Software Standalone applications

Standalone applications

All of the tools listed on this website are designed for Windows operating systems. If you experience any problem with one of the applications please make a short description of it in the bug report section, anonymous reports are also accepted.

IMPORTANT!
Under Windows Vista and Windows 7/8 you might have to run the applications as administrator in order to provide appropriate communication with the database. To do that right click on the application shortcut or directly on the executable file and select the option "Run as administrator".

Systems biology

Solvary

Solvary is an application for the study of complex mathematical models in a form of ODE.
Glycomics tools

GlycoGene

GlycoGene can predict the set of glycans which will most likely occur on the surface of the cell based on glycosyltransferases expression level and a database of known glycan structures. Additionally it creates a detailed report on the changes in glycosyltransferase expression levels connecting them to structures in the creation of which they are involved.
Microarray tools

CDF Creator

CDF Creator allows to make custom Affymetrix microarray Chip Definition Files (CDFs) selecting probes that should be used in the study and assigning them to gene-specific sets. To prepare the basic CDF version only a list of probesets with individual probe coordinates is required.

CEL File Converter

Tool which allows to convert Affymetrix CEL files between various formats in a very fast and easy way. Available formats are: - text: GCOS Text file format (version 3) - xda: GCOS XDA binary file format (version 4) - agcc: AGCC binary format

Cel File Explorer

This simple application allows extracting raw expression intensities out of multiple Affymetrix CEL files based on a given list of probe coordinates or probeset IDs. The application supports CEL files in various formats and both official and custom CDF files for probeset based expression intensity extraction.

GaMRed

GaMRed is designed to estimate the noise level of large numerical datasets using Gaussian mixture models. This approach can be used to reduce the number of features in microarray or RNA-Seq experiment data, although the method is applicable to any dataset where large number of features was measured for any number of samples.


MicroImage

MicroImage removes different kinds of Affymetrix microarray image artifacts represented with probes from the damaged region of the array based on probeset expression data. It can work with various microarray types and different library (CDF) files performing the entire process of artifacts removal by creating new CEL files with minimum user assistance.


NucleoDix

This program removes multiple probesets corresponding to one gene due to specificity of official Affymetrix library files, by removing outlier signals using the Dixons outliers test followed by signal averaging. It searches for gene repeats based on multiple different symbols like Affymetrix ProbesetID, gene symbol, Reference Sequence ID or any other provided by the user.
Sequence analysis and gene annotations

NucleoAnnot

With this application you can very easily browse available PubMed literature related to specific groups or individual genes and build sophisticated search queries. Additionally the application includes a very fast gene ID converter and many different kinds of annotation analysis options based on current NCBI, KEGG and GO databases with a one click updating procedure.


NucleoSeq

NucleoSeq is a nucleotide sequence analysis application with an option to automatically download sequence data from Reference Sequence database based on various gene ID's. The analysis can include only parts of the sequence like CDS or 5'/3'-UTRs allowing to search for specific motifs or motifs provided as a PWM according to Jaspar database format.