Search Results for "sql command line" - Page 5

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of...

mzSquash is a compression tool for mzML files, an XML-based standard developed by HUPO PSI (http://www.psidev.info) for spectrometer output. All development has ceased. The tool may be useful educationally, but is not a recommended utility.

Grid-Enabled Molecular Simulation Repository (GEMS)

The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.

TreeSoft is a collection of softwares that build or manipulate phylogenetic trees.

A polynomial-time algorithm for constructing level-2 phylogenetic networks from dense sets of rooted triplets.

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

Reports the difference between different SNP values in terms of Transcription Binding efficiencies.

A library and associated applications for searching for patterns in protein structures and measuring geometric parameters.

The TandemSearcher is a Java based application for searching for tandem repeats in the DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).

PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.

The ExactFDR software package is an improvement of permutation-based False Discovery Rate (FDR) estimation methods that takes advantage from exact p-value computations for analyzing Genome-wide association studies data

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

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.

The YeastsIdentification is a Java based application for searching for unique DNA sequences. It is based on the Burrows-Wheeler Transform (BWT).

The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.

AgentCell is an agent-based model of cellular biochemical processes and biological behavior.

A platform for the integration of deterministic and stochastic models, for the simulation of the integrated models and for interactive exploration of the model behaviour.

Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.

The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.

Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.

Bioinformatics tools and applications for the analysis of genomic sequence data.

OBOES (Open Biomedical Ontology-Based Enrichment and Search) is an information-theory-based platform that embeds new integrative methods allowing biologists to evaluate new hypotheses.

The program siRNArules 1.0 can predict active short interfering RNA (siRNA) with a rather high efficiency (see published paper on this in RNA journal). This project aims to develop new versions, siRNArules 2.0 etc.

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)