The metabolomics standards initiative (msi) will develop a Core Information for Metabolomics Reporting (CIMR) recommendation and a more formal and semantically defined corresponding ontology (msi-ontology).
The ONTO-SPARQL library contains sparql-queries for loading OBO-ontologies, and for browsing and searching through them. The results of the queries are returned in XML or a HTML-interface. They can be used by end-users and programmers.
MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system
EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries and provides several layers of annotation based on Entrez Gene to allow the user to highlight useful genes and manage cDNA library projects.
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Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
This is a mathematical/informatical/biologocal aproach to System-research. The aim is to write a progrramm that simulates a world with as many mathematical methods as possible at once.
Discrete Event System Specification (DEVS) combined with System Biology Markup Language (SBML) project: a Java-based tool to solve complex biology processes. Support by RTSync Corporation and Arizona Center for Integrated Modeling & Simulation (ACIMS)
Here is a repository of libraries automatically generated by Patlac::Xml2cpp software.
All of these libraries are c++ translation of their respective xsd schema. They include classes with accessors, saxparser with iteration mode and xml serialization.
Parallel IBDWS is an upgrade from IBDWS that utilizes parallel processing. Also, the incorporation of DNA sequence data has been added since the last code release
Ditto Edge Server is a lightweight standalone server for resource-constrained edge environments, based on the core Ditto Edge SDK.
With Ditto Edge Server, you can join devices as small as a Raspberry Pi to a local mesh network and synchronize data across edge environments.
Ditto's Edge SDK is the only thing your edge devices need to ensure your application is operational in any environment, regardless of network conditions.
TACS (Trust Ant Colony System) is a Trust model for P2P, Ad-hoc and Wireless Sensor networks (also valid for multi-agent systems) based on the bio-inspired algorithm ACS (Ant Colony System).
IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info
A web-based groupware application for Linux with PHP, MySQL, Apache, SSL oriented to forensic laboratories.
Applicazione scritta per Linux con PHP, MySQL, Apache, SSL, finalizzata alla condivisione di dati nei laboratori forensi.
Large set of functions for biological records (ECG, EEG, phono), datastore, datamining and analysis (HRV, QT, RR, ST). The application is written in Java, so that it is assumed to work on all devices. It runs as a desktop or client-server application. It
Adamant is a java application for annotation of microarray array designs. The software enables MIAME-compliant annotation of sequences spotted onto arrays and can produce output files in MAGE-ML and other data formats used by public microarray data repos
BushMan is a web interface and a quality assurance tool for biological sequence assembly.
It is a small application that helps process chromatograms, and it assembles using Phred and Phrap. It produces a FASTA formatted consensus sequence.
WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.
NOTE: The IntAct package is now hosted at google code: http://intact.googlecode.com IntAct is an open source package to store and manipulate molecular interaction data.
Life Science Identifier (LSID) Specification is a globally unique identifying scheme for information resources on the life sciences domain. It is based on Internet standards such as DNS, URN, HTTP, RDF, SOAP, WSDL, and web services.
GeneIndex is a parallel program using MPI. It finds frequencies and positions of all words of a certain length in a DNA sequence. Large genome will be an ideal target of GeneIndex.
Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
dna2abc turns DNA sequences into musical sequences. The key feature is the rule editor; a rule is a regular expression paired with a Tcl script. dna2abc scans a DNA sequence, testing each regular expression: if it matches, the Tcl script is run.