Software List

Our software categorized in:

Anti Spam

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.

Wirebrush4SPAM

Wirebrush for SPAM is an extreme efficient open source spam filtering middleware based on the SpamAssassin technology.

Cheminformatics

D2-MCS

D2-MCS is an R framework to automatically predict the biological activity of chemical compounds regarding to theirs chemical substructures.

Data Analysis

bdpar

bdpar (Big Data Preprocessing Architecture) is a a tool to easily build customized data flows to pre-process large volumes of information from different sources.

Frameworks

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.

Compi

Compi is an extremely simple application framework for portable computational pipelines.

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.

BDP4J

BDP4J (Big Data Pipelining For Java) is a simple pipeline implementation derived from the pipeline of Mallet with some interesting features, achieving a product that is different from the Mallet pipeline implementation.

General Research Tools

DiscoverRegex

DiscoverRegex is an automatic generator of regular expressions using Genetic Programming written in C.

PubDown

Pubdown is a practical search engine that allows making queries against PubMed or Scopus, including the retrieval of the list of the available papers and downloading their PDF full texts to a local repository.

Genomics

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.).

GeneCommittee

GeneCommittee is a web-based interactive tool for giving specific support to the study of the discriminative classification power of custom hypothesis in the form of biological relevant gene sets.

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.

DEWE

DEWE is a bioinformatic tool to perform genetic differential expression analysis of RNA-Seq data, including two built-in workflows: HISAT2 or Bowtie2, StringTie and R packages (Ballgown and edgeR).

Microarrays & NGS

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.

bicycle

bicycle (bisulfite-based methylcytosine caller) is a NGS bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data.

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.

Natural Language Processing

NLPA

NLPA (Natural Language Pre-processing Architecture) is a plugin designed to operate in conjuction with BDP4J and able to extract texts from Twitter, Youtube Comments, text files, raw email files (.eml) or WARC (Web Archive) files.

Networking

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.

FilterTLK

FilterTLK is a tool for creating rules for the Berkeley Packet Filter (BPF).

Phylogenetics & Sequence Analysis

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.

B+

B+ is an online database of Positively Selected Sites discovered with ADOPS.

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.

SEDA

SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences.

BLASTERJS

A BioJS component to display BLAST single and multiple alignments.

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).

Proteomics & Mass Spectrometry

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.

S2P

S2P is an open source application for fast and accurate processing of 2D-gel and MALDI-based mass spectrometry protein data.

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.

 

Software Development

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).

Java TraceIt!

Java TraceIt! Is a debugger and optimizer for Java programs developed mainly in Java.

Systems Biology

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.

PCQuorum

The main focus of this project is to reconstruct the interplay modulating the bacterial fungal cross-talk between Pseudomonas aeruginosa and Candida albicans in VAP (Ventilator-Associated Pneumonia) infection.

Teaching & Education

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.

ALT

ALT (Algorithm Learning Tool) is an online tool for the intuitive and step by step graphical display of computer algorithms written in Java.

Text Mining

@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.

BioAnnote

BioAnnote is a desktop application able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase.

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.

Markyt Evaluation System

Markyt evaluation system supports the evaluation of automatic entity and relationship predictions, typically within the scope of a community text mining challenge.

Translational Biomedicine

PanDrugs

PanDrugs provides a bioinformatics platform to prioritize anticancer drug treatments according to individual genomic data.

MAHMI

The MAHMI Project (Mechanism of action of the human microbiome: from genetic sequences to immunomodulatory peptides), proposes a step forward on the description and characterization of potential bioactive peptides encrypted in larger bacterial proteins.

BEW

Biofilms Experiment Workbench (BEW) is a novel software workbench for the operation and analysis of Biofilms experimental data. BEW enables full management and analysis of Experiments and Inter-Lab Experiments.

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.

MultiTasking Cubes

MultiTasking Cubes (MTC) is a project for developing a tool that may be used for cognitive rehabilitation, based on the therapeutic game Memomdado.

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.

 

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