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The site for people who want to learn to use Perl.

McGraw-Hill Hyperbook

Guida ipertestuale all'apprendimento della programmazione: C, Perl e Java.

The Perl CD Bookshelf

Biology

Animations

Extremely conserved (non-coding) sequences in vertebrate genomes

Genome Sizes

http--nematoda.bio.nyu.edu8080-iBrowse_miRNA-cookieSessionChecker.jsp

MicroArray

An (Opinionated) Guide to Microarray Data Analysis

Public domain (free) programs for microarray data analysis

MedMiner

The MedMiner filters will extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query. This tool combines the GeneCards and PubMed search engines with user input and automated server-side scripts in an integrated text filtering system.

MatchMiner

MatchMiner is a set of tools that enables the user to translate between disparate ids for the same gene. It uses data from the UCSC, LocusLink, Unigene, OMIM, Affymetrix and Jackson data sources to determine how different ids relate. Supported id types include, gene symbols and names, IMAGE and FISH clones, GenBank accession numbers and UniGene cluster ids.

Gene Expression Omnibus (GEO) Main page

Gene Expression Omnibus: a gene expression/molecular abundance repository.

EBI Databases - ArrayExpress Home

ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED recommendations.

GeneCruiser

GeneCruiser provides integrated access to the gene and microarray feature information freely available from public databases.

GNF SymAtlas

Genomics Institute of the Novartis Research Foundation (GNF). SymAtlas is a web-application for publishing experimental gene functionalization datasets integrated with a flexibly searchable gene-centric database of public and proprietary annotations.

AliasServer

Bioinformatics project for synonym identifiers search

Cancer Program Data Sets

Access to datasets described in Cancer program publications.

Resourcerer

Provides annotation based on the TIGR Gene Indices (TGI) for commonly available microarray resources, including widely used clone sets and Affymetrix GeneChip Arrays.

SOURCE Batch Search

The batch extract interface for SOURCE allows retrieval of a subset of the data available in SOURCE for many entries at once. This function will be useful to users who are interested in large sets of genes or clones (such as those present on DNA microarrays).

Clone|Gene ID Converter

IDconverter is a tool that converts gene, clone or protein IDs to other IDs.

CHIP Bioinformatics Services | unCHIP!

unCHIP is a web-based interface that allows you to query a database providing information on Affymetrix probe set numbers.

Mayday - Download

Microarray Data Analysis. It is a workbench for visualization, analysis and storage of microarray data.

Clusters and communities: overlapping dense groups in networks

CFinder offers a fast and efficient method for clustering data represented by large graphs, such as genetic or social networks and microarray data. CFinder is a free software for finding overlapping dense groups of nodes in networks, based on the Clique Percolation Method, CPM, of Palla et. al. Nature (2005).

BASIS

Biology of ageing e-science integration and simulation system. BASIS is a new project developing web-based services for quantitative study of the biology of ageing.

MicroRNA

MicroInspector

MicroRNA targets by Tuschl

MicroRNAdb

A Comprehensive Database for MicroRNAs that allows you to browse microRNA genes in all species.

MiRAlign

MiRBaseSequences

Searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry.

PicTar

PicTar is an algorithm for the identification of microRNA targets.

N-iBrowse

N-Browse is a graphical interactive viewer that builds networks from heterogeneous functional genomic data. The aim of this project is to provide intuitive, Web-based access to functional data from large-scale genomic projects.

MiRNAMap

Collection of published miRNAs from the microRNA registry and predict putative miRNA precursors by RNAz which is based on genome-wide mapping of conserved RNA secondary

TarBase

Tarbase is a database that provides a means of searching through a comprehensive set of experimentally supported microRNA targets in at least 8 organisms.

Argonaute

Argonaute - a database for gene regulation by microRNAs

Systems Biology

cPath Home

Cancer Pathway Database. cPath aims to be a freely available cancer pathway database. Currently, only information about protein-protein interactions collected from major interaction databases that support the PSI-MI format is available.

Cytoscape

Cytoscape is an open source and portable computer program which is useful for integrating data, and for visualizing and performing calculations on molecular interaction networks. Many useful capabilities are built into the platform's core, and a simple plugin architecture allows for the rapid development, and easy integration, of separately developed code.

David 2.0

Database For Annotation, Visualization and Integrated Discovery. DAVID 2.0 is designed around the "DAVID Gene Concept", a graph theory evidence-based method to agglomerate species-specific gene/protein identifiers from a variety of public genomic resources including NCBI, PIR and Uniprot/SwissProt.

KEGG PATHWAY Database

Kyoto Encyclopedia of Genes and Genomes. KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.

Reactome

The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.

Atlas of hematology

This Atlas has the goal of supplying hematologists, laboratory technicians, medical school students, biologists as well as professionals working in the field of morphology of blood cells.

BIND

The Biomolecular Interaction Network.

Harvester

Bioinformatic harvester at EMBL.

CGAP

The Cancer genome Anatomy Project. The goal of the NCI's Cancer Genome Anatomy Project is to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient.

PEPR Portal

Public Expression Profiling Resource. PEPR is an experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform.

PRL

Pathguide: the Pathway Resource List. It contains information about 220 biological pathway resources.

UTResource

Internet Resources for Sequence analysis of 5' and 3' Untranslated Regions of Eukaryotic miRs.

VeraAndSam

Variability and ERror Assessment, it estimates error model parameters from replicated, preprocessed experiments. Significance of Array Measurement, uses error model to improve the accuracy of the expression ratio.

wCluto

wCLUTO is a web-enabled data clustering application that is designed for the clustering and data-analysis requirements of gene-expression datasets.

Web Signal Scan Service

Finds and lists homologies of published signal sequences with the input DNA sequence.

JASPAR

JASPAR is a collection of transcription factor DNA-binding preferences, modelled as position-specific weight matrices (PSSMs).

MPromDb

Mammalian Promoter Database is an integrated novel database for gene promoters with experimentally supported annotation of transcription start sites (TSS), cis-regulatory elements, CpG islands and ChIP-chip experimental results with intuitively visualized presentation.

RCSB-Protein Data Bank

Sungear

Sungear enables rapid, visually interactive exploration of large sets of genomic data. It allows browsing of gene sets by experiment membership, gene annotation, and ontological term. The purpose of Sungear is to make otherwise complicated queries quick and visually intuitive.

WEGO Document

Web Gene Ontology Annotation Plotting is a useful tool for plotting GO annotation results.

Genome Browser Gateway

The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information

 

GOTERM

GOToolBox

This site provides a series of programs allowing the functional investigation of groups of genes, based on the Gene OntologyTM ressource.

GoMiner

GoMiner is a tool for biological interpretation of 'omic' data including data from gene expression microarrays.

GOTM

GOTree Machine is a web-based platform for interpreting microarray data or other interesting gene sets using Gene Ontology.

GenMAPP

Gene Map Annotator and Pathway Profiler. GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes.

GeneNote

GeneNote is a full-genome database of expression in healthy human tissues. We present the full transcriptome for both known and novel genes

Other Links..

BALL Website

BALLView is a standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS.

HPRD

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.