Timeline
2024
April 15
- KMeans: First version of K-Means Algorithm is now available for all users
- Identification: A slider with prediction confidence cut-off values to Identification results view is added. Cut-off can be edited and saved
- Prediction Models improvements:
- First version of re-train prediction models with new samples is now available for premium users
- Now optimizaction information, if available, is displayed
- Users can now uploading zip files with open format files in it. Folder hierarchy is kept
- Collection: Add editor options to Usage Notes and Abstract fields
- Training: Youden Index is now available in ROC curve in training.
February 15
- Ribopeaks: First version of Ribopeaks integration in experiment detail view
- Alignment: Now spectra can be aligned by selecting reference peaks
- Validation: Users now can compare one category versus the others to obtain all metrics
- Correlation Analysis: Heatmap is now included in pairwise mode
- Biomarker Analysis: Wilcoxon-Mann-Whitney test is now available
- Global Prediction Bases are now available for Premium MALDI users.
January 24
- Experiment new workflow: First version of the experiment view redesign project, which includes a data flow pipeline for selecting the three main processes before the peak matrix (Preprocessing, Outlier, and Train/Test set splitting).
- Outlier: With the new experiment workflow, selected outlier samples will be skipped in subsequent actions.
January 10
- Task list: First version of Task list functionality to check the state of the user tasks in the last 2 days
- Antibiotic Analysis Detection Module: Enabled test module for new Imipenen values
- Studies: Now studies can be archived
- Reproducibility tests: ANOVA results are now displayed for analysis with more than two categories
- Premium/Basic accounts: Now user can distinguish between MALDI and FTIR premium when accesing to the different modules
- Correlation Analysis: User now can export a unique excel file with the results of all groups
2023
December 7
- Antibiotic Analysis Detection
- Module enable for all Premium Users
- Works with or without multicenter projects
- Mabritec Central:
- Mabritec Central is now available for all Premium Users
- Mabritec Central has now its own box in Bioanalsysis screen
- Average Spectra from Replicates: Advanced mode is now available. Now samples with the same name but in different folders are not mixed when grouping replicates.
- Performance: Improvements in “preprocessing” steps and “peak matrix generation” steps performance
November 9
- FTIR: “Extended Polysaccharide” (1300-800) region is now available as preset in FTIR mode
- Correlation analysis: Correlation analysis is now available with MALDI-TOF data
- Train/Test datasets:
- New method for splitting data into train and test datasets is added
- Info of splitted sets can be download as csv
- Category table info is now displayed at experiment detail view
- When params have no changed, a button is now available to resplit the data into two different datasets
- Find Peaks Algorithm: Dynamic Threshold algorithm is now available
- Biomarker Analysis:
- New option to discriminate one category from the rest in ROC analysis is now available
- Now users can now directly create a new peak matrix in a new step in Biomarker Analsyis with selected peaks
- Number of samples of each category is now displayed
- Validation: Now samples categories in categories step of the validation process are now recognized automatically
- Dendrogram: A toggle button is added to show/hid the cut-off value
- SVM: Poly Kernel option is now available
- Correlation/Distance Heatmap: Now color is from blut to red space. Gaps are added between cells
September 18
September 5
- Export and import files to/from Mabritec tool is now available.
- Imported identification from Mabritec are now displayed in Clover MSDAS.
August 4
- Hierarchical Clustering:
- Cut-off value can be now calculated in automatic or optimal mode.
- Features dendrogram is now available when you build a matrix with peaks.
- Outlier detection:
- A table with summarized analysis is now added.
- User can now modify the STD value limits.
- Samples can now be marked and saved as outliers within an experiment.
