Spectre is a versatile tool used for analysis of MALDI-MSI data sets.
For the sake of simplicity, the toolset provided is available to be used through web application interface, which is currently a work-in-progress.
In order to build and run the application, please refer to the installation section.
The project is currently in its early stage. However, it comprises the implementation of our own spectra modelling based on Gaussian Mixture Models, and Divisive IK-means algorithm for unsupervised segmentation, which can be used for efficient dataset compression, as well as for knowledge discovery. Aformentioned algorithms have already been published and refering links have been enclosed under references section.
Also, several classification and clusterization methods will be provided soon, along with supporting statistics.
The Web service is all the time available here. If you still would like to host it yourself, please contact us by e-mail. We will provide you with exhaustive explanation.
The application is available online here.
Right now, our web application allows only for an interactive visualization of some of the data we were using in the research, along with Divisive Intelligent K-means algorithm results. More features will get documented when they appear.
Please contact us by e-mail. We will answer you in details.
Short contribution guide is actively constructed on the project's wiki as the development progresses.
This project was generated with Angular CLI version 1.0.0-rc.2.
In order to install Angular CLI, please run scripts/InstallNodeDev.ps1 using Windows Powershell.
If the script doesn't have permission to run, please execute Set-ExecutionPolicy Unrestricted command to enable running scripts from Powershell, run InstallNodeDev.ps1, and finish with Set-ExecutionPolicy Restricted (default value) if you will.
Troubleshooting:
- If nodejs.msi couldn't have been successfully downloaded and installed, please install it manually and the rest of the script should run just fine.
Run ng serve for a dev server. Navigate to http://localhost:4200/. The app will automatically reload if you change any of the source files.
If calling ng serve causes errors regarding uninstalled packages, please delete src\Spectre.Angular2Client\node_modules directory, enter src\Spectre.Angular2Client\ and run npm install.
Run ng generate component component-name to generate a new component. You can also use ng generate directive/pipe/service/class/module.
Run ng build to build the project. The build artifacts will be stored in the dist/ directory. Use the -prod flag for a production build.
Run ng test to execute the unit tests via Karma.
Run ng e2e to execute the end-to-end tests via Protractor.
Before running the tests make sure you are serving the app via ng serve.
To get more help on the Angular CLI use ng help or go check out the Angular CLI README.
This software is part of contribution made by Data Mining Group of Silesian University of Technology, rest of which is published here.
- Marczyk M, Polanska J, Polanski A: Comparison of Algorithms for Profile-Based Alignment of Low Resolution MALDI-ToF Spectra. In Advances in Intelligent Systems and Computing, Vol. 242 of Man-Machine Interactions 3, Gruca A, Czachorski T, Kozielski S, editors. Springer Berlin Heidelberg 2014, p. 193-201 (ISBN: 978-3-319-02308-3), ICMMI 2013, 22-25.10.2013 Brenna, Poland
- P. Widlak, G. Mrukwa, M. Kalinowska, M. Pietrowska, M. Chekan, J. Wierzgon, M. Gawin, G. Drazek and J. Polanska, "Detection of molecular signatures of oral squamous cell carcinoma and normal epithelium - application of a novel methodology for unsupervised segmentation of imaging mass spectrometry data," Proteomics, vol. 16, no. 11-12, pp. 1613-21, 2016
- M. Pietrowska, H. C. Diehl, G. Mrukwa, M. Kalinowska-Herok, M. Gawin, M. Chekan, J. Elm, G. Drazek, A. Krawczyk, D. Lange, H. E. Meyer, J. Polanska, C. Henkel, P. Widlak, "Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 2016
- G. Mrukwa, G. Drazek, M. Pietrowska, P. Widlak and J. Polanska, "A Novel Divisive iK-Means Algorithm with Region-Driven Feature Selection as a Tool for Automated Detection of Tumour Heterogeneity in MALDI IMS Experiments," in International Conference on Bioinformatics and Biomedical Engineering, 2016
- A. Polanski, M. Marczyk, M. Pietrowska, P. Widlak and J. Polanska, "Signal partitioning algorithm for highly efficient Gaussian mixture modeling in mass spectrometry," PloS one, vol. 10, no. 7, p. e0134256, 2015