Welcome to the website for software projects created and maintained by the Computational Omics and Systems Biology Group. Below you can find a list of software we have developed, and on the subsequent pages are documentation and links to downloads and source code (hosted on our Github page).
http://compomics.github.io/
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index.html - Compomics Docs | compomics.github.io Reviews
https://compomics.github.io
Welcome to the website for software projects created and maintained by the Computational Omics and Systems Biology Group. Below you can find a list of software we have developed, and on the subsequent pages are documentation and links to downloads and source code (hosted on our Github page).
compomics.github.io
pladipus - Compomics Docs
http://compomics.github.io/projects/pladipus.html
Latest version: 1.2.1. Pladipus system is an affordable cluster computing framework allowing for distributed processing, management and analyses for bio-informatics pipelines. Here, we propose a free framework named Pladipus. To start using Pladipus please see the Pladipus wiki. Pladipus can be installed in a variety of ways. We strongly recommend using the installer. Unzip it in your user home folder and you’re ready to go! The pladipus logo was created by Elodie Adam. At 15:41 on 2017-03-08.
fragmentation-analyzer - Compomics Docs
http://compomics.github.io/projects/fragmentation-analyzer.html
What is Fragmentation Analyzer? Supported Text File Format. Barsnes et al: Proteomics 2010 Mar;10(5):1087-90. As part of a paper, please include the reference above. For further analysis of proteomics data we also recommend checking out SearchGUI. What is Fragmentation Analyzer? Is a tool for analyzing MS/MS fragmentation data. Currently nine different analysis types are supported:. Spectra Visualization - visualize the MS/MS spectra with fragment ion annotation, zooming and manual de-novo-sequencing.
xilmass - Compomics Docs
http://compomics.github.io/projects/xilmass.html
Xilmass is a novel algorithm to identify cross-linked peptides. Xilmass uses a new way to compose the search database and a new scoring function that scores each experimental spectrum against complete theoretical spectra. Xilmass can be used for both labeled and unlabeled cross-linkers. Go to top of page. Go to top of page. Download the Xilmass algorithm here. Go to top of page. At 15:41 on 2017-03-08.
peptide-shaker - Compomics Docs
http://compomics.github.io/projects/peptide-shaker.html
Bioinformatics for Proteomics Tutorial. Vaudel et al. Nature Biotechnol. 2015 Jan;33(1):22 24. If you use PeptideShaker as part of a publication, please include this reference. V1162 - All platforms. Click on a figure to see the full size version). PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X! PeptideShaker currently supports nine different analysis tasks:. For further help see the Bioinf...
jsparklines - Compomics Docs
http://compomics.github.io/projects/jsparklines.html
JSparklines makes it straightforward to visualize numbers in Java tables by the use of sparklines. All that is needed is a couple of lines of code. The charts are created using JFreeChart. And added to the table columns using custom TableCellRenderers. Supports more than 30 types of charts/renderers. Including bar chart, line charts, stacked bar charts, bar charts with error bars, pie charts, scatter plots, interval charts, area charts, heat maps and box plots. V108 - All platforms. How to use JSparklines.
TOTAL PAGES IN THIS WEBSITE
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Thilo Muth | CompOmics
https://compomics.com/people/thilo-muth
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. RT @ N2N UGent.
Paola Masuzzo | CompOmics
https://compomics.com/people/paola-masuzzo
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. RT @ N2N UGent. JTraML:...
Kenneth Verheggen | CompOmics
https://compomics.com/people/kenneth-verheggen
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. RT @ N2N UGent. JTraML:...
Nicolas Housset | CompOmics
https://compomics.com/people/nicolas-housset
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. While I have certainly ...
Niels Hulstaert | CompOmics
https://compomics.com/people/niels-hulstaert
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. RT @ N2N UGent. Build a...
Lennart Martens | CompOmics
https://compomics.com/people/lennart-martens
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. Phone: 32 9 264 93 58.
Sven Degroeve | CompOmics
https://compomics.com/people/sven-degroeve
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. RT @ N2N UGent.
Ana Silva | CompOmics
https://compomics.com/people/ana-silva
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. A year spent working on...
Davy Maddelein | CompOmics
https://compomics.com/people/davy-maddelein
Computational Omics and Systems Biology Group, VIB-UGent. Proteomics bioinformatics positions for InSPECtor grant. BITS – MS data processing – 19.11.2012. University of Cape Town Proteomic Bioinformatics Workshop September 2012. ISAS Dortmund June 2012. FinnProt Protein Identification by MS/MS workshop 26.10.2011. KVCV Proteomics Informatics 19.09.2011. The EBI Bioinformatics Roadshow Prague 2011. Data management and standardization in cell migration research Ghent 3/5 March 2014. RT @ N2N UGent.
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CompOmics | Computational Omics and Systems Biology Group, VIB-UGent
Computational Omics and Systems Biology Group, VIB-UGent. Computational Omics and Systems Biology Group. The Computational Omics and Systems Biology Group, headed by Prof. Dr. Lennart Martens. Is part of the Department of Biochemistry. Of the Faculty of Medicine and Health Sciences. And the VIB-UGent Center for Medical Biotechnology. Both in Ghent, Belgium. Approaches) with an aim towards establishing solid data stores, processing methods and tools to enable downstream systems biology research. HUPOST ne...
index.html - Compomics Docs
Welcome to the website for software projects created and maintained by the Computational Omics and Systems Biology Group ( Compomics. Below you can find a list of software we have developed, and on the subsequent pages are documentation and links to downloads and source code (hosted on our Github. A lims system to automate and expedite proteomics data management, processing and analysis. Open-source java library for computational proteomics. Manipulating fasta sequence databases. Graphical user interface...
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