Open Source Perl Scientific/Engineering Software - Page 17

Meta Assembler for de novo assembly results. GARM (Genome Assembly Reconciliation and Merging) is a pipeline to merge results from different assemblers or results from different DNA sequencing technologies.

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.

GEOSS (Gene Expression Open Source System), formerly known as GeneX Va, provides a web-based interface for the storage and analysis of Affymetrix GeneChipŽ and other microarray data. It has been developed by engineers at the GeneChip/Microarray Bioinform

GEOSS: Gene Expression Open Source System (used to be called Genex Va) GEOSS is a secure, multiuser, gene expression database and analysis package. GEOSS is distinguished by a well developed web based user interface, and analysis/reporting.

an object-oriented API to access spatial data from Perl scripts, defines a set of classes and conventions to access spatial data independent of underlying file format or access method, based on OpenGIS Abstract Specification (see http://www.opengis.org)

GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

GNU Potato Caboose is a suite of programs and scripts designed for collecting trip data (origin/destination info) in support of the Canadian Commuter Challenge. It is easily adapted to other jurisdictions.

Genetic programming environment to inference context free grammars base on positive and negative examples of language.

LibGPIB is a library of C++ classes which can be used to program various GPIB controllers and instruments including GPIB-ENET, GPIB-232-CT-A, and the NI488-GPIB cards.

GPLIGC is a program for analysis and 3D visualization of GPS tracklogs (in igc format) as recorded by flight data recorders used by glider pilots.

The GPS Ride Plot project is software to convert a downloaded GPS track and generate a map image in PNG format. This has been used primarily to plot bicycle rides. It can also plot almost any GPS track and has done so for cars, trolleys or jet airliners.

GPSR is a resource for genomics, proteomics and systems biology. The aim of this project is to build comprehensive resources in the field of bioinformatics.

GSMCard is a sim card manager, it can save and restore phonebook, change and unblock pin code.

GTdb - Modular genotype database for all markers. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.

Gaussian Output Tools is a package of simple scripts to extract data from Gaussian output files.

Gdraw is an genome visualization tool, including a GUI application and a Perl library. The GUI application creates the drawing interactively. It can also create the drawing by import annotated sequence files (such as Genbank, EMBL). Its backend library can be used in user-written perl scripts to create highly customized drawings.

The GenDB system for the annotation of prokaryote genomes. The Perl/MySQL/Apache based system supports cmd-line mode annotation, integrating dozens of bioinformatics tools, but also provides a user-friendly web interface for community annotation efforts

GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead and complexity of managing the data and the biological entities at hand. GenOO-HTS has been designed to be flexible, easily extendable with modular structure and minimal requirements for external tools and libraries.

GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss.

A gene and protein homology database toolset that uses existing data from ensembl and entrezgene online databases.

The goal of the GeneText project is the development of a software package that will enable users to dynamically generate an information summary page from multiple sources given a search term. Fields of interest are biology, genetics and bioinformatics.

GeneX is an gene expression database system with an integrated toolset that enables researchers to store, analyze, and communicate their data.

The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.

GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.