July 19
June 21
- Hierarchical Clustering & Dendrogram
- PCA at HC: Now PCA data is displayed when retrieving HC
- Size plot and graphs can be now edited by the user
- Dendrogram: Color squares can be now edited by the user
- Cut-off: User can set a custom cutoff value to detect the clusters
- Summary Table: A new table is displayed summarizing the content of the detected cluster and how the actual categories/classes are distributed
- Categories as Dendrogram Metadata: One or several columns can be displayed next to the dendrogram. Each column has one coloured rectangle per spectrum. Each rectangle color matches one of the actual categories/classes labelled for the spectrum. This way, it is easy to visually check the detected clusters (unsupervised) and the actual clusters (supervised categories/classes)
- Dual Tech: MALDI & FTIR
- Now you can add your preferred technology at SignUp view
- At User Profile section you can change now your preferred technology
- Filter in Study List so MALDI-TOF or FTIR can be selected
- Antibiotic Hydrolysis Analysis
- Support for Meropenem
May 19
- Premium users mode is now activated. All module and features are now unlimited for premium users.
- FT-IR data.
- FTIR Quality Control Module: First version of QC test for FTIR data.
- Inclusion of new default ranges and internal improvements in range selection with FTIR data.
- FTIR Reproducibility Module: First Version of reproducibility Analysis for FTIR data.
- Algorithms.
- Balanced Accuracy metric at confusion matrix is now calculated and displayed in confusion matrices.
- PCA: Edit size, color and shape of displayed dots.
- Analysis.
- t-test is now available in biomarker analysis as univariate analysis.
- MALDI Biomarker Analysis Module have been redesigned.
- SNP pairwise distance heatmap: First version of Single Nucleotide Polymorphism heatmap.
May 18
https://doi.org/10.1128/jcm.01751-22
April 4
January 30
- Armonisation between FTIR workflow and Clover MSDAS have been updated.
- Rubberband algorithm has been added as Baseline correction algorithm.
- New normalization algorithms:
- Vector Normalization
- Amide I Normalization
- Amide II Normalization
- Predefined ranges for absorbance mass filtering:
- Membrane lipids [3000-2800]
- Proteins [1800-1500]
- Polysaccharides [1200-900]
January 5
https://doi.org/10.1128/jcm.01110-22
2022
November 28
- Outliers Detection Module first version release. PCA Reconstruction and Spectra Correlation analysis have been implemented.
- Shapley Values plot includes now a bar plot to show the shapley values mean.
- New file size upload limit is upgrade to 300MB.
- Validation & Identification modules run now asynchronously. You can leave the screen and recover the result later.
- Hyperparameters at classification can be now choosen manually or calculated via autotune algorithm.
- ROC and Precision-Recall curves displayed up to 4 decimals for AUC values and can be downloaded in CSV format.
- Error Rate have been added as a metric.
- LightGBM have been adjusted on how hyperparameters are optimized.
- In the ROC curve table at Biomarker Analysis module, you can click now on the table rows for selecting masses. Once they are selected, a peak matrix can be automatically generated by using those masses.
September 7
Major updates
- Multitask mode: Now supervised classifiers run in asynchronous mode. Therefore, the user can leave or close the page/tab safely or work in other tasks, because the result will be there next time the classifier page is accessed.
- Performance improvements: Algorithms now work in dedicated processes.
- Random Forest: Newly optimized hyperparameters are: number of estimators, max features, max tree depth, min split size, min number of samples per leaf.
- LightGBM: Adjustments on hyperparameters optimization. Shapley feature importances optimization.
- Biomarker Analysis: In the ROC curve table, the user can click on the table rows for selecting masses. Once they are selected, a peak matrix can be automatically generated by using those masses as biomarkers.
Minor updates
- TIC normalization: is now performed using the area under the entire spectrum.
- Find Peaks Graph: The user can click on a detected peak for displaying a label with the mass value.
- Biomarker Analysis: When a row is clicked in the ROC curve table, now it is also filtered in the Peak Distribution table.
Contact Information | Clover Bioanalytical Software
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(34) 958 991 543
Office
- Edif. Centro de Empresas PTS.
- Av. del Conocimiento, 41
- 18016 Granada, Spain