Software

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Resource Description
Resource Description Project Developers
AMMO-Prot
Search tool for representing three-dimensional protein structures. Where such structure does not exist they are generated by computer algorithms.
ASP
Project ASP (Amine System Project) is an interdisciplinary project that try to combine research efforts on Molecular Biology (Procel) and one on Computer Science (Khaos) to present solutions appropriate to the existing problems in Systems Biology.
Atenea
Online platform for supporting artistic research in such fields as terminology, conceptualization and critics.
AutoDock + jMetal
Molecular docking is a method for structure-based drug design which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) in order to produce a stable complex. The goal of molecular docking techniques is to find states with a minimum biding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques for that purpose. We propose the integration of AutoDock with jMetalCpp, an optimization framework thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems. The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems.
Bioqueries
A Wiki based on Linked Data technology where you can edit, construct, publish and manage data. Bioqueries Wiki is a new format to access and share queries based on Linked Data technology. This technology is a new methodology to connect data from different biological data sources to make easy of obtaining crossing information without using crossing references between biological databases and performing relationship between different information useful for biologists and students too. This objective of this website is the participation of a great amount of biologists as it possible. This website is a place of sharing queries about life sciences domain where users can edit and even construct their particular query with the option of making publish or unpublish their own bioqueries. This wiki is a new method to make easy the access for biologist to connecting data. Users interested in complex and specific queries to database to obtain crossing information have a wide of available queries to access to information included in the cloud of Linked Data technology. These queries are classified in hierarchies that belong from different databases and areas like metabolism, genetic, medical information, proteomic etc. Bioqueries wiki is a common space designed to academic biologists, students and researchers. It is a community whose objective is the participation and collaboration of their members. While users are participating in this wiki, biologist users immerse in Linked Data world, a project that was born in 2008 year and his rate of growth has been incremented by year and it has transformed in Linked data community. Moreover, this wiki allows users to learn more about this type of technology based on data. As a welcome way, in the frontal page you can find the most recent contents included in wiki and the most famous content visited by the community. We are still adding new queries every day.
CursoSWS
Website for the Course on Semantic Web Services awarded by the University of Málaga.
DBOWL
Persistent and Scalable reasoner for OWL-DL ontologies. DBOWL allows to store ontologies in a relational database (ontologies with a great number of instances) and to reason with them. It also supports extended conjunctive queries and SPARQL.
DBTech
Website for the network DBTech Net, a database expert network which is supported by european academy and industry. One of the goals of this network is to develop educational material to diseminiate knowledge on databases which is interesting for students and for companies.
Extending SAWSDL
A proposal for automatically annotating Semantic Web Services acording to the SAWSDL standard.
GeoTrip
Web Geographical Information System for supporting mobile users which has capabilities for recommending georeferenced contents.
GOAL
Genetics for Ontology ALignments. Software tool for optimizing ontology matching functions.
ICARIA
ICARIA Project. From Semantic Web to Systems Biology.
ICARO
ICARO Project. Integration, Queries, Resource Analisis and Ontologies for the Semantic Web.
INB
Tool for the location and execution of BioMOBY Web Services developed in collaboration with the Department of Computer Architecture department from the University of Malaga.
iNGS Logo
iNGS
Personalized medicine can be considered as a medical approach which proposes the customization of healthcare involving medical decisions, treatments etc. that are applied to a patient individually and tailored to that patient. This medical methodology is possible due to the rapid advances in technology in areas such as genomics, transcriptomics, proteomics, metabolomics, etc. In this context, it is important to mention that the development of sequencing approaches of personal human genomes and the detection of DNA variations by means of a reference human genome that was unveiled in 2003-2004 (Human Genome Sequencing Consortium International, 2004) are both huge contributions that should be integrated into the personal "omics" (in this case, genomics) of each patient. Nonetheless, clinical interpretation of whole-genome and NGS (Next Generation Sequencing) genetic findings are currently very low-throughput because of a lack of computational tools/software to integrate all this information. In this sense, the reason for the current bottleneck of whole-genome and whole-exome sequencing projects is the management of structured data and sophisticated computational analysis of the experimental data obtained. Therefore, we have started designing a platform for integrating, firstly, existing genome analysis tools and then adding more annotations than those currently provided from the findings of these tools in public databases. As a first experiment with this platform (http://khaos.uma.es/iNGS), we have developed a Web tool for running multiple analysis tasks. All findings of these analysis tools are completed with public data to generate a simple report to complete information provided by genome interpretation and annotation tool results.
JMetal Logo
JMetal
jMetal is an object-oriented Java-based framework for multi-objective optimization with metaheuristics (http://jmetal.sourceforge.net). Maven packages available at: http://mvnrepository.com/artifact/org.uma.jmetal
Kasbi
Tool for retrieving integrated information from existing databases. This tool includes the capacity for reasoning on the collected data to improve the data analysis processes.
KOMF
The Matching Framework. A tool for researching the composition of complex algorithms for matching ontologies.
Kpath
Kpath, a database that integrates information related to metabolic pathways. kpath also provides a navigational interface that enables not only the browsing, but also the deep use of the integrated data to build metabolic networks based on existing disperse knowledge. Its user interface has been used to showcase relationships that can be inferred from the information available in several public databases.
MaF
The Matching Framework. A tool for researching the composition of complex algorithms for matching ontologies.
PIE
Educational Innovation Project financed by the University of Malaga for the introduction of innovation mechanisms in the subjects related to data management on the Web.
Protopia
Tool for recoverying and analysing relationships between proteins, including the graphical representations of interaction networks.
RedDB
Website from the RedBD Excellence Network.
SBMM
Systems Biology Metabolic Modeling Assistant is a tool for metabolic information retrieval that it can be analyzed by means of its representation in SBML graphs.
SD-Core
The Semantic Directory Core provides an implementation of the concept of Semantic Directory, who allows to the management of metadata ontologies and resources, including the relation between them by means of correspondence relations.
SemESB
Implementación de la arquitectura de referencia descrita en OASIS A proposal for the development a Service Oriented Semantic Bus.
SemFit
A proposal for computing distances between ontologies, using alignments between ontologies and the profile of the user, expressed as a set of relevant concepts.
VSB
Ontology Viewer that allows users to represent different levels, from the semantic fields to the instances of the ontologies.
Yeasts
YeastMed