling
Start Date: 30th May 2016
End Date: 31st May 2016
Event Website: http://www.h-its.org/de/research/sdbv/veranstaltungen/kinetics-on-the-move-practical-workshop-on-data-for-computational-modelling/
Country: Not specified
City: Heidelberg
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 ...
Start Date: 9th Dec 2015
End Date: 10th Dec 2015
Event Website: Not specified
Country: Germany
City: Munich
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 ...
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, ...
Start Date: 9th Dec 2014
End Date: 11th Dec 2014
Event Website: http://www.swat4ls.org/workshops/berlin2014/
Country: Germany
City: Berlin
Systems Biology is one of the most prominent newly emerging interdisciplinary science areas. By connecting fields such as genomics, proteomics, cell biology, medicine, molecular biology, biochemistry and genetics, with mathematics, bioinformatics, engineering and computation, it 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 eventually of whole cells are generated, which are ...
Country: Austria
City: Innsbruck
7th All hands PALs + SEEK users meeting will be co-located with Computational Modeling in Biology Network (COMBINE) meeting taking place from 16th to 20th of September 2013 in Paris. COMBINE is an initiative to coordinate the development of the various community standards and formats, details to meeting agenda and location here: http://mbine.org/events/COMBINE_2013
We plan to arrive on Wednesday, 18th, to participate in COMBINE on Thursday and Friday morning, and to have PALs- only sessions on ...
Start Date: 18th Sep 2013
End Date: 20th Sep 2013
Event Website: Not specified
Country: France
City: Paris
The next All Hands PALs meeting will take place on Thursday 29th and Friday 30th November 2012 in Heidelberg. The meeting will start on Thursday morning (arriving in Heidelberg on Wednesday evening), and finishing after lunch on Friday, so that you can get to home before weekend starts.
Meeting agenda
Thursday 29th November 9:15 Arriving at HITS 9:30 – 10:00 Introduction to PALs meeting 10:00 – 10:45 Review of new SEEK features. 10:45 – 11:00 Coffee break 11:00 – 12:00 An update on SEEK BioSamples ...
Start Date: 29th Nov 2012
End Date: 30th Nov 2012
Event Website: Not specified
Country: Germany
City: Heidelberg
We've presented SEEK at the ICSB / PLATFORM Computational Tools and Algorithms on 20th of August 2012 in Toronto, Canada
Country: Canada
City: Toronto
The third annual COMBINE meeting took place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 through Sunday Aug. 19, 2012
Start Date: 15th Aug 2012
End Date: 19th Aug 2012
Event Website: http://co.mbine.org/events/COMBINE_2012
Country: Canada
City: Toronto
The 5th annual All Hands PALs meeting will take place on 21-22 of May 2012 in Rostock/Warnemünde. The main purpose of the meeting is to update the PALs on the latest developments in SysMO-SEEK and to identify new features and priorities arrising from work in the SysMO projects .
Meeting agenda:
Monday 21st of May
Morning - What's new in SEEK 9:15 – 9:45 Arrival, Introduction and welcome to new people (Wolfgang) 9:45 – 10:45 New features in SEEK & Roles (Stuart) 10:45 – 11:15 Coffee break 11:15 ...
Start Date: 21st May 2012
End Date: 22nd May 2012
Event Website: Not specified
Country: Germany
City: Rostock/Warnemünde
The next SySMO SEEK users meeting will be held in Berlin on March 26-27 2012. Since our last users workshop focused on modeling issues, this one will focus on experimental data and its linking to models. Meeting info is also available at our web page details here http://www.sysmo-db.org/node/53. Detailed agenda can be downloaded here https://seek.sysmo-db.org/data_files/937
Meeting will take place at the Beuth Hochschule für Technik Berlin http://www.beuth-hochschule.de/1654/, accomodation hotel ...
Start Date: 26th Mar 2012
End Date: 27th Mar 2012
Event Website: https://seek.sysmo-db.org/site_announcements/16
Country: Germany
City: Berlin
Agenda Saturday 27th August
9:15 Pick up from Hotelo hotel 9:30 – 10:00 Arrive at HITS, coffee 10:00 – 10:15 Introduction 10:15 – 11:45 Lightning Talks by PALS and SysMO-DB team *(for details see Introduction to Lightning Talks and ISBE session at PALs meeting on 27th of August in Heidelberg associated to this event http://seek.sysmo-db.org/data_files/902 ) 11:45 – 12:15 Coffee break 12: 15 – 13:00 Review of new SEEK features (presentation available as data file associated to this event here ...
Start Date: 26th Aug 2011
End Date: 27th Aug 2011
Event Website: Not specified
Country: Germany
City: Heidelberg
Best practices in research data management and stewardship training on 17 June 2021
Day 4. FAIRDOMHub and Zenodo Hands On Instructions (by Olga Krebs and Aleksey Kolodkin)
Creators: Olga Krebs, Alexey Kolodkin
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
MESI-STRAT data collection for public repository ENA
Maintainers: Olga Krebs, Sofya Marchenko, Leon Regin, Pamela Riemer, Mirja Tamara Prentzell
Number of items: 0
Tags: Sequence, RNA, human cell culture, Cancer, drug