Search Results for "distributed computing"

The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as...

...MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. Written in pure Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for Big Data processing.

...This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs.

Vappio is a framework for building virtual appliances that supports distributed data processing in cloud computing environments using Sun Grid Engine or Hadoop. The primary target application of Vappio is bioinformatics.

Ergatis is a web-based utility used to create, run, and monitor reusable computational analysis pipelines, utilizing the Workflow engine. It contains pre-built components for common bioinformatics analysis tasks.

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. ...

Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine.

Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)

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.

Microbase is a Grid infrastructure for deploying massively parallel applications. Our notification-driven task scheduler supports the enactment of complex data processing workflows, such as those commonly used in bioinformatics.

Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.

A system based on the multiagent approach, to help the biologists with the manual annotation task on genome sequencing projects

Source code for the Chemical Informatics and Cyberinfrastructure Collaboratory project.

The primary goal of the JES is to develop Distributed Configuration Service for client/server,clusters,grids,agent based architectures.

Gridder is a group of portlets that simplify the use and administration of grid services. Especially for job submission management. Gridder also extends and documents the functionality of the OGCE Bundle. It is plenty of useful documentation.

GridSweeper makes it easy to perform batch runs of scientific simulation programs on computational grids/distributed resource management systems.

OpenEMS™ is the multi platform Grid framework to seamlessly aggregate all your multi platform resources into a virtual super computer.

Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)

Cluster Networks are a new style of neural simulation / neural network modeling, that models networks of neural populations ("clusters") that transform and transmit information using precisely-timed, graded bursts ("pulses" or "volleys") of firing.

IslandEv distributes a Genetic Algorithm (like <a href="/projects/jaga">JaGa</a>) across a network (see <a href="/projects/distrit">DistrIT</a>) using an island based coevolutionary model in which neighbouring islands swap migrating individuals every

The Java Batch System (JBS) is a batch queueing system in the tradition of NQS and PBS for internal (Java-based) and system batch jobs. Stand-alone operation and integration with existing batch queueing systems, initially OpenPBS, is supported.

The objective of the Life Sciences Identifier (LSID) project is to develop a reference implementation of the LSID standards proposal currently being developed by the Technical Architecture Group of the I3C (www.i3c.org).

Info Sapient will be an Open Source, Common License 0.5, 100% Pure Java based program that is a mechanism for the expression and execution of business rules.

An open-sourced distributed computing client for exploring the results of the Human Genome Project.

A generalized and flexible pipeline management software.