AIBench is a lightweight, non-intrusive, MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output. This basic idea provides a powerful programming model to fast develop applications given that:
The logic can be decoupled from the user interface.
The interconnection of operations can also be decoupled based in the idea of “experiments”.
The programmer is forced to “think-before-program”, easing the code reuse.
CLUMMED (CLUstering on Mobile MEdical Devices)
The clustering of documents provides a mechanism for effective and intuitive navigation through the organization of the recovery results. When the system returns a large number of documents, organizing them in a small number of groups is very useful, especially on mobile devices with reduced screens. CLUMMED is a retrieval system for biomedical domain with post-retrieval clustering based in Lucene and Weka (K-Means algorithm).
AsGeRe (Asistente para la generación de Resúmenes)
AsGeRe is an application that supports the manual extractive summarization, focusing on the biomedical field. These summaries are called Gold Standard and are necessary in the evaluation process of automatic summaries generation systems to establish a benchmark.
The application is able to preprocess the text, identify biomedical concepts included, identify the language, divide the text into sentences and shows the frequency distribution of the concepts that appear, as support for the creation of the summary.
BioAnnote
BioAnnote is a desktop application is able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase.
Users can introduce biomedical documents and obtain annotations for the relevant terms, such as diseases, symptoms and treatments. In addition, users can retrieve more detailed information for each recognized entity (making use of an integrated web browser), including related topics, external links, related bibliography and paper abstracts.
BioViewMed
Viewmed is a web tool that helps the user to define their information needs, to know how to express better to search string through the visual aid of a graph that shows related concepts to an initial concept. It is based on UMLS Metathesaurus (accessed through a web service) and on Freebase (accessed through the API and MQL). With the information from the ontologies builds a XML intermediate file, from which the applet is generated with the graph of mecical concepts.
Gene Committee
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. Provided with a straightforward and intuitive interface, GeneCommittee is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.
WhichModel
WhichModel 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. Provided with a straightforward and intuitive interface, WhichModel is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.
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
PileLine & PileLine GUI
PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments (i.e. pileup, BED,GFF, or VCF files). PileLine is designed to be memory efficient by performing on-disk operations over sorted GP files directly.
PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser. With this intuitive graphical desktop application you can run the following tasks:
Processing commands of GP files, like seek, join, annotate and filtering.
Perform 2-samples and n-samples point somatic mutation calling (via the
PileLine 2smc and nsmc commands).
Browse GP files in an interactive local genome browser.
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-MS analysis, which compares the results of the direct and inverse experiments and quickly identifies reproducible peptides (i.e. those that have similar direct and inverse ratios) that should be used to subsequent and accurate protein absolute quantification.
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 the soft ionisation technique Matrix Assisted Laser Desorption/Ionisation (MALDI) coupled with mass spectrometry. The MLibrary compares the results of the experimental data with theoretic values included in the database. It simplifies the interpretation of the mass spectrometry data and reduces the amount of time required to analyse the results manually.
The developed MLibrary software takes as input several mass spectra coming from the MALDI-MS(/MS) analyses and aids the researcher to (i) identify the possible presence of AAS in the sample, in single MS mode, by comparison with the AAS theoretic values included in the MS database and (ii) to confirm their identification, in the MS/MS mode, by comparison of the fragmentation pattern against a MS/MS database.
ADOPS
ADOPS (Automatic Detection of Positively Selected Sites) is a novel software pipeline implemented with the goal of providing an automatic and flexible tool for detecting positively selected amino acid sites from a set of unaligned nucleotide sequence data.
The pipeline uses third-party well established tools to perform several steps involved in the process of detecting positively selected sites: (i) alignment of the sequences using T-coffee, (ii) inference of phylogenetic trees with MrBayes and (iii) detection of positively selected amino acid sites using codeml. ADOPS software implements a graphical user interface that provides an integrated view of all the results including intermediate stages (such as the tree used and convergence statistics).
