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Hours: 1338.40

Project Date User Activity Issue Comment Hours
Pathogen outbreak study - Pseudomonas single isolate WGS 10/07/2019 Katie Lennard Analysis Time spent up until 30/9/2019 88.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 10/04/2019 Jon Ambler Analysis Support #90: QC of aligned reads 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 10/04/2019 Jon Ambler Analysis Support #100: Time seres analysis 24.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 10/04/2019 Jon Ambler Analysis Support #100: Time seres analysis 16.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 10/04/2019 Jon Ambler Analysis Support #92: Differential expression analysis 16.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 09/18/2019 Thys Potgieter Analysis Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization different normalization and imputation techniques tested - Median, Quantile, and None compared. Slides generated. Median better than Quantile, KNN appears better than BPCA for gene set enrichment but not protein differential abundance 4.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 09/17/2019 Thys Potgieter Analysis Feature #98: Sample processing with MetaMorpheus Sample Calibration run with MetaMorpheus 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 09/17/2019 Thys Potgieter Analysis Feature #98: Sample processing with MetaMorpheus Pilot run with 4 samples 2.00 Actions
Microbiota profiling of cows milk with and without traditional fermentation 09/04/2019 Katie Lennard Analysis Up until 3/9/2019 20.00 Actions
The impact of fire and herbivores on soil microbes 09/04/2019 Katie Lennard Meeting Time spent up until 3/9/2019 13.00 Actions
Pathogen outbreak study - Pseudomonas single isolate WGS 09/03/2019 Katie Lennard Analysis Time spent until 2/9/2019 86.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 08/08/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Contaminant versus total protein content visualization figure (Added to QC component of pipeline) 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 08/05/2019 Thys Potgieter Analysis Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Runs for cells and tissues completed, QC figures added to meeting presentation, output moved to research drive. 3.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 08/05/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Gene and protein ID added to differential abundance analysis output, unit tests. 3.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/25/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Exclude samples from downstream analysis using config file 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/23/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Boxplots for peptide identifications, scatterplots of sample protein intensities against median (QC). 4.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/19/2019 Thys Potgieter Development Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization Bayes PCA tested, configurable normalization method in pipeline. Box plots improved to exclude outliers in plots 4.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Jon Ambler Investigation Support #90: QC of aligned reads 3.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Jon Ambler Analysis Support #92: Differential expression analysis 6.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Thys Potgieter Analysis Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Methods summary presentation created and sent to Relebohile 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Thys Potgieter Development Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Data analyzed, experimental design file created for cells and tissues separately. 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Thys Potgieter Development Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Bug fixes and unit tests for mqmetaproteomics pipeline 6.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Thys Potgieter Analysis Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu Quality control - samples less than 1 percent assigned spectra excluded. normalization and imputation methods tested. 6.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 07/02/2019 Thys Potgieter Analysis Support #85: MaxQuant run of raw proteomics data MaxQuant run restarted, experiment names added 2.00 Actions
Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) 06/24/2019 Jon Ambler Development Support #92: Differential expression analysis Creating the design_formula file needed to create DESeqDataSet 5.00 Actions
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