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MCX is a GPU-accelerated, general-purpose, physically-accurate and feature-rich 3-D light transport simulator. It is one of the fastest simulators because it can use tens of thousands of GPU threads to simulate photons in parallel.
...The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server.
Manuscripts in submission:
https://arxiv.org/abs/1703.09852
https://arxiv.org/abs/1608
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Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested.
IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
...This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows users to annotate, for example, draft genome contigs or different genomes concatenated in multi-fasta file in a single step.
FIAP works on all UNIX-like operating systems (tested on Ubuntu 14.04 LTS and Mac OS 10.9.4).
Multi-SETI@home Monitor. This program was written to monitor SETI@home and BOINC activity that may be running on multiple computers over a network without having to cross mount file systems. Runs on Windows/Linux/Unix.
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
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The Multi-purpose Automated Genome Project Investigation Environment (MAGPIE, http://magpie.ucalgary.ca/), is a software package for the automated curation and presentation of DNA and protein sequences. Freely available under terms of Apache license v2.0
BCAR is a library for the associative classification, which denotes "Boosting
Class Association Rules". BCAR provides a general tool for classification tasks
with various types of input data.
A MUD "totally" written in Perl. It runs an engine which relies on a extensible Perl MudLib and interprets user-programmable scripts in a fashion that reminds the old-time LPC MUD, but now everything is in Perl. It uses Perl v.5.10.0 and SQLite 3.3.7.
Webtunnel is an HTTP tunnel with some unique features: it runs in the context of a web server; it uses simple requests/responses for proxy traversal; and it is multi-threaded to allow many parallel connections to many destinations simultaneously.
STARS is an alternative interface to staden for studying polymorphisms in short sequences with batch processing, manual editing, trace viewing and data management. STARS was initially designed for Multi Locus Sequence Typing of bacteria.
The Internet Censor is a multi-platform, Internet clustering program, for which the resulting data will be used in the creation of a non-profit content-filtering Internet Search Engine for children.