Investigations

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160 Investigations visible to you, out of a total of 464

We performed topological analysis on pathways from a harmonised dataset containing pathways from the COVID-19 Disease Map, WikiPathways, and Reactome. The analysis was done using Vanted, SBGN-ED, and LMME which support the import and export of several standard formats (such as SBML, and SBGN-ML).

Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated 2022 as bioRxiv https://doi.org/10.1101/105437v2, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU TiMet project, https://fairdomhub.org/projects/92.

This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. NB ...

Metadata

Investigation: _I_Test

Short Name: Test

Title: Test investigation

Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Members of the genus Aromatoleum are cosmopolitan in diverse habitats and utilize a broad range of recalcitrant organic molecules coupled to denitrification or O2-respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we here studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate and acetate utilized under nitrate-reducing vs. oxic conditions. Multi-OMICS (transcriptome, proteome and metabolome) ...

Submitter: Meina Neumann-Schaal

Studies: No Studies

Assays: No Assays

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Studies: _S_Show

Assays: _A_Work-R

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Studies: _S_Show

Assays: _A_Work-R

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Studies: _S_Show

Assays: _A_Work-R

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Studies: _S_Show

Assays: _A_Work-R

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Submitter: Andrej Blejec

Studies: _S_Show

Assays: _A_Work-R

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

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 ...

No description specified

Submitter: James Wordsworth

Studies: No Studies

Assays: No Assays

Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 02_FieldTrials Title: Field trials Description: Field trials - spraying CPB larvae on potato field with the insecticidal dsRNA validated for effectiveness in the laboratory trials Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Short Name: 01_LabTrials Title: Laboratory trials Description: Selection of targets and their validation in trials performed in the laboratories and greenhouse at NIB Phenodata: ./phenodata_20210113.txt pISA Investigation creation date: 2021-01-13 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Because enzyme activity depends very much on the reaction conditions, it is crucial to report all these metadata (see for example the STRENDA Guidelines:https://www.beilstein-strenda-db.org/strenda/public/guidelines.xhtml).

Another challenge in experiments to determine enzyme reaction parameters is the choice of suitable substrate concentrations to enable optimal kinetic fits and the informed choice of a kinetic model.

A Jupyter notebook is given to assist in the choice of substrate concentrations ...

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work is published in Urquiza-Garcia and Millar, Testing the inferred transcription rates of a dynamic, gene network model in absolute units, In Silico Plants, 2021.

Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (first version U2017.1; published as U2019.1) model, rescales ...

Multiscale and multicellular simulation of SARS-CoV-2 infection uncover points of intervention to evade apoptosis.

Summary:

Our framework enables the simulation of the dynamics of signaling pathways that include the relevant players in SARS-CoV-2 infection, at the level of the individual cell and of the cell population. These different players encompass the virus, epithelial and immune cells. The model focuses on apoptosis and suggests two knock out alterations that force apoptosis of the ...

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 ...

An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure these properties are ...

The COVIDminer text mining project (https://rupertoverall.net/covidminer/) reads the published literature concerning SARS-CoV-2 and COVID-19 to extract statements about (primarily molecular) interactions. Using the API associated with this project, putative interactors can be automatically retrieved for the existing COVID-19 Disease Maps. New interactions are prioritised based on their frequency in the literature and the topological importance of the interaction targets to provide a focussed set ...

Submitter: Rupert Overall

Studies: No Studies

Assays: No Assays

We further used the transcriptome dataset from the GEO database with accession number GSE147507 (Blanco-Melo et al., 2020) to extract the series number 5 from the dataset, consisting of 2 conditions in triplicate, A549 cells treated with a mock and A549 infected with SARS-CoV-2, measured 24 hours after treatment. Phosphoproteomic data of mock-treated and SARS-CoV2 infected cells were extracted from (Stukalov et al., 2020). We then applied our pipeline described in M&M X. This work notably ...

In this investigation, we aim to develop automatic workflows to pinpoint drug targets carrying genomic variants at high frequency in the population

In this investigation we aim to develop automatic workflows to analyze COVID19 Omics data to understand and predict the molecular pathways depicting host-virus interaction.

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