Biocomputing Unit / Software

SOFTWARE

Our group develops the following software:

	"X-Windows-based Microscopy Image Processing Package" (Xmipp) , is a specialized suite of image processing programs primarly aimed at obtaining the three-dimensional reconstruction of biological specimens from large sets of projection images obtained by transmission electron microscopy.
	GENECODIS is a web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list.
	ENGENE is a versatile, web-based and platform independent exploratory data analysis tool for gene expression data that aims at storing, visualizing and processing large sets of expression patterns. engene (standing for Gene Engine) integrates a variety of analysis tools for visualizing, pre-processing and clustering expression data.
	FuzzySOM: Fuzzy Self-Organizing Map application.
	ChIPCodis: Mining complex regulatory systems in yeast by concurrent enrichment analysis of Chip-on-chip data.
	S-flexfit: Superfamily-based flexible fitting
	CentrosomeDB: A Human Centrosomal Proteins Database
	bioNMF online is a windows-based stand-alone tool for performing non-negative matrix factorization of biological data. This application is a useful tool for bioinformatics researchers that need to use the NMF algorithm in an easy and efficient way. There is also a stand-alone version of bioNMF.
	bUnwarpJ: ImageJ plugin for bidirectional elastic registration of two images.
	Sent is a web-based tool to brings structure and semantics to a list of genes by means of literature analysis. It takes a list of genes given as input and returns a collection of functionally related groups along with a list of words that provide them with a functional description.
	Moara is a project developed by BioComputing unit at Centro Nacional de Biotecnologia (CNB) for gene mentiona and normalization in biological texts.
	"The Command Line Mate" (Colimate) is a language for automatic Graphic User-Interface generation, based on command line definitions.