Search Results for "multi-threaded"

PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data.

A software package that implements the probabilistic record linkage technique (PRL). This is a new, improved, open-source, multi-platform version of the previously available program, by the same authors.

MuffinEC is an error correction software capable of handling all types of errors (insertion deletions, mismatches and unknown bases). It officially supports four technologies (Illumina, 454, ion Torrent and PacBio - experimental) and it also has a generic setup for others (old and/or new). It is released under LGPL version 3.0. MuffinEC can use multicore systems, thanks to its OpenMP implementation. We are developing the 2nd version of MuffinEC. The beta version is already available...

JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later.

StochPy - Stochastistic modeling in Python - is an easy-to-use package, which provides several stochastic simulation algorithms and unique analysis techniques, which can be used for stochastic simulations of biochemical systems.

...DeDAY supports both interval-censored data and exact event-time data. Using MLE (Maximum Likelihood Estimate), DeDAY fits statistic model to the data. DeDAY also calculates the variances and the multi-dimensional confidence limits of model parameters. DeDAY is free for academic users.

BioDare (Biological Data Repository) was developed under the multi-site ROBuST project (http://hallidaylab.bio.ed.ac.uk/ROBuST.html) to support data exchange inside the project. It is a web application which allows data-sharing (including public dissemination), data-processing and analysis, with the main focus on time-series data produced in circadian experiments. The main features of BioDare are: - an online repository for experimental data accompanied by extensive metadata - generation of secondary data (normalized, detrended, averaged …) - graphical output of data, secondary data and rhythm analysis - simple text-based search throughout metadata - biology- and conditions-aware search for data - data aggregation and export - group-based privacy settings for collaborative research

...It performs approximate Bayesian computation for stochastic models having latent dynamics defined by stochastic differential equations (SDEs) and not limited to the "state-space" modelling framework. Both one- and multi-dimensional SDE systems are supported and partially observed systems are easily accommodated. Variance components for the "measurement error" affecting the data/observations can be estimated. A 50-pages Reference Manual is provided with two case-studies implemented and discussed. The methodology is based on the research article available at http://arxiv.org/abs/1204.5459 Author's research page is http://www.maths.lth.se/matstat/staff/umberto/

The flNeuronTool allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D interactive visualization-assisted environment, which is a powerful tool for analysis of complex neuronal images.

NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.

As an NIAID Bioinformatics Resource Center (BRC) Pathema contains in depth curatorial analysis of six target organisms from the list of NIAID category A-C pathogens. Pathema also offers single-genome and comparative multi-genome analyses as well as displ

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.

Open Source project for visualizing protein structure. Written in C++ with Qt and OpenGL the software is designed to be multi-platform (Linux, FreeBSD and Windows). On web: www.msprot.com Copyright 2008 Federal University of Sao Paulo - UNIFESP

Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.

Inter University Multi-Modal Imaging

RReportGenerator aims to provide a simple and user-friendly multi-platform graphical user interface (GUI) allowing to run routine statistical analysis using R via predefined analysis scenarios to produce reports in pdf-format.

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr.

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).

R Tools for Biologists (RT4Bio) is a multi-functional package writen in R language developed in the Laboratory of Behavioral and Computational Ecology at State University of Montes Claros - MG - Brazil. Formerly known as RRJ.

This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

TAS (Transcription Analysis System) is a multi-tier framework for running parameterized SQL queries. Users can analyze new data or new combinations of data with a few clicks in a GUI. Potentially complex/repetitive database interaction is all automated

Anthill is a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from the complex adaptive systems area.