Software List |
Our software categorized in: WARCProcessor WARCProcessor is a platform independent integrative tool providing specific support to scientists that need to perform experiments in the field of web spam research. Grindstone4SPAM Grindstone for SPAM is an open source, lightweight tool set designed to aid on develop SpamAssasin based filters and improve the general performance of them. STRep STRep is a repository management software providing advanced features for sharing spam filtering corpora/datasets. AIBench AIBench is a Java application framework, a leading language with a huge set of libraries for almost anything. In addition, AIBench is 100% integrated with Maven. You can create an application starting from the archetype. GC4S GC4S is an open-source library that provides a bioinformatics-oriented collection of GUI Components for (Java) Swing. jARVEST jARVEST (Java web harvesting library) is a simple web harvesting or web scraping framework. jARVEST is implemented via a powerful JRuby-based domain specific language (DSL), allowing you to develop harvesters with minimum code. DiscoverRegex DiscoverRegex is an automatic generator of regular expressions using Genetic Programming written in C. PathJam PathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists, integrating pathway-related annotations from several public sources (Reactome, KEGG, Biocarta, etc.). WhichGenes WhichGenes is a bioinformatics gene set building tool that allows the user to create and manage custom genesets extracted from several sources (Gene Ontology, KEGG, Biocarta, Reactome, etc.). nextpresso nextpresso implements a pipeline to perform a complete analysis of RNA-seq data, including quantification and differential expression with HTseq-count and DESeq2, quantification and differential expression with Cuffnorm/Cuffdiff, among others. geneCBR GeneCBR is software tool that allows the use of combined techniques that can be applied to gene selection, clustering, knowledge extraction and prediction. PileLine & PileLineGUI PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by NGS experiments (pileup, BED,GFF, or VCF files). PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser. RUbioSeq+ RUbioSeq-GUI a graphical user interface (GUI) for RUbioSeq that works as a web application (i.e. in a browser) and allows users to use RUbioSeq in a user-friendly way. nextpresso nextpresso implements a pipeline to perform a complete analysis of RNA-seq data, including quantification and differential expression with HTseq-count and DESeq2, quantification and differential expression with Cuffnorm/Cuffdiff, among others. JaBaCATS JaBaCATS is a set of basic java tools for developers who need Certificate Authority (CA) root certificates and user certificates signed by the CA. ALTER ALTER stands for (ALignment Transformation EnviRonment) and it is a set of software components to transform between Multiple Sequence Alignment file formats. ADOPS ADOPS is a desktop application that implements a workflow for Automatic Detection Of Positively Selected Sites using T-Coffee, MrBayes and CodeML. BDBM BDBM (BLAST DataBase Manager) provides a graphical user interface that allows you to create high quality sequence datasets using the tools included (EMBOSS, bedtools, and NCBI's BLAST, Splign & Compart, and ProSplign & ProCompart). EvoPPI EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for distinct species. EvoPPI allows two types of queries: (i) same species comparisons, and (ii) distinct species comparisons. P4P P4P (Peptidomes for Phylogenies) is a web service conceived for bacterial strain classification based on peptide datasets. These datasets are obtained from proteins by the in silico action of the three main human gut endoproteases (pepsin, trypsin and chemotrypsin). GenomeFastScreen GenomeFastScreen is a Compi pipeline that automates the process of identifying genes that likely show PSS, and thus, should be studied in detail, starting from a set of FASTA files, one per genome, containing all coding sequences. IPSSA IPSSA (Integrated Positively Selected Sites Analyses) is a Compi pipeline to automatically identify positively selected amino acid sites using three different methods, namely CodeML, omegaMap, and FUBAR. Mass-Up Mass-Up is an open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. LA-iMageS LA-iMageS is an open source application to generate 2D/3D images for the elements present in a set from ICP-MS spectra. DPD: Decision Peptide Driven The DPD (Decision Peptide-Driven) tool implements an application for assisting the user in a specific protocol for protein quantification based on 18O labeled inverse labeling and MALDI-TOF mass spectrometry analysis. MLibrary The MLibrary software tool is a database search engine developed to assist the user in the detection and identification of small compounds, such as anabolic androgenic steroids (AAS), using MALDI-TOF mass spectrometry. BiMS BiMS (biclustering for mass spectrometry data) is a Java application designed to allow the application of biclustering algorithms to mass spectrometry datasets.
 
PUWI: PHP Unit Web Interface PUWI (PHPUnit Web Interface) is a tool that provides a web interface to PHPUnit framework, allowing to re-execute unit tests and handle results visibility (show only failed tests). Gleukos Gleukos is a public web-based resource that aims to provide a comprehensive portrait of the glycolytic abilities of bacteria, in articular those encrypted in the protein complement of the human microbiome. SINGulator SINGulator is a novel application that aims to model the diffusional motion of individual biomolecules and intermolecular interactions in continuous three-dimensional cellular environments with agent-based reaction-diffusion algorithms. Analytics and Recommendations plugin 4 Moodle The Analytics and Recommendations plugin for Moodle environment is a tool for giving specific support to both students and teachers. @Note @Note is a Biomedical Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. BioClass BioClass is a platform for the application of reasoning models in text classification issues, designed to work with the results obtained from an information retrieval process in a text database, where documents can be relevant or not for a specific issue. Markyt Markyt is a Web-based multi-purpose annotation tool. With this annotation tool you can annotate from simple documents (without any formatting) to HTML documents. Documents can have embedded: images, diagrams, videos, etc. With all power of HTML. PanDrugs PanDrugs provides a bioinformatics platform to prioritize anticancer drug treatments according to individual genomic data. DREIMT DREIMT is a bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data. Antimicrobial Combination Network Antimicrobial Combination Network is an online database focused on antimicrobial combinations that have been experimentally tested against Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Listeria monocytogenes and Candida albicans. SDS SDS (Smart Drug Search) is an advanced search engine for the screening of up-to-date information on drug-related experimental studies. InNoCBR InNoCBR is a software tool for automatic HAIs (Hospital-acquired Infections) surveillance. It is currently deployed in the Ourense University Hospital Complex (Spain) as well as in other Galician hospitals. |