Open Source Perl Scientific/Engineering Software for Linux - Page 4

metaf2xml can download, parse and decode aviation routine weather reports (METAR, SPECI, SAO), aerodrome forecasts (TAF), synoptic observations (SYNOP), observations from buoys (BUOY) and meteorological reports from aircrafts (AMDAR). Data can also be taken from decoded BUFR messages. The extracted data can be written as XML or passed to a user-defined function (all done in Perl). It also provides XSLT style sheets to convert the XML to plain language (text, HTML), or XML with different schemas. A web-based (CGI) user interface can be used to download and display up-to-date weather data from NOAA, Ogimet, and other sources.

Moodss is a modular monitoring application, composed of a GUI and a daemon, which supports any device or process for which a module can be developed. Complete dashboards with graphical viewers, thresholds, SQL database archiving, ... can be managed.

primedb is a project that attempt to generation prime numbers fast and saving them to a database(Mysql or else) for prime research: finding large number of prime,prime factorization,Goldbach's conjecture,twin prime conjecture...

GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features

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.

mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html.

MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.

Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals.

DocDB is a powerful and flexible collaborative web based document server which maintains a versioned list of documents. Information maintained in the database includes, author(s), title, topic(s), abstract, access restriction information, etc.

A Custom Sequence Locus Typer for Classifying Microbial Genotypic and Phenotypic Attributes. Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240

PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters.

This project has come to an end. If you want, you can download the sources and continue from there. The repository will be wiped clean by the end of 2017.

PHPXref is a developers tool, written in Perl, that will cross reference and extract inline documentation from a collection of PHP scripts. It generates simple HTML output suitable for browsing offline.

ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS.

Aquifer Analysis Tools

AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase.

COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download

Gpsdrive is a car (bike, ship, plane) navigation system. Displaying your position on a map and a lot of other functions are implemented. It works with vector maps from http://www.OpenStreetMap.de/

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. 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

The MetCal/SPA package provides diagnostic resources for users and developers of meteorological apps. The Shared Procedure Archive is a dynamic set of file I/O, analysis routines and APIs for third party packages accessible through the MetCal GUI.

General Number Field Sieve implementation

Collaborative infrastructure for Collaborative Product Development (manufacturing) within Extended and Virtual Enterprise.

Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.

SunlightLB is an open-source 3d lattice Boltzmann code which can be used to solve a variety of hydrodynamics problems, including passive scalar transport problems.

An object orientated Perl applications framework for dealing with VOEvent messages.