Open Source Perl Data Management Systems

MRTG is a free, open-source tool designed to monitor and measure the traffic load on network links. It generates HTML pages containing graphical representations (PNG images) of network traffic, providing visual insights into bandwidth usage over time. Originally developed to monitor router traffic, MRTG has evolved to graph various network devices and other metrics.

XMLTV is a suite of utilities to obtain, generate, and post-process TV listings data in XMLTV format. It provides tools to gather television listings, process listings data, and help organize TV viewing.

xoscope is a digital oscilloscope using input from a sound card or EsounD and/or a ProbeScope/osziFOX and will soon support Bitscope hardware. Includes 8 signal displays, variable time scale, math, memory, measurements, and file save/load.

DVCS Ripper is a security and forensics toolkit that reconstructs source code repositories accidentally exposed on web servers. It understands multiple version-control systems—Git, Mercurial, Bazaar, and Subversion—and crawls their metadata directories to rebuild full history where possible. The utilities handle partial or blocked directory listings by guessing object paths and assembling missing pieces from loose files. Investigators and red-teamers use it to demonstrate the risk of deploying .git/ or .svn/ alongside web content, recovering not just code but also secrets committed by mistake. Outputs are normalized into usable repos so diffing, blame, and log analysis work as if you had pulled from the canonical remote. While powerful, it’s intended for legitimate testing and incident response, reinforcing best practices like build-time artifact generation and strict web server access rules.

FlowViewer provides a convenient web-based user interface to Mark Fullmer’s flow-tools suite and CMU's netflow data capture/analyzer, SiLK. The inclusion of the underlying SiLK tool set enables FlowViewer users to continue to use the tool with the newer IPFIX netflow data protocol, which includes support for IPv6 and Cisco's v9 and FNF netflow. FlowViewer has been developed for NASA’s Earth Sciences Data and Information System (ESDIS) networks, and credit goes to NASA for their usual outstanding support of innovation. The FlowViewer tools provide additional graphing and tracking features by utilizing open source software including Thomas Boutrell’s gd, Lincoln Stein's GD, Martien Verbruggen's GD::Graph, and Tobias Oetiker’s RRDtool. FlowViewer v4.6 fixes non-UTC local time environments for FlowViewer and FlowGrapher, and $no_devices_or_exporters FlowMonitor_Collector problem. **Note: SiLK must be v3.8.0 or later. Version 3.9 handles sFlow data.

Flame graphs are a visualization of profiled software, allowing the most frequent code-paths to be identified quickly and accurately. They can be generated using my open source programs, which create interactive SVGs. See the Updates section for other implementations. Recently I've been helping with d3-flame-graph. The x-axis shows the stack profile population, sorted alphabetically (it is not the passage of time), and the y-axis shows stack depth, counting from zero at the bottom. Each rectangle represents a stack frame. The wider a frame is is, the more often it was present in the stacks. The top edge shows what is on-CPU, and beneath it is its ancestry. The colors are usually not significant, picked randomly to differentiate frames. Flame charts were first added by Google Chrome's WebKit Web Inspector (bug). While inspired by flame graphs, flame charts put the passage of time on the x-axis instead of the alphabet.

NOTE: Code commits are FROZEN on SourceForge: New code is now at <http://github.com/Xastir/Xastir>. Real-time tracking & messaging of stations via radio/internet APRS data streams, w/125 map formats supported. Linux/FreeBSD/Solaris/MacOSX/Windows in any of 7 languages. Can also be used for mobile mapping w/GPS. MAILING LISTS ARE AT: PROJECT->WEB SITE.

The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.

As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/

The goal of the Perl OBD-II Logger project is to create a flexible and efficient application that can capture and log OBD-II Mode 0x01 PID data from an automotive scantool. It is designed with accurate and efficient PID data logging in mind, and provides NO support for reading or resetting diagnostic trouble codes. By default, the output log file contains time-stamped PID values in a simple Comma Separated Values (CSV) format that can be readily imported into popular data analysis or spreadsheet applications. (Output to an SQLite3 database file is also available). It is written in Perl, so it runs in any computing environment with a working Perl interpreter. The program supports scantools that are based on the ELM Electronics ELM327 or OBD Solutions STN1110 programmed microcontrollers. It has been tested with scantools using legacy RS-232 serial, serial over USB, and Bluetooth hardware interfaces. Perl OBD-II Logger even runs on the popular Raspberry Pi computer!

AquaTerm is a Mac OS X grahics renderer. It allows command line applications written in ObjC, C, FORTRAN, Lisp, Perl or Python to display vector graphics, text and images using a simple API. Adapters for gnuplot, PGPLOT, and PLplot exists as well.

A Perl object-oriented library for plotting graphs with Gnuplot.

g2 is an easy to use, portable and powerful 2D graphics library. It provides a comprehensive set of functions for simultaneous generation of graphical output on different types of devices.

Krona allows hierarchical data to be explored with zoomable HTML5 pie charts. Krona charts can be created using an Excel template or Krona Tools, which includes support for several bioinformatics tools and raw data formats.

Vcd2txt is an utility to parse value change dump (VCD) files and convert them to an easily readable (plain-text) table of signals. In contrast to GTKwave, simulation of hardware circuits can be performed fully on the command line.

EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets. It is designed for scaling beyond Petabytes and 10^13 objects. http://fantom.gsc.riken.jp/4/edgeexpress

CNV-WebStore is an integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Contact system admin at http://cnv-webstore.uantwerpen.be for installation scripts

Graph handling and layout software developed for helping scientific research. The interface uses Perl, the algorithms are in C++. Creates and shows 3D and 2D graph layouts (several algorithms). Has a scripting interface for graph handling.

OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.

PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create).

TraffStats: network Traffic Statistic - is a monitoring and traffic analysis software, using SNMP to collect data from any enabled device. - has the ability to generate graphs (using jpgraph) with the option to compare and sum up different devices.

ZENBU is a data integration, data processing, and visualization web system based around three main web interfaces : an expression data enhanced genome browser interface, a secured user system for data upload and secured data sharing, and a data explorer interface to find and manipulate data across the many supported experimental data types and to find shared user configurations ZENBU is built as a web2.0 client/server application with javascript web clients and c++ server infrastructure.

miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together well-established software in a single bundle, allowing a complete analysis from raw data. All the capabilities can be easily and simultaneously enabled at will, regardless the step in the workflow.

scriptLattes is an open-source system to create academic reports of groups based on curricula vitae of the Brazilian Lattes Database.

The ADQ project aims to provide device drivers and a terminal based data acquisition and control program for the Meilhaus ME26 data acquisition board and the Meilhaus ME53 relay boards. The data can also be displayed in real time with a Web page.