ADOPS is ideal for research projects involving the analysis of tens of genes. Although a good and easy to use graphical interface is provided, the entire pipeline can be run using a command line option as well thus being adequate to process hundreds or thousands of genes as well. ADOPS software can be freely downloaded from http://sing.ei.uvigo.es/ADOPS/.
Software
AIBench
AIBench is a lightweight, non-intrusive, MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output. This basic idea provides a powerful programming model to fast develop applications given that:
CLUMMED (CLUstering on Mobile MEdical Devices)
The clustering of documents provides a mechanism for effective and intuitive navigation through the organization of the recovery results. When the system returns a large number of documents, organizing them in a small number of groups is very useful, especially on mobile devices with reduced screens. CLUMMED is a retrieval system for biomedical domain with post-retrieval clustering based in Lucene and Weka (K-Means algorithm).
AsGeRe (Asistente para la generación de Resúmenes)
AsGeRe is an application that supports the manual extractive summarization, focusing on the biomedical field. These summaries are called Gold Standard and are necessary in the evaluation process of automatic summaries generation systems to establish a benchmark.
The application is able to preprocess the text, identify biomedical concepts included, identify the language, divide the text into sentences and shows the frequency distribution of the concepts that appear, as support for the creation of the summary.
BioAnnote
BioAnnote is a desktop application is able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase.
Users can introduce biomedical documents and obtain annotations for the relevant terms, such as diseases, symptoms and treatments. In addition, users can retrieve more detailed information for each recognized entity (making use of an integrated web browser), including related topics, external links, related bibliography and paper abstracts.
BioViewMed
Viewmed is a web tool that helps the user to define their information needs, to know how to express better to search string through the visual aid of a graph that shows related concepts to an initial concept. It is based on UMLS Metathesaurus (accessed through a web service) and on Freebase (accessed through the API and MQL). With the information from the ontologies builds a XML intermediate file, from which the applet is generated with the graph of mecical concepts.
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. Provided with a straightforward and intuitive interface, GeneCommittee is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.
WhichModel 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. Provided with a straightforward and intuitive interface, WhichModel is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.
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
PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments (i.e. pileup, BED,GFF, or VCF files). PileLine is designed to be memory efficient by performing on-disk operations over sorted GP files directly.
PileLine GUI is a front-end of the PileLine toolkit, plus a genome browser. With this intuitive graphical desktop application you can run the following tasks:
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-MS analysis, which compares the results of the direct and inverse experiments and quickly identifies reproducible peptides (i.e. those that have similar direct and inverse ratios) that should be used to subsequent and accurate protein absolute quantification.
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 the soft ionisation technique Matrix Assisted Laser Desorption/Ionisation (MALDI) coupled with mass spectrometry. The MLibrary compares the results of the experimental data with theoretic values included in the database. It simplifies the interpretation of the mass spectrometry data and reduces the amount of time required to analyse the results manually.
The developed MLibrary software takes as input several mass spectra coming from the MALDI-MS(/MS) analyses and aids the researcher to (i) identify the possible presence of AAS in the sample, in single MS mode, by comparison with the AAS theoretic values included in the MS database and (ii) to confirm their identification, in the MS/MS mode, by comparison of the fragmentation pattern against a MS/MS database.
ADOPS (Automatic Detection of Positively Selected Sites) is a novel software pipeline implemented with the goal of providing an automatic and flexible tool for detecting positively selected amino acid sites from a set of unaligned nucleotide sequence data.
The pipeline uses third-party well established tools to perform several steps involved in the process of detecting positively selected sites: (i) alignment of the sequences using T-coffee, (ii) inference of phylogenetic trees with MrBayes and (iii) detection of positively selected amino acid sites using codeml. ADOPS software implements a graphical user interface that provides an integrated view of all the results including intermediate stages (such as the tree used and convergence statistics).
ADOPS is ideal for research projects involving the analysis of tens of genes. Although a good and easy to use graphical interface is provided, the entire pipeline can be run using a command line option as well thus being adequate to process hundreds or thousands of genes as well. ADOPS software can be freely downloaded from http://sing.ei.uvigo.es/ADOPS/.