Hannah O'Keefe
SEEK ID: https://fairdomhub.org/people/1188
Location:
United Kingdom
ORCID:
https://orcid.org/0000-0002-0107-711X
Joined: 31st Oct 2018
Expertise: Not specified
Tools: Not specified
Roles
Project administrator
- Fairdom Hub documents
- RStudio-Shiny and Java_API connection testing
- Outreach - Simulation of breast cancer development using an agent based modelling approach
- Outreach - Breast Cancer RStudio-Shiny application
- Outreach - Senescence RStudio-Shiny application
- Outreach - Simulation of cellular senescence using an agent based modelling approach
Asset housekeeper
Asset gatekeeper
Programme administrator
Their tagsRelated items
Development of a NetLogo simulation and RStudio-Shiny web application surrounding cellular senescence for outreach. Aimed at GCSE/A-level students
Projects: Not specified
Web page: Not specified
testing access to fairdom hub documents. data files etc via the API in various programming languages
Projects: Fairdom Hub documents, RStudio-Shiny and Java_API connection testing
Web page: Not specified
A small application which simulates the development of breast cancer
Projects: Outreach - Simulation of breast cancer development using an agent based modelling approach, Outreach - Breast Cancer RStudio-Shiny application
Web page: Not specified
Systems modelling molecular mechanisms of ageing
Projects: Systems modelling age-related changes in the maintenance of dermal extra-cellular matrix: mechanisms and interventions, Are microRNAs key mediators of cartilage destruction in osteoarthritis?, Dynamic interplay between nuclei and mitochondria in ageing cells, Outreach - Senescence RStudio-Shiny application, Outreach - Simulation of cellular senescence using an agent based modelling approach
Web page: https://www.ncl.ac.uk/camb/staff/profile/darylshanley.html
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, 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, Fluid flow project, Smart Garden Watering System, The role of different fatty acids, AQUACIRCLE, IDIM, Sampling vicinity of industrial settings for pathogens and GMO identification, RNA-seq data for paper, RNA-seq data
Web page: Not specified
Programme: Independent Projects
Public web page: Not specified
This project aims to develop an agent based model using the Netlogo package which can then be used for outreach in schools and the wider community. This model represents cellular senescence in skin with the potential for users to explore the effects of combination treatments in silico.
Programme: Newcastle University Systems Modelling of Ageing
Public web page: Not specified
Web application developed using RStudio-Shiny for outreach. Incorporates information, videos and images, worksheets and simulations surrounding cellular senescence and therapy. Incorporates NetLogo simulation from "Outreach - Simulation of cellular senescence using an agent based modelling approach" project.
Programme: Newcastle University Systems Modelling of Ageing
Public web page: Not specified
Overall, we will measure in-vitro and model in-silico the short-term biochemical network dynamics of extra cellular matrix maintenance (ECM) in populations of young, old and senescent dermal fibroblasts. We have shown in previous work that differences in network dynamics are highly informative and provide a means to identify parts of the network that could be targeted to restore healthy function.
The work will be first carried out in 2D culture of human dermal fibroblasts then extended to a novel ...
This project aims to develop an agent based model using the Netlogo package which can then be used for outreach in schools and the wider community. This model represents the development of breast cancer with the potential for users to explore the effects of combination treatments in silico.
Programme: Breast Cancer Simulation
Public web page: Not specified
Start date: 1st Jun 2019
End date: 1st Aug 2019
Web application developed using RStudio-Shiny for outreach. Incorporates information, videos and images, worksheets and simulations surrounding breast cancer development and therapy. Incorporates NetLogo simulation from "Outreach - Simulation of breast cancer development using an agent based modelling approach" project.
Programme: Breast Cancer Simulation
Public web page: Not specified
documents for use with RStudio-Shiny and java API testing
Programme: API_testing_projects
Public web page: Not specified
testing fairdom API in Java and R programming language for use in Breast cancer outreach project
Programme: API_testing_projects
Public web page: Not specified
Small set of values for entering into NetLogo simulation
Creator: Hannah O'Keefe
Submitters: Daryl Shanley, Hannah O'Keefe
DownloadSmall set of values for entering into NetLogo Simulation
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Very simple unrealistic values for Metformin kinetics (Km). For use in a simple graphical model.
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Very simple unrealistic values for Fisetin kinetics (Km). For use in a simple graphical model.
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Very simple unrealistic values for Everolimus kinetics (Km). For use in a simple graphical model.
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Very simplistic unrealistic values for tamoxifen Kinetics (Km). For use in a simple graphical model.
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Model of selective destruction in a single population of cells with differing sensitivities for growth
Creators: James Wordsworth, Daryl Shanley, Hannah O'Keefe
Submitter: James Wordsworth
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
NetLogo desktop version of Breast cancer development agent based model
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
desktop version of NetLogo model of cellular senescence in dermal layer of skin
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
fifth worksheet for RStudio-Shiny application, relating to the following pages:
simulation2 concluding question (all pages, simulations, worksheets)
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
fourth worksheet for RStudio-Shiny application, relating to the following pages:
Therapies and senescence simulation1
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
third worksheet for RStudio-Shiny application, relating to the following pages:
Senescence in tissue biology
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
second worksheet for RStudio-Shiny application, relating to the following pages:
Cellular senescence
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
first worksheet for RStudio-Shiny application, relating to the following pages:
Systems Biology
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
fifth worksheet for RStudio-Shiny application, relating to the following pages:
simulation2 concluding question (all pages, simulations, worksheets)
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
fourth worksheet for RStudio-Shiny application, relating to the following pages:
computational modelling simulation1
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
third worksheet for RStudio-Shiny application, relating to the following pages:
treatment options drug resistance
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Second worksheet for RStudio-Shiny application, relating to the following pages:
Risk factors, features and biomarker cancer characteristics
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
first worksheet for RStudio-Shiny application, relating to the following pages:
what is breast cancer breast cancer types
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
