Open Source Perl Scientific/Engineering Software - Page 10

Albion is a digital document archive presentation package. Features include a searchable database, an integrated spell checker, and automatic thumbnail generation. As native Perl as possible, the database/photos/search-function can be delivered on CD!

Symbolic Algebra using Perl

Algorithm::MatchingModel is a perl library for running match simulations and statistics for two-sided matching problems. It includes classes for a preference factory, algorithm plug-ins, and gathering statistics between rounds.

Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. Allelome.PRO offers increased sensitivity to analyse lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data.

A rule-based modelling framework for allosteric proteins and biochemical networks.

AmphetaRate is the first RSS recommendation server. It calculates your likes/dislikes to create a personalized RSS recommendation feed. We also currently provide an aggregator based on AmphetaDesk to communicate to AmphetaRate.

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.

Anubadok: The Bengali Machine Translator. A machine translation system for English to Bengali.

Based on the Buckwalter Morphological Analyzer (Version 1.0) for doing Arabic stemming and POS tagging. Includes a rewrite of the original Perl script, with better documentation and more flexible options, and a C++ interface (usable as a library or app).

ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines

Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424.

This is a project regarding parsing data from different(general) sources and representing it in form of graphs.

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. Website: http://bioinformatics.ubc.ca/atlas

A collection of many different perl-scripts doing math-stuff, including date and time scripts.

Linear Programming (LP) has been used in the case of the Federalist Papers whose authorship had been disputed. The task here will be to use the Cell Broadband Engine to do likewise with papers whose authorship is disputed.

Flowcharts not telling you what you want to know about some C source code? Try a State Dependency map! Every C source file is an implemention of a state machine. Implicit in the definition of a state machine is a network of dependencies between the states. The Automalator * deconstructs the C code into the core state machine * collates the transactions into the dependency net * generates a diagram-format file with the states and dependencies as the nodes and edges. Pre-requisites * Perl - tested with versions 5.12.3, 5.14.2 and 5.20.2, Windows, Linux and MAC * Get the Automalator by downloading the zip, or checking out or exporting the SVN trunk * copy the source code of interest into "project.c" * windows - double-click "src2map.bat" * linux & MAC - navigate the command line to the "project" folder, then run "src2map.sh" * open "project.gml" file with diagramming software.

ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.

The central problem to be addressed in this project concerns a multidisciplinary (linguistics and computational linguistics) investigation into sharing of knowledge and resources between closely-related languages, specifically relating to the automatic processing of compounds. Specifically, we will explore the possibility to create new knowledge about closely-related languages, and efficiently develop additional, more advanced resources for (a) compound segmentation; and (b) the semantic analysis of compounds; as such, the project will be divided into two interrelated subprojects, to be executed simultaneously. The focus in this project will be on Afrikaans (with Dutch as the closely-related, well-sourced language), which will lay grounds for future work on other closely-related language pairs.

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.

The BEE Project is a suite of tools supporting Business Intelligence project implementation including ETL tool and OLAP server and a thin client. The ROLAP server ensures multipass SQL generation and powerful cache management (utilizes MySQL RDBMS).

The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses. See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595). You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there.

BIGpre: a quality assessment package for next-genomics sequencing data

BIGrat: a genome assembly tool for pyrosequencing-based re-sequencing

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.

BIRAP (Bacterial Intergenic Region Analysis Pipeline) is an open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output from SAMtools for RNA-seq data and peptide/ePST locus file (GFF) from the Proteogenomic Mapping tool for prote-ogenomics data along with the genome and existing in silico annotation. When information regarding the locus of promot-ers and terminators in the genome (in .coords format) is pro-vided, the pipeline will also help identify non-coding RNA.